Changes between Initial Version and Version 1 of Ticket #5525


Ignore:
Timestamp:
Nov 2, 2021, 11:45:24 AM (4 years ago)
Author:
Eric Pettersen
Comment:

Reported by Arnold Muccini

May be easier to debug in daily build, where 'property' attribute errors give proper traceback.

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #5525

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Structure Comparison
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Morph problem

  • Ticket #5525 – Description

    initial v1  
    5252> close session
    5353
    54 > open
    55 > C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2-Arf1/dimer/complex_dimer.pdb
    56 
    57 Summary of feedback from opening
    58 C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2-Arf1/dimer/complex_dimer.pdb 
    59 --- 
    60 warning | Ignored bad PDB record found on line 43136 
    61 END 
    62  
    63 Chain information for complex_dimer.pdb #1 
    64 --- 
    65 Chain | Description 
    66 A C | No description available 
    67 B D | No description available 
    68  
    69 
    70 > color byhetero
    71 
    72 > color bychain
    73 
    74 > close session
    75 
    76 > open C:/Users/Arnold/Downloads/postprocess.mrc
    77 
    78 Opened postprocess.mrc, grid size 300,300,300, pixel 1.65, shown at level
    79 0.00536, step 2, values float32 
    80 
    81 > volume #1 level 0.0239
    82 
    83 > volume #1 step 1
    84 
    85 > close session
    86 
    87 > open C:/Users/Arnold/Downloads/open_dimer-FINAL-
    88 > coot-0_real_space_refined_204.pdb
    89 
    90 Chain information for open_dimer-FINAL-coot-0_real_space_refined_204.pdb #1 
    91 --- 
    92 Chain | Description 
    93 A B | No description available 
    94  
    95 
    96 > hide #!1 models
    97 
    98 > close #1
    99 
    100 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    101 > figures/closed_dimer-FINAL-coot-1_real_space_refined_202.pdb
    102 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    103 > figures/open_dimer-FINAL-coot-0_real_space_refined_204.pdb
    104 
    105 Chain information for closed_dimer-FINAL-coot-1_real_space_refined_202.pdb #1 
    106 --- 
    107 Chain | Description 
    108 A B | No description available 
    109  
    110 Chain information for open_dimer-FINAL-coot-0_real_space_refined_204.pdb #2 
    111 --- 
    112 Chain | Description 
    113 A B | No description available 
    114  
    115 
    116 > mmaker #1 on #2
    117 
    118 > matchmaker #1 on #2
    119 
    120 Expected a keyword 
    121 
    122 > mmaker #1 to #2
    123 
    124 Parameters 
    125 --- 
    126 Chain pairing | bb 
    127 Alignment algorithm | Needleman-Wunsch 
    128 Similarity matrix | BLOSUM-62 
    129 SS fraction | 0.3 
    130 Gap open (HH/SS/other) | 18/18/6 
    131 Gap extend | 1 
    132 SS matrix |  |  | H | S | O 
    133 ---|---|---|--- 
    134 H | 6 | -9 | -6 
    135 S |  | 6 | -6 
    136 O |  |  | 4 
    137 Iteration cutoff | 2 
    138  
    139 Matchmaker open_dimer-FINAL-coot-0_real_space_refined_204.pdb, chain A (#2)
    140 with closed_dimer-FINAL-coot-1_real_space_refined_202.pdb, chain B (#1),
    141 sequence alignment score = 5277.9 
    142 RMSD between 775 pruned atom pairs is 0.985 angstroms; (across all 1129 pairs:
    143 10.144) 
    144  
    145 
    146 > hide #!2 models
    147 
    148 > ui tool show "Show Sequence Viewer"
    149 
    150 > sequence chain #1/A #1/B
    151 
    152 Alignment identifier is 1 
    153 Drag select of 1 residues 
    154 
    155 > ui tool show "Color Actions"
    156 
    157 > color sel #ddecf9ff
    158 
    159 > color sel #ccccccff
    160 
    161 > color sel #c8c5c8ff
    162 
    163 > color sel #787718ff
    164 
    165 > color sel #8c9297ff
    166 
    167 > color sel #9ac2f5ff
    168 
    169 > color sel #9cc3f4ff
    170 
    171 > color sel #f4e379ff
    172 
    173 Drag select of 1 residues 
    174 
    175 > color sel #ffffffff
    176 
    177 > color sel #d7eaf8ff
    178 
    179 > color sel #7886a2ff
    180 
    181 > color sel #ccccccff
    182 
    183 > color sel #f0f0f0ff
    184 
    185 > color sel #8e9193ff
    186 
    187 > color sel #f7fbfcff
    188 
    189 > color sel #f1ebe6ff
    190 
    191 > color sel #f2e5dfff
    192 
    193 > color sel #e1c4b2ff
    194 
    195 > color sel #e3d2c8ff
    196 
    197 > color sel #f2e5dfff
    198 
    199 > color sel #f6f2eeff
    200 
    201 > color sel #e1c4b2ff
    202 
    203 > color sel #cce4f7ff
    204 
    205 > color sel #867878ff
    206 
    207 > color sel #f0f0f0ff
    208 
    209 > color sel #ffffffff
    210 
    211 > color sel #90ee90ff
    212 
    213 > color sel #4d4f52ff
    214 
    215 > color sel #9ac2f5ff
    216 
    217 > color sel #f5e27bff
    218 
    219 > color sel #f4e379ff
    220 
    221 > color sel #4275aeff
    222 
    223 > color sel #3c79afff
    224 
    225 > color sel #4377a7ff
    226 
    227 > color sel #ece691ff
    228 
    229 > color sel #9ac2f5ff
    230 
    231 > color sel #f4e379ff
    232 
    233 > color sel #4377a7ff
    234 
    235 > color sel #9ac2f5ff
    236 
    237 > color sel #ffffffff
    238 
    239 > color sel #f8f8f8ff
    240 
    241 > color sel #f0f0f0ff
    242 
    243 > color sel #ffffffff
    244 
    245 > color sel #91c37dff
    246 
    247 > color sel #ccccccff
    248 
    249 > color sel #187778ff
    250 
    251 > color sel #928986ff
    252 
    253 > color sel #9ac2f5ff
    254 
    255 > color sel #ffffffff
    256 
    257 > color sel #b3eaf8ff
    258 
    259 > color sel #90ee90ff
    260 
    261 > color sel #979899ff
    262 
    263 > color sel #4377a7ff
    264 
    265 > select clear
    266 
    267 > lighting soft
    268 
    269 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    270 > figures/closed_dimer-FINAL.ccp4
    271 
    272 Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
    273 level 1.11, step 2, values float32 
    274 
    275 > volume #3 step 1
    276 
    277 > volume #3 level 16.41
    278 
    279 > surface zone #3 nearAtoms #1 newMap True
    280 
    281 Expected a keyword 
    282 
    283 > volume zone #3 nearAtoms #1 range 3 newMap true
    284 
    285 > hide #!4 models
    286 
    287 > show #!3 models
    288 
    289 > hide #!3 models
    290 
    291 > show #!4 models
    292 
    293 > color zone #4 near #1 distance 20
    294 
    295 > color sel #9ac2f5ff
    296 
    297 > color zone #4 near #1 distance 20
    298 
    299 > select clear
    300 
    301 > hide #!4 models
    302 
    303 > preset cartoons/nucleotides cylinders/stubs
    304 
    305 Changed 0 atom styles 
    306 Preset expands to these ChimeraX commands:
    307 
    308    
    309    
    310     show nucleic
    311     hide protein|solvent|H
    312     surf hide
    313     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    314     cartoon
    315     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    316     cartoon style ~(nucleic|strand) x round
    317     cartoon style (nucleic|strand) x rect
    318     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    319     cartoon style nucleic x round width 1.6 thick 1.6
    320     nucleotides stubs
    321 
    322  
    323 
    324 > preset "overall look" publication
    325 
    326 Preset expands to these ChimeraX commands:
    327 
    328    
    329    
    330     set bg white
    331     graphics silhouettes t
    332 
    333  
    334 
    335 > show #!4 models
    336 
    337 > hide #!1 models
    338 
    339 > hide #!4 models
    340 
    341 > show #!2 models
    342 
    343 > ui tool show "Show Sequence Viewer"
    344 
    345 > sequence chain #2/A #2/B
    346 
    347 Alignment identifier is 1 
    348 Drag select of 1 residues 
    349 
    350 > color sel #f4e379ff
    351 
    352 Drag select of 2 residues 
    353 
    354 > color sel #e1c4b2ff
    355 
    356 > select clear
    357 
    358 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    359 > figures/open_dimer-FINAL.ccp4
    360 
    361 Opened open_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
    362 level 0.978, step 2, values float32 
    363 
    364 > volume #5 level 9.627
    365 
    366 > volume #5 step 1
    367 
    368 > volume #5 level 17.41
    369 
    370 > volume zone #5 nearAtoms #2 range 3 newMap true
    371 
    372 > color zone #6 near #2 distance 20
    373 
    374 > hide #!6 models
    375 
    376 > show #!6 models
    377 
    378 > hide #!6 models
    379 
    380 > show #!6 models
    381 
    382 > color zone #6 near #2 distance 20
    383 
    384 Drag select of 1 residues, 6 open_dimer-FINAL.ccp4 zone 
    385 
    386 > color sel #9ac2f5ff
    387 
    388 > color zone #6 near #2 distance 20
    389 
    390 > select clear
    391 
    392 > hide #!6 models
    393 
    394 > hide #!2 models
    395 
    396 > show #!6 models
    397 
    398 > show #!4 models
    399 
    400 > hide #!4 models
    401 
    402 > hide #!6 models
    403 
    404 > show #!4 models
    405 
    406 > surface zone #4 #6 size 5
    407 
    408 Expected a keyword 
    409 
    410 > surface dust #4 #6 size 5
    411 
    412 > hide #!4 models
    413 
    414 > show #!6 models
    415 
    416 > hide #!6 models
    417 
    418 > show #!4 models
    419 
    420 > hide #!4 models
    421 
    422 > show #!6 models
    423 
    424 > hide #!6 models
    425 
    426 > show #!4 models
    427 
    428 > show #!6 models
    429 
    430 > close #1
    431 
    432 > close #2
    433 
    434 > close #3
    435 
    436 > close #4
    437 
    438 > close #5
    439 
    440 > close #6
    441 
    442 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    443 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    444 
    445 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #1 
    446 --- 
    447 Chain | Description 
    448 A B | No description available 
    449  
    450 
    451 > preset "initial styles" "original look"
    452 
    453 Preset implemented in Python; no expansion to individual ChimeraX commands
    454 available. 
    455 
    456 > preset "initial styles" cartoon
    457 
    458 Preset implemented in Python; no expansion to individual ChimeraX commands
    459 available. 
    460 
    461 > lighting simple
    462 
    463 > lighting simple
    464 
    465 > lighting soft
    466 
    467 > lighting simple
    468 
    469 > lighting shadows true
    470 
    471 > lighting shadows false
    472 
    473 > graphics silhouettes false
    474 
    475 > lighting shadows true
    476 
    477 > lighting shadows false
    478 
    479 > lighting flat
    480 
    481 > lighting flat
    482 
    483 > lighting shadows true intensity 0.5
    484 
    485 > lighting flat
    486 
    487 > lighting flat
    488 
    489 > lighting simple
    490 
    491 > graphics silhouettes false
    492 
    493 > ui tool show "Show Sequence Viewer"
    494 
    495 > sequence chain /A /B
    496 
    497 Alignment identifier is 1 
    498 
    499 > select clear
    500 
    501 > select clear
    502 
    503 Drag select of 2 residues 
    504 
    505 > color sel #f4e379ff
    506 
    507 > color sel #4377a7ff
    508 
    509 > color sel #e1c4b2ff
    510 
    511 > select clear
    512 
    513 > color sel #9ac2f5ff
    514 
    515 > select clear
    516 
    517 > lighting shadows true
    518 
    519 > graphics silhouettes true
    520 
    521 > lighting shadows false
    522 
    523 > preset cartoons/nucleotides ribbons/slabs
    524 
    525 Changed 0 atom styles 
    526 Preset expands to these ChimeraX commands:
    527 
    528    
    529    
    530     show nucleic
    531     hide protein|solvent|H
    532     surf hide
    533     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    534     cartoon
    535     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    536     cartoon style ~(nucleic|strand) x round
    537     cartoon style (nucleic|strand) x rect
    538     nucleotides tube/slab shape box
    539 
    540  
    541 
    542 > preset cartoons/nucleotides cylinders/stubs
    543 
    544 Changed 0 atom styles 
    545 Preset expands to these ChimeraX commands:
    546 
    547    
    548    
    549     show nucleic
    550     hide protein|solvent|H
    551     surf hide
    552     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    553     cartoon
    554     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    555     cartoon style ~(nucleic|strand) x round
    556     cartoon style (nucleic|strand) x rect
    557     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    558     cartoon style nucleic x round width 1.6 thick 1.6
    559     nucleotides stubs
    560 
    561  
    562 
    563 > lighting soft
    564 
    565 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    566 > figures/complex_dimer-FINAL.ccp4
    567 
    568 Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
    569 level 1.63, step 2, values float32 
    570 
    571 > close #2
    572 
    573 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    574 > figures/closed_dimer-FINAL.ccp4
    575 
    576 Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
    577 level 1.11, step 2, values float32 
    578 
    579 > volume #2 level 13.94
    580 
    581 > volume #2 step 1
    582 
    583 > surface dust #4 #6 size 5
    584 
    585 No surfaces specified 
    586 
    587 > volume zone #2 nearAtoms #1 range 3 newMap true
    588 
    589 > color zone #3 near #1 distance 20
    590 
    591 > hide #!3 models
    592 
    593 > hide #1 models
    594 
    595 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    596 > figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
    597 
    598 Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #4 
    599 --- 
    600 Chain | Description 
    601 A B | No description available 
    602  
    603 
    604 > ui tool show "Show Sequence Viewer"
    605 
    606 > sequence chain #4/A #4/B
    607 
    608 Alignment identifier is 1 
    609 Drag select of 1 residues 
    610 
    611 > color sel #f4e379ff
    612 
    613 Drag select of 1 residues 
    614 
    615 > color sel #e1c4b2ff
    616 
    617 > color sel #9ac2f5ff
    618 
    619 > select clear
    620 
    621 > preset cartoons/nucleotides cylinders/stubs
    622 
    623 Changed 0 atom styles 
    624 Preset expands to these ChimeraX commands:
    625 
    626    
    627    
    628     show nucleic
    629     hide protein|solvent|H
    630     surf hide
    631     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    632     cartoon
    633     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    634     cartoon style ~(nucleic|strand) x round
    635     cartoon style (nucleic|strand) x rect
    636     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    637     cartoon style nucleic x round width 1.6 thick 1.6
    638     nucleotides stubs
    639 
    640  
    641 
    642 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    643 > figures/open_dimer-FINAL.ccp4
    644 
    645 Opened open_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
    646 level 0.978, step 2, values float32 
    647 
    648 > volume #5 level 5.92
    649 
    650 > volume #5 step 1
    651 
    652 > volume #5 level 18.9
    653 
    654 > volume zone #5 nearAtoms #4 range 3 newMap true
    655 
    656 > hide #4 models
    657 
    658 > show #4 models
    659 
    660 > color zone #6 nearAtoms #5 distance 20
    661 
    662 Expected a keyword 
    663 
    664 > color zone #6 near #5 distance 20
    665 
    666 > show #!5 models
    667 
    668 > hide #!6 models
    669 
    670 > hide #!5 models
    671 
    672 > show #!6 models
    673 
    674 > color zone #6 near #4 distance 20
    675 
    676 > lighting soft
    677 
    678 > lighting full
    679 
    680 > lighting soft
    681 
    682 > lighting flat
    683 
    684 > lighting soft
    685 
    686 > graphics silhouettes false
    687 
    688 > graphics silhouettes true
    689 
    690 > lighting shadows true intensity 0.5
    691 
    692 > lighting shadows false
    693 
    694 > lighting shadows true
    695 
    696 > lighting soft
    697 
    698 > hide #4 models
    699 
    700 > hide #!6 models
    701 
    702 > show #1 models
    703 
    704 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    705 
    706 > hide #1 models
    707 
    708 > show #!3 models
    709 
    710 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    711 
    712 > hide #!3 models
    713 
    714 > show #4 models
    715 
    716 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    717 
    718 > hide #4 models
    719 
    720 > show #!6 models
    721 
    722 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    723 
    724 > hide #!6 models
    725 
    726 > show #1 models
    727 
    728 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    729 
    730 > hide #1 models
    731 
    732 > show #!3 models
    733 
    734 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    735 
    736 > hide #!3 models
    737 
    738 > show #4 models
    739 
    740 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    741 
    742 > hide #4 models
    743 
    744 > show #!6 models
    745 
    746 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    747 
    748 > hide #!6 models
    749 
    750 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    751 > figures/complex_dimer-FINAL.ccp4
    752 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    753 > figures/complex_dimer-FINAL-coot-7.pdb
    754 
    755 Chain information for complex_dimer-FINAL-coot-7.pdb #8 
    756 --- 
    757 Chain | Description 
    758 A C | No description available 
    759 B | No description available 
    760 D | No description available 
    761  
    762 Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
    763 level 1.63, step 2, values float32 
    764 
    765 > volume #7 level 4.258
    766 
    767 > volume #7 step 1
    768 
    769 > hide #!8 models
    770 
    771 > show #!8 models
    772 
    773 > hide #!7 models
    774 
    775 > ui tool show "Show Sequence Viewer"
    776 
    777 > sequence chain #8/A #8/C
    778 
    779 Alignment identifier is 1 
    780 
    781 > select #8/A:545
    782 
    783 4 atoms, 3 bonds, 1 residue, 1 model selected 
    784 
    785 > color sel #f4e379ff
    786 
    787 > select #8/A:799
    788 
    789 7 atoms, 7 bonds, 1 residue, 1 model selected 
    790 
    791 > select clear
    792 
    793 > select #8/A:550
    794 
    795 9 atoms, 8 bonds, 1 residue, 1 model selected 
    796 
    797 > color sel #e1c4b2ff
    798 
    799 > color sel #9ac2f5ff
    800 
    801 > select clear
    802 
    803 > select #8/C
    804 
    805 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected 
    806 
    807 > select #8/B
    808 
    809 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    810 
    811 > select #8/A
    812 
    813 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected 
    814 
    815 > select clear
    816 
    817 > select #8/D
    818 
    819 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    820 
    821 > color (#!8 & sel) #ffffffff
    822 
    823 > color (#!8 & sel) #000053ff
    824 
    825 > color (#!8 & sel) #f0f0f0ff
    826 
    827 > color (#!8 & sel) #ffffffff
    828 
    829 > color (#!8 & sel) #222222ff
    830 
    831 > color (#!8 & sel) #ffffffff
    832 
    833 > color (#!8 & sel) #505a8dff
    834 
    835 > color (#!8 & sel) #899affff
    836 
    837 > color (#!8 & sel) #808feeff
    838 
    839 > color (#!8 & sel) #7b89e1ff
    840 
    841 > color (#!8 & sel) #7583d5ff
    842 
    843 > color (#!8 & sel) #727fcdff
    844 
    845 > color (#!8 & sel) #707cc9ff
    846 
    847 > color (#!8 & sel) #6f7bc6ff
    848 
    849 > color (#!8 & sel) #606dbfff
    850 
    851 > color (#!8 & sel) #8091faff
    852 
    853 > color (#!8 & sel) #7c8df5ff
    854 
    855 > color (#!8 & sel) #7d8df6ff
    856 
    857 > color (#!8 & sel) #7d8ef7ff
    858 
    859 > color (#!8 & sel) #7d8ef8ff
    860 
    861 > color (#!8 & sel) #7e8ff9ff
    862 
    863 > color (#!8 & sel) #7c8df4ff
    864 
    865 > color (#!8 & sel) #e2e2e2ff
    866 
    867 > color (#!8 & sel) #ffffffff
    868 
    869 > color (#!8 & sel) #808fe2ff
    870 
    871 > color (#!8 & sel) #8c9dffff
    872 
    873 > color (#!8 & sel) #8595f8ff
    874 
    875 > color (#!8 & sel) #8291f2ff
    876 
    877 > color (#!8 & sel) #8090efff
    878 
    879 > color (#!8 & sel) #7d8ce7ff
    880 
    881 > color (#!8 & sel) #7987deff
    882 
    883 > color (#!8 & sel) #7582d4ff
    884 
    885 > color (#!8 & sel) #151723ff
    886 
    887 > color (#!8 & sel) #6a75bcff
    888 
    889 > color (#!8 & sel) #1c1c1cff
    890 
    891 > color (#!8 & sel) #5560a7ff
    892 
    893 > color (#!8 & sel) #7280dbff
    894 
    895 > color (#!8 & sel) #7281dbff
    896 
    897 > select clear
    898 
    899 > select #8/B
    900 
    901 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    902 
    903 > color sel #4377a7ff
    904 
    905 > color sel #7281dbff
    906 
    907 > select clear
    908 
    909 > preset cartoons/nucleotides cylinders/stubs
    910 
    911 Changed 0 atom styles 
    912 Preset expands to these ChimeraX commands:
    913 
    914    
    915    
    916     show nucleic
    917     hide protein|solvent|H
    918     surf hide
    919     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    920     cartoon
    921     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    922     cartoon style ~(nucleic|strand) x round
    923     cartoon style (nucleic|strand) x rect
    924     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    925     cartoon style nucleic x round width 1.6 thick 1.6
    926     nucleotides stubs
    927 
    928  
    929 
    930 > volume zone #7 nearAtoms #8 range 3 newMap true
    931 
    932 > color zone #9 near #7 distance 20
    933 
    934 > color zone #9 near #8 distance 20
    935 
    936 > volume #9 level 6.374
    937 
    938 > volume #9 level 9.196
    939 
    940 > volume #9 level 12.72
    941 
    942 > volume #9 level 19.43
    943 
    944 > hide #!8 models
    945 
    946 > surface dust # 9 size 5
    947 
    948 > show #!8 models
    949 
    950 > hide #!8 models
    951 
    952 > hide #!9 models
    953 
    954 > show #!8 models
    955 
    956 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    957 
    958 > hide #!8 models
    959 
    960 > show #!9 models
    961 
    962 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    963 
    964 > hide #!9 models
    965 
    966 > show #!8 models
    967 
    968 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    969 
    970 > hide #!8 models
    971 
    972 > show #!9 models
    973 
    974 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    975 
    976 > hide #!9 models
    977 
    978 > show #!8 models
    979 
    980 > hide #!8 models
    981 
    982 > show #!8 models
    983 
    984 > save C:\Users\Arnold\Desktop\image8.png supersample 3
    985 
    986 > hide #!8 models
    987 
    988 > show #!9 models
    989 
    990 > save C:\Users\Arnold\Desktop\image9.png supersample 3
    991 
    992 > hide #!9 models
    993 
    994 > show #!8 models
    995 
    996 > hide #!8 models
    997 
    998 > show #!7 models
    999 
    1000 > hide #!7 models
    1001 
    1002 > show #!3 models
    1003 
    1004 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1005 
    1006 > hide #!3 models
    1007 
    1008 > show #4 models
    1009 
    1010 > show #!5 models
    1011 
    1012 > hide #!5 models
    1013 
    1014 > show #!6 models
    1015 
    1016 > hide #!6 models
    1017 
    1018 > show #!7 models
    1019 
    1020 > hide #!7 models
    1021 
    1022 > show #1 models
    1023 
    1024 > hide #1 models
    1025 
    1026 > show #1 models
    1027 
    1028 > hide #1 models
    1029 
    1030 > show #1 models
    1031 
    1032 > hide #4 models
    1033 
    1034 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1035 
    1036 > hide #1 models
    1037 
    1038 > show #!3 models
    1039 
    1040 > hide #!3 models
    1041 
    1042 > show #4 models
    1043 
    1044 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    1045 
    1046 > hide #4 models
    1047 
    1048 > show #!9 models
    1049 
    1050 > hide #!9 models
    1051 
    1052 > show #!7 models
    1053 
    1054 > hide #!7 models
    1055 
    1056 > show #!8 models
    1057 
    1058 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1059 
    1060 > hide #!8 models
    1061 
    1062 > show #1 models
    1063 
    1064 > show #4 models
    1065 
    1066 > hide #4 models
    1067 
    1068 > show #4 models
    1069 
    1070 > hide #4 models
    1071 
    1072 > show #4 models
    1073 
    1074 > hide #4 models
    1075 
    1076 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1077 
    1078 > hide #1 models
    1079 
    1080 > show #4 models
    1081 
    1082 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    1083 
    1084 > hide #4 models
    1085 
    1086 > show #!9 models
    1087 
    1088 > hide #!9 models
    1089 
    1090 > show #!8 models
    1091 
    1092 > hide #!8 models
    1093 
    1094 > show #!8 models
    1095 
    1096 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1097 
    1098 > hide #!8 models
    1099 
    1100 > open C:/Users/Arnold/Downloads/AF-P47102-F1-model_v1.pdb
    1101 
    1102 AF-P47102-F1-model_v1.pdb title: 
    1103 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    1104 (P47102) [more info...] 
    1105  
    1106 Chain information for AF-P47102-F1-model_v1.pdb #10 
    1107 --- 
    1108 Chain | Description 
    1109 A | arf guanine-nucleotide exchange factor 1 
    1110  
    1111 
    1112 > open C:/Users/Arnold/Downloads/lipids_slice.pdb
    1113 
    1114 > hide #11 models
    1115 
    1116 > show #11 models
    1117 
    1118 > hide #10 models
    1119 
    1120 > show #10 models
    1121 
    1122 > select #10
    1123 
    1124 11218 atoms, 11405 bonds, 1408 residues, 1 model selected 
    1125 
    1126 > ui mousemode right "translate selected models"
    1127 
    1128 > ~select #10
    1129 
    1130 Nothing selected 
    1131 
    1132 > ui mousemode right swapaa
    1133 
    1134 > ui mousemode right swapaa
    1135 
    1136 > hide #10 models
    1137 
    1138 > select #11
    1139 
    1140 313093 atoms, 317626 bonds, 3369 residues, 1 model selected 
    1141 
    1142 > hide sel atoms
    1143 
    1144 > show sel atoms
    1145 
    1146 > style sel stick
    1147 
    1148 Changed 313093 atom styles 
    1149 
    1150 > select clear
    1151 
    1152 > close #11
    1153 
    1154 > show #!3 models
    1155 
    1156 > show #4 models
    1157 
    1158 > hide #4 models
    1159 
    1160 > show #1 models
    1161 
    1162 > hide #!3 models
    1163 
    1164 > hide #1 models
    1165 
    1166 > show #1 models
    1167 
    1168 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1169 
    1170 > hide #1 models
    1171 
    1172 > show #4 models
    1173 
    1174 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    1175 
    1176 > hide #4 models
    1177 
    1178 > show #!8 models
    1179 
    1180 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    1181 
    1182 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    1183 
    1184 > hide #!8 models
    1185 
    1186 > show #!5 models
    1187 
    1188 > hide #!5 models
    1189 
    1190 > show #4 models
    1191 
    1192 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    1193 
    1194 > hide #4 models
    1195 
    1196 > show #1 models
    1197 
    1198 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    1199 
    1200 > show #!9 models
    1201 
    1202 > hide #!9 models
    1203 
    1204 > show #!8 models
    1205 
    1206 > hide #!8 models
    1207 
    1208 > show #!7 models
    1209 
    1210 > hide #!7 models
    1211 
    1212 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    1213 
    1214 Chain information for ger2.pdb #11 
    1215 --- 
    1216 Chain | Description 
    1217 A | No description available 
    1218 C | No description available 
    1219  
    1220 
    1221 > swapaa mousemode #1/A:561 GLN
    1222 
    1223 > select #11
    1224 
    1225 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    1226 
    1227 > swapaa mousemode #11/C:64 ALA
    1228 
    1229 > ui mousemode right translate
    1230 
    1231 > ui mousemode right "translate selected models"
    1232 
    1233 Drag select of 12 atoms, 446 residues, 10 bonds 
    1234 
    1235 > hide sel atoms
    1236 
    1237 > select clear
    1238 
    1239 > ui tool show "Fit in Map"
    1240 
    1241 Fit molecule ger2.pdb (#11) to map closed_dimer-FINAL.ccp4 (#2) using 2988
    1242 atoms 
    1243 average map value = 8.317, steps = 232 
    1244 shifted from previous position = 9.24 
    1245 rotated from previous position = 42.6 degrees 
    1246 atoms outside contour = 2063, contour level = 13.94 
    1247  
    1248 Position of ger2.pdb (#11) relative to closed_dimer-FINAL.ccp4 (#2)
    1249 coordinates: 
    1250 Matrix rotation and translation 
    1251 0.93550398 0.15724014 0.31639822 249.10411821 
    1252 0.19555749 -0.97626931 -0.09303492 328.72846253 
    1253 0.29426104 0.14890858 -0.94405332 329.51008491 
    1254 Axis 0.98368142 0.09000417 0.15578869 
    1255 Axis point 0.00000000 144.22327553 154.42235547 
    1256 Rotation angle (degrees) 172.93596315 
    1257 Shift along axis 325.95996886 
    1258  
    1259 
    1260 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    1261 > figures/2k5u.pdb
    1262 
    1263 2k5u.pdb title: 
    1264 Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
    1265 info...] 
    1266  
    1267 Chain information for 2k5u.pdb 
    1268 --- 
    1269 Chain | Description 
    1270 12.1/A | adp-ribosylation factor 1 
    1271 12.2/A 12.3/A 12.4/A 12.5/A 12.6/A 12.7/A 12.8/A 12.9/A 12.10/A 12.11/A
    1272 12.12/A 12.13/A 12.14/A 12.15/A 12.16/A | adp-ribosylation factor 1 
    1273  
    1274 
    1275 > close #12.2-16
    1276 
    1277 > matchmaker #12 to #11
    1278 
    1279 Parameters 
    1280 --- 
    1281 Chain pairing | bb 
    1282 Alignment algorithm | Needleman-Wunsch 
    1283 Similarity matrix | BLOSUM-62 
    1284 SS fraction | 0.3 
    1285 Gap open (HH/SS/other) | 18/18/6 
    1286 Gap extend | 1 
    1287 SS matrix |  |  | H | S | O 
    1288 ---|---|---|--- 
    1289 H | 6 | -9 | -6 
    1290 S |  | 6 | -6 
    1291 O |  |  | 4 
    1292 Iteration cutoff | 2 
    1293  
    1294 Matchmaker ger2.pdb, chain A (#11) with 2k5u.pdb, chain A (#12.1), sequence
    1295 alignment score = 695 
    1296 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    1297 5.084) 
    1298  
    1299 
    1300 > hide #11 models
    1301 
    1302 > hide #1 models
    1303 
    1304 > preset cartoons/nucleotides cylinders/stubs
    1305 
    1306 Changed 0 atom styles 
    1307 Preset expands to these ChimeraX commands:
    1308 
    1309    
    1310    
    1311     show nucleic
    1312     hide protein|solvent|H
    1313     surf hide
    1314     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    1315     cartoon
    1316     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    1317     cartoon style ~(nucleic|strand) x round
    1318     cartoon style (nucleic|strand) x rect
    1319     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    1320     cartoon style nucleic x round width 1.6 thick 1.6
    1321     nucleotides stubs
    1322 
    1323  
    1324 
    1325 > preset cartoons/nucleotides cylinders/stubs
    1326 
    1327 Changed 0 atom styles 
    1328 Preset expands to these ChimeraX commands:
    1329 
    1330    
    1331    
    1332     show nucleic
    1333     hide protein|solvent|H
    1334     surf hide
    1335     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    1336     cartoon
    1337     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    1338     cartoon style ~(nucleic|strand) x round
    1339     cartoon style (nucleic|strand) x rect
    1340     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    1341     cartoon style nucleic x round width 1.6 thick 1.6
    1342     nucleotides stubs
    1343 
    1344  
    1345 Drag select of 43 atoms, 196 residues, 44 bonds 
    1346 
    1347 > hide sel atoms
    1348 
    1349 > select clear
    1350 
    1351 > select #12
    1352 
    1353 2952 atoms, 2981 bonds, 182 residues, 2 models selected 
    1354 
    1355 > color sel #4377a7ff
    1356 
    1357 > color sel #7281dbff
    1358 
    1359 > color sel #7383ddff
    1360 
    1361 > color sel #7484deff
    1362 
    1363 > color sel #7484dfff
    1364 
    1365 > color sel #7686e2ff
    1366 
    1367 > color sel #7788e5ff
    1368 
    1369 > color sel #798ae8ff
    1370 
    1371 > color sel #7a8beaff
    1372 
    1373 > color sel #7b8bebff
    1374 
    1375 > color sel #7b8cecff
    1376 
    1377 > color sel #7c8deeff
    1378 
    1379 > color sel #7d8eefff
    1380 
    1381 > color sel #7d8ef0ff
    1382 
    1383 > color sel #7e8ff1ff
    1384 
    1385 > color sel #7f90f3ff
    1386 
    1387 > color sel #7f91f4ff
    1388 
    1389 > color sel #8091f5ff
    1390 
    1391 > color sel #8193f7ff
    1392 
    1393 > color sel #8193f8ff
    1394 
    1395 > color sel #8294f9ff
    1396 
    1397 > color sel #8294faff
    1398 
    1399 > color sel #8396fcff
    1400 
    1401 > color sel #8496fdff
    1402 
    1403 > color sel #8497feff
    1404 
    1405 > color sel #8597ffff
    1406 
    1407 > color sel #8497feff
    1408 
    1409 > color sel #8496fdff
    1410 
    1411 > color sel #8294f9ff
    1412 
    1413 > color sel #7f90f3ff
    1414 
    1415 > color sel #7d8eefff
    1416 
    1417 > color sel #7a8beaff
    1418 
    1419 > color sel #7889e7ff
    1420 
    1421 > color sel #7889e6ff
    1422 
    1423 > color sel #7686e2ff
    1424 
    1425 > color sel #7484dfff
    1426 
    1427 > color sel #7383dcff
    1428 
    1429 > color sel #6f7ed4ff
    1430 
    1431 > color sel #6e7dd3ff
    1432 
    1433 > color sel #6d7cd1ff
    1434 
    1435 > color sel #6c7bcfff
    1436 
    1437 > color sel #6b7aceff
    1438 
    1439 > color sel #6a78cbff
    1440 
    1441 > color sel #6876c7ff
    1442 
    1443 > color sel #6471bfff
    1444 
    1445 > color sel #6270bdff
    1446 
    1447 > color sel #626fbcff
    1448 
    1449 > color sel #606db8ff
    1450 
    1451 > color sel #5d6ab3ff
    1452 
    1453 > color sel #5c68b0ff
    1454 
    1455 > color sel #5a67adff
    1456 
    1457 > color sel #5965aaff
    1458 
    1459 > color sel #5763a7ff
    1460 
    1461 > color sel #5662a6ff
    1462 
    1463 > color sel #5662a5ff
    1464 
    1465 > color sel #525e9eff
    1466 
    1467 > color sel #505b9aff
    1468 
    1469 > color sel #4f5a98ff
    1470 
    1471 > color sel #4e5996ff
    1472 
    1473 > color sel #4e5895ff
    1474 
    1475 > color sel #4d5894ff
    1476 
    1477 > color sel #4c5793ff
    1478 
    1479 > color sel #4b5691ff
    1480 
    1481 > color sel #4b5590ff
    1482 
    1483 > color sel #4b5691ff
    1484 
    1485 > color sel #505b9aff
    1486 
    1487 > color sel #525e9eff
    1488 
    1489 > color sel #5460a2ff
    1490 
    1491 > color sel #5662a5ff
    1492 
    1493 > color sel #5763a7ff
    1494 
    1495 > color sel #5965abff
    1496 
    1497 > color sel #5a67adff
    1498 
    1499 > color sel #5c69b1ff
    1500 
    1501 > color sel #5d6ab3ff
    1502 
    1503 > color sel #5f6cb6ff
    1504 
    1505 > color sel #606eb9ff
    1506 
    1507 > color sel #6270bdff
    1508 
    1509 > color sel #6471bfff
    1510 
    1511 > color sel #6573c2ff
    1512 
    1513 > color sel #6775c5ff
    1514 
    1515 > color sel #6876c7ff
    1516 
    1517 > color sel #6877c8ff
    1518 
    1519 > color sel #6b7aceff
    1520 
    1521 > color sel #6c7bcfff
    1522 
    1523 > color sel #6c7bd0ff
    1524 
    1525 > color sel #6f7ed4ff
    1526 
    1527 > color sel #707fd6ff
    1528 
    1529 > color sel #7180d8ff
    1530 
    1531 > color sel #7281daff
    1532 
    1533 > color sel #7383ddff
    1534 
    1535 > color sel #7484dfff
    1536 
    1537 > color sel #7586e1ff
    1538 
    1539 > color sel #7788e5ff
    1540 
    1541 > color sel #7889e7ff
    1542 
    1543 > color sel #7b8bebff
    1544 
    1545 > color sel #7b8cecff
    1546 
    1547 > color sel #7d8eefff
    1548 
    1549 > color sel #7d8ef0ff
    1550 
    1551 > color sel #7e8ff1ff
    1552 
    1553 > color sel #7f90f3ff
    1554 
    1555 > color sel #7f91f4ff
    1556 
    1557 > color sel #8091f5ff
    1558 
    1559 > color sel #8193f7ff
    1560 
    1561 > color sel #8294f9ff
    1562 
    1563 > color sel #8294faff
    1564 
    1565 > color sel #8396fcff
    1566 
    1567 > color sel #8497feff
    1568 
    1569 > color sel #8597ffff
    1570 
    1571 > select clear
    1572 
    1573 > select ::name="MYR"
    1574 
    1575 42 atoms, 41 bonds, 1 residue, 1 model selected 
    1576 
    1577 > show sel atoms
    1578 
    1579 > show sel atoms
    1580 
    1581 > select ::name="GDP"
    1582 
    1583 40 atoms, 42 bonds, 1 residue, 1 model selected 
    1584 
    1585 > color sel byhetero
    1586 
    1587 No model chosen to save relative to 
    1588 
    1589 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    1590 > figures/figures.cxs includeMaps true
    1591 
    1592 > select ::name="GDP"
    1593 
    1594 40 atoms, 42 bonds, 1 residue, 1 model selected 
    1595 
    1596 > show sel atoms
    1597 
    1598 > color sel byhetero
    1599 
    1600 > color sel #ffaaffff
    1601 
    1602 > color sel byhetero
    1603 
    1604 > select clear
    1605 
    1606 > select ::name="MYR"
    1607 
    1608 42 atoms, 41 bonds, 1 residue, 1 model selected 
    1609 
    1610 > color sel byhetero
    1611 
    1612 > select clear
    1613 
    1614 > show #1 models
    1615 
    1616 > hide #!12 models
    1617 
    1618 > show #!5 models
    1619 
    1620 > hide #!5 models
    1621 
    1622 > show #!6 models
    1623 
    1624 > hide #!6 models
    1625 
    1626 > show #!7 models
    1627 
    1628 > hide #!7 models
    1629 
    1630 > show #!6 models
    1631 
    1632 > hide #!6 models
    1633 
    1634 > show #!5 models
    1635 
    1636 > hide #!5 models
    1637 
    1638 > show #4 models
    1639 
    1640 > hide #1 models
    1641 
    1642 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    1643 
    1644 Chain information for ger2.pdb #13 
    1645 --- 
    1646 Chain | Description 
    1647 A | No description available 
    1648 C | No description available 
    1649  
    1650 
    1651 > hide #4 models
    1652 
    1653 > show #!5 models
    1654 
    1655 > hide #!5 models
    1656 
    1657 > show #!6 models
    1658 
    1659 > select #13
    1660 
    1661 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    1662 Fit molecule ger2.pdb (#13) to map open_dimer-FINAL.ccp4 (#5) using 2990 atoms 
    1663 average map value = 2.65, steps = 112 
    1664 shifted from previous position = 5.18 
    1665 rotated from previous position = 14.5 degrees 
    1666 atoms outside contour = 2575, contour level = 18.898 
    1667  
    1668 Position of ger2.pdb (#13) relative to open_dimer-FINAL.ccp4 (#5) coordinates: 
    1669 Matrix rotation and translation 
    1670 0.83150660 -0.32310828 -0.45188252 334.47827146 
    1671 -0.40828316 -0.90705896 -0.10270785 338.75699998 
    1672 -0.37669833 0.26989828 -0.88614519 332.68541347 
    1673 Axis 0.95652433 -0.19300676 -0.21865407 
    1674 Axis point 0.00000000 183.98124055 223.78732810 
    1675 Rotation angle (degrees) 168.76866172 
    1676 Shift along axis 181.81119216 
    1677  
    1678 
    1679 > select clear
    1680 
    1681 > select #13
    1682 
    1683 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    1684 Fit molecule ger2.pdb (#13) to map open_dimer-FINAL.ccp4 (#5) using 2990 atoms 
    1685 average map value = 9.852, steps = 260 
    1686 shifted from previous position = 7.6 
    1687 rotated from previous position = 37.6 degrees 
    1688 atoms outside contour = 2146, contour level = 18.898 
    1689  
    1690 Position of ger2.pdb (#13) relative to open_dimer-FINAL.ccp4 (#5) coordinates: 
    1691 Matrix rotation and translation 
    1692 0.89467687 -0.43384390 0.10645546 293.26294690 
    1693 -0.44670038 -0.87072757 0.20565084 303.40477431 
    1694 0.00347334 -0.23154475 -0.97281805 345.05274987 
    1695 Axis -0.97296277 0.22918294 -0.02861163 
    1696 Axis point 0.00000000 206.04153636 147.44800737 
    1697 Rotation angle (degrees) 167.01639027 
    1698 Shift along axis -225.67125473 
    1699  
    1700 
    1701 > select #6
    1702 
    1703 2 models selected 
    1704 
    1705 > select clear
    1706 
    1707 > hide #!6 models
    1708 
    1709 > show #!6 models
    1710 
    1711 > hide #!6 models
    1712 
    1713 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    1714 > figures/2k5u.pdb
    1715 
    1716 2k5u.pdb title: 
    1717 Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
    1718 info...] 
    1719  
    1720 Chain information for 2k5u.pdb 
    1721 --- 
    1722 Chain | Description 
    1723 14.1/A | adp-ribosylation factor 1 
    1724 14.2/A 14.3/A 14.4/A 14.5/A 14.6/A 14.7/A 14.8/A 14.9/A 14.10/A 14.11/A
    1725 14.12/A 14.13/A 14.14/A 14.15/A 14.16/A | adp-ribosylation factor 1 
    1726  
    1727 
    1728 > close #14.2-16
    1729 
    1730 > matchmaker #14 to #13
    1731 
    1732 Parameters 
    1733 --- 
    1734 Chain pairing | bb 
    1735 Alignment algorithm | Needleman-Wunsch 
    1736 Similarity matrix | BLOSUM-62 
    1737 SS fraction | 0.3 
    1738 Gap open (HH/SS/other) | 18/18/6 
    1739 Gap extend | 1 
    1740 SS matrix |  |  | H | S | O 
    1741 ---|---|---|--- 
    1742 H | 6 | -9 | -6 
    1743 S |  | 6 | -6 
    1744 O |  |  | 4 
    1745 Iteration cutoff | 2 
    1746  
    1747 Matchmaker ger2.pdb, chain A (#13) with 2k5u.pdb, chain A (#14.1), sequence
    1748 alignment score = 695 
    1749 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    1750 5.084) 
    1751  
    1752 
    1753 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    1754 > figures/2ksq.pdb
    1755 
    1756 2ksq.pdb title: 
    1757 The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
    1758 info...] 
    1759  
    1760 Chain information for 2ksq.pdb 
    1761 --- 
    1762 Chain | Description 
    1763 15.1/A | adp-ribosylation factor 1 
    1764 15.2/A 15.3/A 15.4/A 15.5/A 15.6/A 15.7/A 15.8/A 15.9/A 15.10/A 15.11/A
    1765 15.12/A 15.13/A 15.14/A 15.15/A 15.16/A 15.17/A 15.18/A 15.19/A 15.20/A | adp-
    1766 ribosylation factor 1 
    1767  
    1768 Drag select of 5382 atoms, 3600 residues, 4965 bonds 
    1769 
    1770 > matchmaker #15 to #15
    1771 
    1772 Specify a single 'to' model only 
    1773 
    1774 > matchmaker #15 to #14
    1775 
    1776 Parameters 
    1777 --- 
    1778 Chain pairing | bb 
    1779 Alignment algorithm | Needleman-Wunsch 
    1780 Similarity matrix | BLOSUM-62 
    1781 SS fraction | 0.3 
    1782 Gap open (HH/SS/other) | 18/18/6 
    1783 Gap extend | 1 
    1784 SS matrix |  |  | H | S | O 
    1785 ---|---|---|--- 
    1786 H | 6 | -9 | -6 
    1787 S |  | 6 | -6 
    1788 O |  |  | 4 
    1789 Iteration cutoff | 2 
    1790  
    1791 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.1), sequence
    1792 alignment score = 767.7 
    1793 RMSD between 95 pruned atom pairs is 1.117 angstroms; (across all 180 pairs:
    1794 8.424) 
    1795  
    1796 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.2), sequence
    1797 alignment score = 785.8 
    1798 RMSD between 95 pruned atom pairs is 1.110 angstroms; (across all 180 pairs:
    1799 7.715) 
    1800  
    1801 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.3), sequence
    1802 alignment score = 772.6 
    1803 RMSD between 94 pruned atom pairs is 1.129 angstroms; (across all 180 pairs:
    1804 7.309) 
    1805  
    1806 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.4), sequence
    1807 alignment score = 765.4 
    1808 RMSD between 97 pruned atom pairs is 1.068 angstroms; (across all 180 pairs:
    1809 8.269) 
    1810  
    1811 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.5), sequence
    1812 alignment score = 776.8 
    1813 RMSD between 95 pruned atom pairs is 1.109 angstroms; (across all 180 pairs:
    1814 8.459) 
    1815  
    1816 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.6), sequence
    1817 alignment score = 785.2 
    1818 RMSD between 95 pruned atom pairs is 1.137 angstroms; (across all 180 pairs:
    1819 8.055) 
    1820  
    1821 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.7), sequence
    1822 alignment score = 777.4 
    1823 RMSD between 100 pruned atom pairs is 1.135 angstroms; (across all 180 pairs:
    1824 9.001) 
    1825  
    1826 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.8), sequence
    1827 alignment score = 782.2 
    1828 RMSD between 96 pruned atom pairs is 1.178 angstroms; (across all 180 pairs:
    1829 8.591) 
    1830  
    1831 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.9), sequence
    1832 alignment score = 749.8 
    1833 RMSD between 100 pruned atom pairs is 1.116 angstroms; (across all 180 pairs:
    1834 9.079) 
    1835  
    1836 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.10), sequence
    1837 alignment score = 786.4 
    1838 RMSD between 101 pruned atom pairs is 1.122 angstroms; (across all 180 pairs:
    1839 8.786) 
    1840  
    1841 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.11), sequence
    1842 alignment score = 769 
    1843 RMSD between 95 pruned atom pairs is 1.117 angstroms; (across all 180 pairs:
    1844 8.678) 
    1845  
    1846 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.12), sequence
    1847 alignment score = 775.6 
    1848 RMSD between 95 pruned atom pairs is 1.081 angstroms; (across all 180 pairs:
    1849 7.518) 
    1850  
    1851 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.13), sequence
    1852 alignment score = 778.6 
    1853 RMSD between 102 pruned atom pairs is 1.069 angstroms; (across all 180 pairs:
    1854 8.329) 
    1855  
    1856 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.14), sequence
    1857 alignment score = 782.2 
    1858 RMSD between 92 pruned atom pairs is 1.079 angstroms; (across all 180 pairs:
    1859 8.049) 
    1860  
    1861 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.15), sequence
    1862 alignment score = 775 
    1863 RMSD between 94 pruned atom pairs is 1.224 angstroms; (across all 180 pairs:
    1864 9.000) 
    1865  
    1866 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.16), sequence
    1867 alignment score = 764.2 
    1868 RMSD between 93 pruned atom pairs is 1.072 angstroms; (across all 180 pairs:
    1869 9.002) 
    1870  
    1871 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.17), sequence
    1872 alignment score = 779.8 
    1873 RMSD between 96 pruned atom pairs is 1.161 angstroms; (across all 180 pairs:
    1874 8.165) 
    1875  
    1876 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.18), sequence
    1877 alignment score = 767.8 
    1878 RMSD between 97 pruned atom pairs is 1.130 angstroms; (across all 180 pairs:
    1879 8.283) 
    1880  
    1881 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.19), sequence
    1882 alignment score = 772 
    1883 RMSD between 95 pruned atom pairs is 1.127 angstroms; (across all 180 pairs:
    1884 8.772) 
    1885  
    1886 Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.20), sequence
    1887 alignment score = 772 
    1888 RMSD between 98 pruned atom pairs is 1.154 angstroms; (across all 180 pairs:
    1889 9.201) 
    1890  
    1891 
    1892 > close #15.2-20
    1893 
    1894 > select clear
    1895 
    1896 > matchmaker #15 to #13
    1897 
    1898 Parameters 
    1899 --- 
    1900 Chain pairing | bb 
    1901 Alignment algorithm | Needleman-Wunsch 
    1902 Similarity matrix | BLOSUM-62 
    1903 SS fraction | 0.3 
    1904 Gap open (HH/SS/other) | 18/18/6 
    1905 Gap extend | 1 
    1906 SS matrix |  |  | H | S | O 
    1907 ---|---|---|--- 
    1908 H | 6 | -9 | -6 
    1909 S |  | 6 | -6 
    1910 O |  |  | 4 
    1911 Iteration cutoff | 2 
    1912  
    1913 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.1), sequence
    1914 alignment score = 653.1 
    1915 RMSD between 107 pruned atom pairs is 1.190 angstroms; (across all 165 pairs:
    1916 3.564) 
    1917  
    1918 
    1919 > hide #13 models
    1920 
    1921 > hide #!14 models
    1922 
    1923 > hide #!15 models
    1924 
    1925 > show #!15 models
    1926 
    1927 > close #15
    1928 
    1929 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    1930 > figures/2ksq.pdb
    1931 
    1932 2ksq.pdb title: 
    1933 The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
    1934 info...] 
    1935  
    1936 Chain information for 2ksq.pdb 
    1937 --- 
    1938 Chain | Description 
    1939 15.1/A | adp-ribosylation factor 1 
    1940 15.2/A 15.3/A 15.4/A 15.5/A 15.6/A 15.7/A 15.8/A 15.9/A 15.10/A 15.11/A
    1941 15.12/A 15.13/A 15.14/A 15.15/A 15.16/A 15.17/A 15.18/A 15.19/A 15.20/A | adp-
    1942 ribosylation factor 1 
    1943  
    1944 
    1945 > show #13 models
    1946 
    1947 > hide #!15 models
    1948 
    1949 > show #!15 models
    1950 
    1951 > hide #!15 models
    1952 
    1953 > hide #13 models
    1954 
    1955 > show #13 models
    1956 
    1957 > show #!15 models
    1958 
    1959 > matchmaker #15 to #13
    1960 
    1961 Parameters 
    1962 --- 
    1963 Chain pairing | bb 
    1964 Alignment algorithm | Needleman-Wunsch 
    1965 Similarity matrix | BLOSUM-62 
    1966 SS fraction | 0.3 
    1967 Gap open (HH/SS/other) | 18/18/6 
    1968 Gap extend | 1 
    1969 SS matrix |  |  | H | S | O 
    1970 ---|---|---|--- 
    1971 H | 6 | -9 | -6 
    1972 S |  | 6 | -6 
    1973 O |  |  | 4 
    1974 Iteration cutoff | 2 
    1975  
    1976 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.1), sequence
    1977 alignment score = 653.1 
    1978 RMSD between 107 pruned atom pairs is 1.190 angstroms; (across all 165 pairs:
    1979 3.564) 
    1980  
    1981 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.2), sequence
    1982 alignment score = 673.5 
    1983 RMSD between 114 pruned atom pairs is 1.167 angstroms; (across all 165 pairs:
    1984 3.522) 
    1985  
    1986 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.3), sequence
    1987 alignment score = 660.3 
    1988 RMSD between 110 pruned atom pairs is 1.141 angstroms; (across all 165 pairs:
    1989 3.603) 
    1990  
    1991 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.4), sequence
    1992 alignment score = 653.1 
    1993 RMSD between 110 pruned atom pairs is 1.124 angstroms; (across all 165 pairs:
    1994 3.563) 
    1995  
    1996 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.5), sequence
    1997 alignment score = 654.9 
    1998 RMSD between 110 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    1999 3.685) 
    2000  
    2001 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.6), sequence
    2002 alignment score = 656.7 
    2003 RMSD between 107 pruned atom pairs is 1.142 angstroms; (across all 165 pairs:
    2004 3.681) 
    2005  
    2006 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.7), sequence
    2007 alignment score = 665.1 
    2008 RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    2009 3.623) 
    2010  
    2011 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.8), sequence
    2012 alignment score = 663.9 
    2013 RMSD between 112 pruned atom pairs is 1.157 angstroms; (across all 165 pairs:
    2014 3.648) 
    2015  
    2016 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.9), sequence
    2017 alignment score = 638.1 
    2018 RMSD between 115 pruned atom pairs is 1.091 angstroms; (across all 165 pairs:
    2019 3.623) 
    2020  
    2021 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.10), sequence
    2022 alignment score = 671.1 
    2023 RMSD between 119 pruned atom pairs is 1.108 angstroms; (across all 165 pairs:
    2024 3.493) 
    2025  
    2026 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.11), sequence
    2027 alignment score = 647.1 
    2028 RMSD between 107 pruned atom pairs is 1.106 angstroms; (across all 165 pairs:
    2029 3.749) 
    2030  
    2031 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.12), sequence
    2032 alignment score = 660.3 
    2033 RMSD between 116 pruned atom pairs is 1.120 angstroms; (across all 165 pairs:
    2034 3.698) 
    2035  
    2036 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.13), sequence
    2037 alignment score = 663.3 
    2038 RMSD between 114 pruned atom pairs is 1.015 angstroms; (across all 165 pairs:
    2039 3.578) 
    2040  
    2041 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.14), sequence
    2042 alignment score = 663.9 
    2043 RMSD between 108 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    2044 3.655) 
    2045  
    2046 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.15), sequence
    2047 alignment score = 656.7 
    2048 RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
    2049 3.660) 
    2050  
    2051 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.16), sequence
    2052 alignment score = 648.9 
    2053 RMSD between 114 pruned atom pairs is 1.154 angstroms; (across all 165 pairs:
    2054 3.728) 
    2055  
    2056 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.17), sequence
    2057 alignment score = 648.9 
    2058 RMSD between 108 pruned atom pairs is 1.173 angstroms; (across all 165 pairs:
    2059 3.507) 
    2060  
    2061 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.18), sequence
    2062 alignment score = 649.5 
    2063 RMSD between 110 pruned atom pairs is 1.120 angstroms; (across all 165 pairs:
    2064 3.716) 
    2065  
    2066 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.19), sequence
    2067 alignment score = 656.7 
    2068 RMSD between 110 pruned atom pairs is 1.136 angstroms; (across all 165 pairs:
    2069 3.583) 
    2070  
    2071 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.20), sequence
    2072 alignment score = 656.7 
    2073 RMSD between 113 pruned atom pairs is 1.167 angstroms; (across all 165 pairs:
    2074 3.587) 
    2075  
    2076 
    2077 > hide #15.1 models
    2078 
    2079 > hide #15.2 models
    2080 
    2081 > hide #15.3 models
    2082 
    2083 > hide #15.4 models
    2084 
    2085 > hide #15.5 models
    2086 
    2087 > hide #!15 models
    2088 
    2089 > show #15.1 models
    2090 
    2091 > hide #!15 models
    2092 
    2093 > hide #15.1 models
    2094 
    2095 > hide #15.6 models
    2096 
    2097 > hide #15.8 models
    2098 
    2099 > hide #15.7 models
    2100 
    2101 > hide #15.20 models
    2102 
    2103 > hide #15.19 models
    2104 
    2105 > hide #15.18 models
    2106 
    2107 > hide #15.17 models
    2108 
    2109 > hide #15.16 models
    2110 
    2111 > hide #15.15 models
    2112 
    2113 > hide #15.14 models
    2114 
    2115 > hide #15.13 models
    2116 
    2117 > hide #15.11 models
    2118 
    2119 > hide #15.12 models
    2120 
    2121 > hide #15.10 models
    2122 
    2123 > hide #15.9 models
    2124 
    2125 > show #15.1 models
    2126 
    2127 > hide #15.1 models
    2128 
    2129 > show #15.2 models
    2130 
    2131 > hide #15.2 models
    2132 
    2133 > show #15.3 models
    2134 
    2135 > hide #15.3 models
    2136 
    2137 > show #15.4 models
    2138 
    2139 > hide #15.4 models
    2140 
    2141 > show #15.5 models
    2142 
    2143 > hide #15.5 models
    2144 
    2145 > show #15.6 models
    2146 
    2147 > hide #15.6 models
    2148 
    2149 > show #15.7 models
    2150 
    2151 > hide #15.7 models
    2152 
    2153 > show #15.8 models
    2154 
    2155 > hide #15.8 models
    2156 
    2157 > show #15.9 models
    2158 
    2159 > hide #15.9 models
    2160 
    2161 > show #15.10 models
    2162 
    2163 > hide #15.10 models
    2164 
    2165 > show #15.11 models
    2166 
    2167 > hide #15.11 models
    2168 
    2169 > show #15.12 models
    2170 
    2171 > hide #15.12 models
    2172 
    2173 > show #15.13 models
    2174 
    2175 > hide #15.13 models
    2176 
    2177 > show #15.14 models
    2178 
    2179 > hide #15.14 models
    2180 
    2181 > show #15.15 models
    2182 
    2183 > show #!14 models
    2184 
    2185 > hide #!14 models
    2186 
    2187 > show #!9 models
    2188 
    2189 > hide #!9 models
    2190 
    2191 > show #!8 models
    2192 
    2193 > hide #!8 models
    2194 
    2195 > show #!7 models
    2196 
    2197 > hide #!7 models
    2198 
    2199 > show #!6 models
    2200 
    2201 > close #15.1-14
    2202 
    2203 > hide #!6 models
    2204 
    2205 > close #15.16-20
    2206 
    2207 > hide #13 models
    2208 
    2209 Drag select of 262 atoms, 180 residues, 241 bonds 
    2210 
    2211 > hide sel atoms
    2212 
    2213 > select clear
    2214 
    2215 > select ::name="MYR"
    2216 
    2217 126 atoms, 123 bonds, 3 residues, 3 models selected 
    2218 
    2219 > select #12
    2220 
    2221 2952 atoms, 2981 bonds, 182 residues, 2 models selected 
    2222 
    2223 > ~select #12
    2224 
    2225 Nothing selected 
    2226 
    2227 > select clear
    2228 
    2229 > select ::name="MYR"
    2230 
    2231 126 atoms, 123 bonds, 3 residues, 3 models selected 
    2232 
    2233 > show sel & #15.15 atoms
    2234 
    2235 > select clear
    2236 
    2237 > select ::name="GTP"
    2238 
    2239 43 atoms, 45 bonds, 1 residue, 1 model selected 
    2240 
    2241 > show sel atoms
    2242 
    2243 > color sel byhetero
    2244 
    2245 > select clear
    2246 
    2247 > hide #!15 models
    2248 
    2249 > select #15
    2250 
    2251 3045 atoms, 3079 bonds, 187 residues, 2 models selected 
    2252 
    2253 > show #!15 models
    2254 
    2255 > color sel #7281dbff
    2256 
    2257 > color sel #7383dcff
    2258 
    2259 > color sel #7281daff
    2260 
    2261 > color sel #6d7cd1ff
    2262 
    2263 > color sel #6674c3ff
    2264 
    2265 > color sel #616ebaff
    2266 
    2267 > color sel #5e6bb5ff
    2268 
    2269 > color sel #5d6ab3ff
    2270 
    2271 > color sel #5c68b0ff
    2272 
    2273 > color sel #5a67adff
    2274 
    2275 > color sel #5a66acff
    2276 
    2277 > color sel #5965abff
    2278 
    2279 > select clear
    2280 
    2281 Drag select of 85 atoms, 180 residues, 86 bonds 
    2282 
    2283 > color sel byhetero
    2284 
    2285 > select clear
    2286 
    2287 > preset cartoons/nucleotides cylinders/stubs
    2288 
    2289 Changed 0 atom styles 
    2290 Preset expands to these ChimeraX commands:
    2291 
    2292    
    2293    
    2294     show nucleic
    2295     hide protein|solvent|H
    2296     surf hide
    2297     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    2298     cartoon
    2299     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    2300     cartoon style ~(nucleic|strand) x round
    2301     cartoon style (nucleic|strand) x rect
    2302     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    2303     cartoon style nucleic x round width 1.6 thick 1.6
    2304     nucleotides stubs
    2305 
    2306  
    2307 
    2308 > select ::name="GTP"
    2309 
    2310 43 atoms, 45 bonds, 1 residue, 1 model selected 
    2311 
    2312 > color sel #ff007fff
    2313 
    2314 > color sel byhetero
    2315 
    2316 > select clear
    2317 
    2318 > hide #!15 models
    2319 
    2320 > hide #15.15 models
    2321 
    2322 > show #1 models
    2323 
    2324 > show #11 models
    2325 
    2326 > hide #11 models
    2327 
    2328 > show #!12 models
    2329 
    2330 > show #13 models
    2331 
    2332 > hide #!12 models
    2333 
    2334 > hide #13 models
    2335 
    2336 > show #!14 models
    2337 
    2338 > show #4 models
    2339 
    2340 > hide #1 models
    2341 
    2342 > show #!15 models
    2343 
    2344 > hide #!14 models
    2345 
    2346 > hide #!15 models
    2347 
    2348 > show #15.15 models
    2349 
    2350 > hide #15.15 models
    2351 
    2352 > show #15.15 models
    2353 
    2354 > hide #!15 models
    2355 
    2356 > show #!14 models
    2357 
    2358 > show #!15 models
    2359 
    2360 > hide #15.15 models
    2361 
    2362 > hide #!15 models
    2363 
    2364 > show #15.15 models
    2365 
    2366 > hide #4 models
    2367 
    2368 > hide #!14 models
    2369 
    2370 > hide #!15 models
    2371 
    2372 > hide #15.15 models
    2373 
    2374 > show #1 models
    2375 
    2376 > show #4 models
    2377 
    2378 > hide #4 models
    2379 
    2380 > show #11 models
    2381 
    2382 > hide #11 models
    2383 
    2384 > show #!12 models
    2385 
    2386 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2387 
    2388 > hide #1 models
    2389 
    2390 > hide #!12 models
    2391 
    2392 > show #13 models
    2393 
    2394 > hide #13 models
    2395 
    2396 > show #!14 models
    2397 
    2398 > select #14
    2399 
    2400 2952 atoms, 2981 bonds, 182 residues, 2 models selected 
    2401 
    2402 > color sel #7281dbff
    2403 
    2404 > color sel byhetero
    2405 
    2406 > color sel #240000ff
    2407 
    2408 > color sel #ccccccff
    2409 
    2410 > color sel #ffffffff
    2411 
    2412 > color sel #d9d9d9ff
    2413 
    2414 > color sel #ffffffff
    2415 
    2416 > color sel #ffaa55ff
    2417 
    2418 > color sel #ffffffff
    2419 
    2420 > color sel #abb8ffff
    2421 
    2422 > color sel #8597ffff
    2423 
    2424 > color sel byhetero
    2425 
    2426 > select clear
    2427 
    2428 > select ::name="GDP"
    2429 
    2430 80 atoms, 84 bonds, 2 residues, 2 models selected 
    2431 
    2432 > color (#14.1 & sel) #ffaaffff
    2433 
    2434 > color sel & #14.1 byhetero
    2435 
    2436 > select clear
    2437 
    2438 > hide #12.1 models
    2439 
    2440 > show #4 models
    2441 
    2442 > hide #4 models
    2443 
    2444 > show #4 models
    2445 
    2446 > show #!2 models
    2447 
    2448 > hide #!2 models
    2449 
    2450 > show #1 models
    2451 
    2452 > hide #1 models
    2453 
    2454 > show #1 models
    2455 
    2456 > hide #1 models
    2457 
    2458 > show #1 models
    2459 
    2460 > hide #1 models
    2461 
    2462 > show #1 models
    2463 
    2464 > hide #4 models
    2465 
    2466 > hide #!14 models
    2467 
    2468 > show #!12 models
    2469 
    2470 > hide #!12 models
    2471 
    2472 > show #12.1 models
    2473 
    2474 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2475 
    2476 > show #!2 models
    2477 
    2478 > hide #!2 models
    2479 
    2480 > hide #12.1 models
    2481 
    2482 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    2483 
    2484 > hide #!12 models
    2485 
    2486 > show #!12 models
    2487 
    2488 > hide #!12 models
    2489 
    2490 > show #4 models
    2491 
    2492 > hide #1 models
    2493 
    2494 > show #!14 models
    2495 
    2496 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    2497 
    2498 > hide #4 models
    2499 
    2500 > hide #!14 models
    2501 
    2502 > show #!9 models
    2503 
    2504 > hide #!9 models
    2505 
    2506 > show #!8 models
    2507 
    2508 > select #8/B
    2509 
    2510 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    2511 
    2512 > select #8/D
    2513 
    2514 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    2515 
    2516 > hide sel atoms
    2517 
    2518 > hide sel cartoons
    2519 
    2520 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    2521 
    2522 > hide #!8 models
    2523 
    2524 > select #8
    2525 
    2526 21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected 
    2527 
    2528 > show #1 models
    2529 
    2530 > ui mousemode right "rotate selected models"
    2531 
    2532 > ui mousemode right rotate
    2533 
    2534 > ui mousemode right translate
    2535 
    2536 > show #12.1 models
    2537 
    2538 > hide #12.1 models
    2539 
    2540 > show #12.1 models
    2541 
    2542 > hide #1 models
    2543 
    2544 > show #1 models
    2545 
    2546 > show #!2 models
    2547 
    2548 > hide #!2 models
    2549 
    2550 > hide #!12 models
    2551 
    2552 > show #4 models
    2553 
    2554 > hide #1 models
    2555 
    2556 > show #!14 models
    2557 
    2558 > hide #12.1 models
    2559 
    2560 > show #!15 models
    2561 
    2562 > hide #!15 models
    2563 
    2564 > show #15.15 models
    2565 
    2566 > hide #15.15 models
    2567 
    2568 > show #15.15 models
    2569 
    2570 > hide #15.15 models
    2571 
    2572 > hide #!14 models
    2573 
    2574 > hide #!15 models
    2575 
    2576 > hide #4 models
    2577 
    2578 > show #4 models
    2579 
    2580 > show #!12 models
    2581 
    2582 > hide #!12 models
    2583 
    2584 > show #12.1 models
    2585 
    2586 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2587 
    2588 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2589 
    2590 > hide #4 models
    2591 
    2592 > hide #!12 models
    2593 
    2594 > show #!14 models
    2595 
    2596 > show #4 models
    2597 
    2598 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    2599 
    2600 > hide #!14 models
    2601 
    2602 > hide #12.1 models
    2603 
    2604 > ~select #8
    2605 
    2606 Nothing selected 
    2607 
    2608 > hide #4 models
    2609 
    2610 > show #!12 models
    2611 
    2612 > hide #!12 models
    2613 
    2614 > show #12.1 models
    2615 
    2616 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    2617 
    2618 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    2619 
    2620 > save C:\Users\Arnold\Desktop\image8.png supersample 3
    2621 
    2622 > hide #12.1 models
    2623 
    2624 > hide #!12 models
    2625 
    2626 > show #1 models
    2627 
    2628 > show #12.1 models
    2629 
    2630 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2631 
    2632 > hide #12.1 models
    2633 
    2634 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    2635 
    2636 > show #4 models
    2637 
    2638 > hide #1 models
    2639 
    2640 > hide #!12 models
    2641 
    2642 > show #!14 models
    2643 
    2644 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    2645 
    2646 > hide #4 models
    2647 
    2648 > show #!2 models
    2649 
    2650 > hide #!2 models
    2651 
    2652 > hide #!14 models
    2653 
    2654 > show #!15 models
    2655 
    2656 > show #15.15 models
    2657 
    2658 > hide #!15 models
    2659 
    2660 > show #1 models
    2661 
    2662 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    2663 
    2664 > hide #1 models
    2665 
    2666 > show #!2 models
    2667 
    2668 > hide #!2 models
    2669 
    2670 > show #!3 models
    2671 
    2672 > hide #!3 models
    2673 
    2674 > show #4 models
    2675 
    2676 > hide #4 models
    2677 
    2678 > show #4 models
    2679 
    2680 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    2681 
    2682 > hide #4 models
    2683 
    2684 > show #4 models
    2685 
    2686 > show #12.1 models
    2687 
    2688 > hide #12.1 models
    2689 
    2690 > show #12.1 models
    2691 
    2692 > hide #4 models
    2693 
    2694 > hide #15.15 models
    2695 
    2696 > hide #12.1 models
    2697 
    2698 > hide #!12 models
    2699 
    2700 > show #1 models
    2701 
    2702 > show #!12 models
    2703 
    2704 > hide #!12 models
    2705 
    2706 > show #12.1 models
    2707 
    2708 > show #11 models
    2709 
    2710 > hide #11 models
    2711 
    2712 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    2713 
    2714 Chain information for ger2.pdb #16 
    2715 --- 
    2716 Chain | Description 
    2717 A | No description available 
    2718 C | No description available 
    2719  
    2720 
    2721 > select #16
    2722 
    2723 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    2724 
    2725 > ui mousemode right "translate selected models"
    2726 
    2727 Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
    2728 2990 atoms 
    2729 average map value = 2.881, steps = 72 
    2730 shifted from previous position = 3.15 
    2731 rotated from previous position = 3.4 degrees 
    2732 atoms outside contour = 2589, contour level = 13.94 
    2733  
    2734 Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
    2735 coordinates: 
    2736 Matrix rotation and translation 
    2737 -0.91511885 -0.20261121 0.34857737 191.41831251 
    2738 0.03540339 0.82084041 0.57005931 133.43896567 
    2739 -0.40162680 0.53401284 -0.74399341 293.87252456 
    2740 Axis -0.04575115 0.95217945 0.30209457 
    2741 Axis point 123.84831938 0.00000000 104.11434027 
    2742 Rotation angle (degrees) 156.80008533 
    2743 Shift along axis 207.07752694 
    2744  
    2745 Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
    2746 2990 atoms 
    2747 average map value = 2.174, steps = 136 
    2748 shifted from previous position = 3.92 
    2749 rotated from previous position = 11.1 degrees 
    2750 atoms outside contour = 2693, contour level = 13.94 
    2751  
    2752 Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
    2753 coordinates: 
    2754 Matrix rotation and translation 
    2755 -0.95811570 -0.20329010 0.20171129 203.21957913 
    2756 -0.01141659 0.73089825 0.68239095 114.52557294 
    2757 -0.28615376 0.65150663 -0.70260597 292.79453452 
    2758 Axis -0.05881058 0.92900290 0.36536957 
    2759 Axis point 121.00023796 0.00000000 108.40830819 
    2760 Rotation angle (degrees) 164.77711778 
    2761 Shift along axis 201.42134211 
    2762  
    2763 
    2764 > matchmaker #16 to #3
    2765 
    2766 No 'to' model specified 
    2767 
    2768 > matchmaker #16 to #4
    2769 
    2770 Parameters 
    2771 --- 
    2772 Chain pairing | bb 
    2773 Alignment algorithm | Needleman-Wunsch 
    2774 Similarity matrix | BLOSUM-62 
    2775 SS fraction | 0.3 
    2776 Gap open (HH/SS/other) | 18/18/6 
    2777 Gap extend | 1 
    2778 SS matrix |  |  | H | S | O 
    2779 ---|---|---|--- 
    2780 H | 6 | -9 | -6 
    2781 S |  | 6 | -6 
    2782 O |  |  | 4 
    2783 Iteration cutoff | 2 
    2784  
    2785 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
    2786 with ger2.pdb, chain C (#16), sequence alignment score = 1010.5 
    2787 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    2788 1.454) 
    2789  
    2790 Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
    2791 2990 atoms 
    2792 average map value = 8.581, steps = 124 
    2793 shifted from previous position = 5.16 
    2794 rotated from previous position = 21.4 degrees 
    2795 atoms outside contour = 2090, contour level = 13.94 
    2796  
    2797 Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
    2798 coordinates: 
    2799 Matrix rotation and translation 
    2800 -0.93445292 -0.15891148 -0.31866108 250.14498889 
    2801 -0.19549211 0.97691904 0.08609311 171.18116813 
    2802 0.29762489 0.14274569 -0.94395079 330.03844216 
    2803 Axis 0.09138035 -0.99406645 -0.05900439 
    2804 Axis point 107.34815589 0.00000000 181.15022546 
    2805 Rotation angle (degrees) 161.94183740 
    2806 Shift along axis -166.78083774 
    2807  
    2808 
    2809 > ~select #16
    2810 
    2811 Nothing selected 
    2812 
    2813 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    2814 > figures/2k5u.pdb
    2815 
    2816 2k5u.pdb title: 
    2817 Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
    2818 info...] 
    2819  
    2820 Chain information for 2k5u.pdb 
    2821 --- 
    2822 Chain | Description 
    2823 17.1/A | adp-ribosylation factor 1 
    2824 17.2/A 17.3/A 17.4/A 17.5/A 17.6/A 17.7/A 17.8/A 17.9/A 17.10/A 17.11/A
    2825 17.12/A 17.13/A 17.14/A 17.15/A 17.16/A | adp-ribosylation factor 1 
    2826  
    2827 
    2828 > close #17.2-16
    2829 
    2830 > matchmaker #17 to #16
    2831 
    2832 Parameters 
    2833 --- 
    2834 Chain pairing | bb 
    2835 Alignment algorithm | Needleman-Wunsch 
    2836 Similarity matrix | BLOSUM-62 
    2837 SS fraction | 0.3 
    2838 Gap open (HH/SS/other) | 18/18/6 
    2839 Gap extend | 1 
    2840 SS matrix |  |  | H | S | O 
    2841 ---|---|---|--- 
    2842 H | 6 | -9 | -6 
    2843 S |  | 6 | -6 
    2844 O |  |  | 4 
    2845 Iteration cutoff | 2 
    2846  
    2847 Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
    2848 alignment score = 695 
    2849 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    2850 5.084) 
    2851  
    2852 
    2853 > hide #12.1 models
    2854 
    2855 > hide #!12 models
    2856 
    2857 > hide #16 models
    2858 
    2859 > show #!14 models
    2860 
    2861 > select ::name="GDP"
    2862 
    2863 120 atoms, 126 bonds, 3 residues, 3 models selected 
    2864 
    2865 > color (#14.1#17.1 & sel) #55ffffff
    2866 
    2867 > color (#14.1#17.1 & sel) #ffaaffff
    2868 
    2869 > color sel & #14.1#17.1 byhetero
    2870 
    2871 > select clear
    2872 
    2873 > hide #!14 models
    2874 
    2875 > show #!12 models
    2876 
    2877 > hide #!12 models
    2878 
    2879 > show #12.1 models
    2880 
    2881 > hide #12.1 models
    2882 
    2883 > show #12.1 models
    2884 
    2885 > hide #!12 models
    2886 
    2887 > hide #12.1 models
    2888 
    2889 > hide #!17 models
    2890 
    2891 > hide #17.1 models
    2892 
    2893 > hide #1 models
    2894 
    2895 > show #!3 models
    2896 
    2897 > hide #!3 models
    2898 
    2899 > show #4 models
    2900 
    2901 > show #13 models
    2902 
    2903 > hide #13 models
    2904 
    2905 > show #!14 models
    2906 
    2907 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    2908 > figures/2k5u.pdb
    2909 
    2910 2k5u.pdb title: 
    2911 Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
    2912 info...] 
    2913  
    2914 Chain information for 2k5u.pdb 
    2915 --- 
    2916 Chain | Description 
    2917 18.1/A | adp-ribosylation factor 1 
    2918 18.2/A 18.3/A 18.4/A 18.5/A 18.6/A 18.7/A 18.8/A 18.9/A 18.10/A 18.11/A
    2919 18.12/A 18.13/A 18.14/A 18.15/A 18.16/A | adp-ribosylation factor 1 
    2920  
    2921 
    2922 > close #18.2-16
    2923 
    2924 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    2925 
    2926 Chain information for ger2.pdb #19 
    2927 --- 
    2928 Chain | Description 
    2929 A | No description available 
    2930 C | No description available 
    2931  
    2932 
    2933 > matchmaker #19 to #4
    2934 
    2935 Parameters 
    2936 --- 
    2937 Chain pairing | bb 
    2938 Alignment algorithm | Needleman-Wunsch 
    2939 Similarity matrix | BLOSUM-62 
    2940 SS fraction | 0.3 
    2941 Gap open (HH/SS/other) | 18/18/6 
    2942 Gap extend | 1 
    2943 SS matrix |  |  | H | S | O 
    2944 ---|---|---|--- 
    2945 H | 6 | -9 | -6 
    2946 S |  | 6 | -6 
    2947 O |  |  | 4 
    2948 Iteration cutoff | 2 
    2949  
    2950 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
    2951 with ger2.pdb, chain C (#19), sequence alignment score = 1010.5 
    2952 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    2953 1.454) 
    2954  
    2955 
    2956 > matchmaker #18 to #19
    2957 
    2958 Parameters 
    2959 --- 
    2960 Chain pairing | bb 
    2961 Alignment algorithm | Needleman-Wunsch 
    2962 Similarity matrix | BLOSUM-62 
    2963 SS fraction | 0.3 
    2964 Gap open (HH/SS/other) | 18/18/6 
    2965 Gap extend | 1 
    2966 SS matrix |  |  | H | S | O 
    2967 ---|---|---|--- 
    2968 H | 6 | -9 | -6 
    2969 S |  | 6 | -6 
    2970 O |  |  | 4 
    2971 Iteration cutoff | 2 
    2972  
    2973 Matchmaker ger2.pdb, chain A (#19) with 2k5u.pdb, chain A (#18.1), sequence
    2974 alignment score = 695 
    2975 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    2976 5.084) 
    2977  
    2978 
    2979 > hide #!18 models
    2980 
    2981 > hide #18.1 models
    2982 
    2983 > hide #19 models
    2984 
    2985 > show #!18 models
    2986 
    2987 > hide #!18 models
    2988 
    2989 > show #18.1 models
    2990 
    2991 > view #!9 clip false
    2992 
    2993 No displayed objects specified. 
    2994 
    2995 > select ::name="GDP"
    2996 
    2997 160 atoms, 168 bonds, 4 residues, 4 models selected 
    2998 
    2999 > color (#14.1#18.1 & sel) #55ffffff
    3000 
    3001 > color (#14.1#18.1 & sel) #ffaaffff
    3002 
    3003 > color sel & #14.1#18.1 byhetero
    3004 
    3005 > select clear
    3006 
    3007 > hide #18.1 models
    3008 
    3009 > hide #!18 models
    3010 
    3011 > hide #!14 models
    3012 
    3013 > hide #4 models
    3014 
    3015 > show #1 models
    3016 
    3017 > show #!12 models
    3018 
    3019 > show #12.1 models
    3020 
    3021 > hide #!12 models
    3022 
    3023 > show #!17 models
    3024 
    3025 > hide #!17 models
    3026 
    3027 > show #17.1 models
    3028 
    3029 > hide #17.1 models
    3030 
    3031 > show #17.1 models
    3032 
    3033 > hide #!17 models
    3034 
    3035 > hide #12.1 models
    3036 
    3037 > hide #17.1 models
    3038 
    3039 > show #17.1 models
    3040 
    3041 > show #12.1 models
    3042 
    3043 > show #!18 models
    3044 
    3045 > hide #!18 models
    3046 
    3047 > show #18.1 models
    3048 
    3049 > hide #18.1 models
    3050 
    3051 > select ::name="GDP"
    3052 
    3053 160 atoms, 168 bonds, 4 residues, 4 models selected 
    3054 
    3055 > color (#12.1#17.1 & sel) #55ffffff
    3056 
    3057 > color (#12.1#17.1 & sel) #ffaaffff
    3058 
    3059 > color sel & #12.1#17.1 byhetero
    3060 
    3061 > select clear
    3062 
    3063 > hide #!17 models
    3064 
    3065 > hide #!12 models
    3066 
    3067 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    3068 
    3069 > hide #17.1 models
    3070 
    3071 > hide #!18 models
    3072 
    3073 > hide #12.1 models
    3074 
    3075 > show #4 models
    3076 
    3077 > hide #1 models
    3078 
    3079 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    3080 
    3081 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    3082 
    3083 > hide #4 models
    3084 
    3085 > show #1 models
    3086 
    3087 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    3088 
    3089 > hide #1 models
    3090 
    3091 > show #1 models
    3092 
    3093 > show #!12 models
    3094 
    3095 > hide #!12 models
    3096 
    3097 > show #12.1 models
    3098 
    3099 > show #17.1 models
    3100 
    3101 > show #18.1 models
    3102 
    3103 > hide #18.1 models
    3104 
    3105 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    3106 
    3107 > hide #!12 models
    3108 
    3109 > hide #12.1 models
    3110 
    3111 > hide #!17 models
    3112 
    3113 > hide #17.1 models
    3114 
    3115 > hide #!18 models
    3116 
    3117 > show #4 models
    3118 
    3119 > hide #1 models
    3120 
    3121 > show #!18 models
    3122 
    3123 > hide #!18 models
    3124 
    3125 > show #18.1 models
    3126 
    3127 > show #!14 models
    3128 
    3129 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    3130 
    3131 > hide #!18 models
    3132 
    3133 > hide #18.1 models
    3134 
    3135 > hide #!14 models
    3136 
    3137 > show #!8 models
    3138 
    3139 > hide #4 models
    3140 
    3141 > select #8/D
    3142 
    3143 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    3144 
    3145 > show sel cartoons
    3146 
    3147 > select clear
    3148 
    3149 > save C:\Users\Arnold\Desktop\image8.png supersample 3
    3150 
    3151 > hide #!8 models
    3152 
    3153 > show #!15 models
    3154 
    3155 > show #15.15 models
    3156 
    3157 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    3158 
    3159 > hide #15.15 models
    3160 
    3161 > hide #!15 models
    3162 
    3163 > show #1 models
    3164 
    3165 > open C:/Users/Arnold/Downloads/AF-P39993-F1-model_v1.pdb
    3166 
    3167 AF-P39993-F1-model_v1.pdb title: 
    3168 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    3169 (P39993) [more info...] 
    3170  
    3171 Chain information for AF-P39993-F1-model_v1.pdb #20 
    3172 --- 
    3173 Chain | Description 
    3174 A | arf guanine-nucleotide exchange factor 2 
    3175  
    3176 
    3177 > close #20
    3178 
    3179 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3180 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3181 
    3182 AF-P47102-F1-model_v1 (1).pdb title: 
    3183 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3184 (P47102) [more info...] 
    3185  
    3186 Chain information for AF-P47102-F1-model_v1 (1).pdb #20 
    3187 --- 
    3188 Chain | Description 
    3189 A | arf guanine-nucleotide exchange factor 1 
    3190  
    3191 
    3192 > matchmaker #20 to #1
    3193 
    3194 Parameters 
    3195 --- 
    3196 Chain pairing | bb 
    3197 Alignment algorithm | Needleman-Wunsch 
    3198 Similarity matrix | BLOSUM-62 
    3199 SS fraction | 0.3 
    3200 Gap open (HH/SS/other) | 18/18/6 
    3201 Gap extend | 1 
    3202 SS matrix |  |  | H | S | O 
    3203 ---|---|---|--- 
    3204 H | 6 | -9 | -6 
    3205 S |  | 6 | -6 
    3206 O |  |  | 4 
    3207 Iteration cutoff | 2 
    3208  
    3209 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    3210 with AF-P47102-F1-model_v1 (1).pdb, chain A (#20), sequence alignment score =
    3211 3608.2 
    3212 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    3213 5.511) 
    3214  
    3215 Drag select of 16 residues 
    3216 
    3217 > ui tool show "Show Sequence Viewer"
    3218 
    3219 > sequence chain #10/A #20/A
    3220 
    3221 Alignment identifier is 1 
    3222 Seqview [ID: 1] region 2 chains [1-207] RMSD: 344.416 
    3223  
    3224 Drag select of 14 residues 
    3225 Seqview [ID: 1] region 2 chains [978-979] RMSD: 388.274 
    3226  
    3227 Seqview [ID: 1] region 2 chains [1-977] RMSD: 310.189 
    3228  
    3229 
    3230 > delete atoms (#20 & sel)
    3231 
    3232 > delete bonds (#20 & sel)
    3233 
    3234 Seqview [ID: 1] region 2 chains [993] RMSD: 391.524 
    3235  
    3236 Seqview [ID: 1] region 2 chains [999-1001] RMSD: 376.840 
    3237  
    3238 Seqview [ID: 1] region 2 chains [998-1408] RMSD: 315.123 
    3239  
    3240 
    3241 > delete atoms (#20 & sel)
    3242 
    3243 > delete bonds (#20 & sel)
    3244 
    3245 > select clear
    3246 
    3247 > select clear
    3248 
    3249 > hide #20 models
    3250 
    3251 > show #20 models
    3252 
    3253 > select #20
    3254 
    3255 155 atoms, 156 bonds, 20 residues, 1 model selected 
    3256 
    3257 > ~select #20
    3258 
    3259 Nothing selected 
    3260 
    3261 > select #20
    3262 
    3263 155 atoms, 156 bonds, 20 residues, 1 model selected 
    3264 
    3265 > preset cartoons/nucleotides cylinders/stubs
    3266 
    3267 Changed 0 atom styles 
    3268 Preset expands to these ChimeraX commands:
    3269 
    3270    
    3271    
    3272     show nucleic
    3273     hide protein|solvent|H
    3274     surf hide
    3275     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    3276     cartoon
    3277     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    3278     cartoon style ~(nucleic|strand) x round
    3279     cartoon style (nucleic|strand) x rect
    3280     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    3281     cartoon style nucleic x round width 1.6 thick 1.6
    3282     nucleotides stubs
    3283 
    3284  
    3285 
    3286 > select clear
    3287 
    3288 > select #20
    3289 
    3290 155 atoms, 156 bonds, 20 residues, 1 model selected 
    3291 
    3292 > color sel #7281dbff
    3293 
    3294 > color sel #4377a7ff
    3295 
    3296 > color sel #ffaaffff
    3297 
    3298 > select clear
    3299 
    3300 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3301 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3302 
    3303 AF-P47102-F1-model_v1 (1).pdb title: 
    3304 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3305 (P47102) [more info...] 
    3306  
    3307 Chain information for AF-P47102-F1-model_v1 (1).pdb #21 
    3308 --- 
    3309 Chain | Description 
    3310 A | arf guanine-nucleotide exchange factor 1 
    3311  
    3312 
    3313 > matchmaker #20 to #1/B
    3314 
    3315 Parameters 
    3316 --- 
    3317 Chain pairing | bb 
    3318 Alignment algorithm | Needleman-Wunsch 
    3319 Similarity matrix | BLOSUM-62 
    3320 SS fraction | 0.3 
    3321 Gap open (HH/SS/other) | 18/18/6 
    3322 Gap extend | 1 
    3323 SS matrix |  |  | H | S | O 
    3324 ---|---|---|--- 
    3325 H | 6 | -9 | -6 
    3326 S |  | 6 | -6 
    3327 O |  |  | 4 
    3328 Iteration cutoff | 2 
    3329  
    3330 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    3331 with AF-P47102-F1-model_v1 (1).pdb, chain A (#20), sequence alignment score =
    3332 2159.3 
    3333 RMSD between 4 pruned atom pairs is 0.236 angstroms; (across all 4 pairs:
    3334 0.236) 
    3335  
    3336 
    3337 > matchmaker #21 to #1/B
    3338 
    3339 Parameters 
    3340 --- 
    3341 Chain pairing | bb 
    3342 Alignment algorithm | Needleman-Wunsch 
    3343 Similarity matrix | BLOSUM-62 
    3344 SS fraction | 0.3 
    3345 Gap open (HH/SS/other) | 18/18/6 
    3346 Gap extend | 1 
    3347 SS matrix |  |  | H | S | O 
    3348 ---|---|---|--- 
    3349 H | 6 | -9 | -6 
    3350 S |  | 6 | -6 
    3351 O |  |  | 4 
    3352 Iteration cutoff | 2 
    3353  
    3354 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    3355 with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
    3356 3579.8 
    3357 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    3358 5.699) 
    3359  
    3360 
    3361 > matchmaker #21 to #1/A
    3362 
    3363 Parameters 
    3364 --- 
    3365 Chain pairing | bb 
    3366 Alignment algorithm | Needleman-Wunsch 
    3367 Similarity matrix | BLOSUM-62 
    3368 SS fraction | 0.3 
    3369 Gap open (HH/SS/other) | 18/18/6 
    3370 Gap extend | 1 
    3371 SS matrix |  |  | H | S | O 
    3372 ---|---|---|--- 
    3373 H | 6 | -9 | -6 
    3374 S |  | 6 | -6 
    3375 O |  |  | 4 
    3376 Iteration cutoff | 2 
    3377  
    3378 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    3379 with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
    3380 3608.2 
    3381 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    3382 5.511) 
    3383  
    3384 
    3385 > ui tool show "Show Sequence Viewer"
    3386 
    3387 > sequence chain #10/A #20/A #21/A
    3388 
    3389 Alignment identifier is 1 
    3390 Drag select of 1 residues 
    3391 Seqview [ID: 1] region 3 chains [1-976] RMSD: 310.105 
    3392  
    3393 
    3394 > delete atoms (#21 & sel)
    3395 
    3396 > delete bonds (#21 & sel)
    3397 
    3398 Seqview [ID: 1] region 3 chains [999-1408] RMSD: 314.967 
    3399  
    3400 
    3401 > delete atoms (#21 & sel)
    3402 
    3403 > delete bonds (#21 & sel)
    3404 
    3405 > hide #1 models
    3406 
    3407 > hide #20 models
    3408 
    3409 > hide #21 models
    3410 
    3411 > show #4 models
    3412 
    3413 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3414 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3415 
    3416 AF-P47102-F1-model_v1 (1).pdb title: 
    3417 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3418 (P47102) [more info...] 
    3419  
    3420 Chain information for AF-P47102-F1-model_v1 (1).pdb #22 
    3421 --- 
    3422 Chain | Description 
    3423 A | arf guanine-nucleotide exchange factor 1 
    3424  
    3425 
    3426 > matchmaker #22 to #1/A
    3427 
    3428 Parameters 
    3429 --- 
    3430 Chain pairing | bb 
    3431 Alignment algorithm | Needleman-Wunsch 
    3432 Similarity matrix | BLOSUM-62 
    3433 SS fraction | 0.3 
    3434 Gap open (HH/SS/other) | 18/18/6 
    3435 Gap extend | 1 
    3436 SS matrix |  |  | H | S | O 
    3437 ---|---|---|--- 
    3438 H | 6 | -9 | -6 
    3439 S |  | 6 | -6 
    3440 O |  |  | 4 
    3441 Iteration cutoff | 2 
    3442  
    3443 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    3444 with AF-P47102-F1-model_v1 (1).pdb, chain A (#22), sequence alignment score =
    3445 3608.2 
    3446 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    3447 5.511) 
    3448  
    3449 
    3450 > matchmaker #21 to #1/B
    3451 
    3452 Parameters 
    3453 --- 
    3454 Chain pairing | bb 
    3455 Alignment algorithm | Needleman-Wunsch 
    3456 Similarity matrix | BLOSUM-62 
    3457 SS fraction | 0.3 
    3458 Gap open (HH/SS/other) | 18/18/6 
    3459 Gap extend | 1 
    3460 SS matrix |  |  | H | S | O 
    3461 ---|---|---|--- 
    3462 H | 6 | -9 | -6 
    3463 S |  | 6 | -6 
    3464 O |  |  | 4 
    3465 Iteration cutoff | 2 
    3466  
    3467 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    3468 with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
    3469 2161.7 
    3470 RMSD between 6 pruned atom pairs is 0.798 angstroms; (across all 6 pairs:
    3471 0.798) 
    3472  
    3473 
    3474 > show #21 models
    3475 
    3476 > hide #21 models
    3477 
    3478 > show #21 models
    3479 
    3480 > hide #21 models
    3481 
    3482 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3483 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3484 
    3485 AF-P47102-F1-model_v1 (1).pdb title: 
    3486 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3487 (P47102) [more info...] 
    3488  
    3489 Chain information for AF-P47102-F1-model_v1 (1).pdb #23 
    3490 --- 
    3491 Chain | Description 
    3492 A | arf guanine-nucleotide exchange factor 1 
    3493  
    3494 
    3495 > hide #22 models
    3496 
    3497 > hide #23 models
    3498 
    3499 > show #23 models
    3500 
    3501 > matchmaker #23 to #1/B
    3502 
    3503 Parameters 
    3504 --- 
    3505 Chain pairing | bb 
    3506 Alignment algorithm | Needleman-Wunsch 
    3507 Similarity matrix | BLOSUM-62 
    3508 SS fraction | 0.3 
    3509 Gap open (HH/SS/other) | 18/18/6 
    3510 Gap extend | 1 
    3511 SS matrix |  |  | H | S | O 
    3512 ---|---|---|--- 
    3513 H | 6 | -9 | -6 
    3514 S |  | 6 | -6 
    3515 O |  |  | 4 
    3516 Iteration cutoff | 2 
    3517  
    3518 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    3519 with AF-P47102-F1-model_v1 (1).pdb, chain A (#23), sequence alignment score =
    3520 3579.8 
    3521 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    3522 5.699) 
    3523  
    3524 
    3525 > hide #23 models
    3526 
    3527 > hide #4 models
    3528 
    3529 > show #!6 models
    3530 
    3531 > hide #!6 models
    3532 
    3533 > show #!7 models
    3534 
    3535 > hide #!7 models
    3536 
    3537 > show #!8 models
    3538 
    3539 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3540 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3541 
    3542 AF-P47102-F1-model_v1 (1).pdb title: 
    3543 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3544 (P47102) [more info...] 
    3545  
    3546 Chain information for AF-P47102-F1-model_v1 (1).pdb #24 
    3547 --- 
    3548 Chain | Description 
    3549 A | arf guanine-nucleotide exchange factor 1 
    3550  
    3551 
    3552 > open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3553 > figures/AF-P47102-F1-model_v1 (1).pdb"
    3554 
    3555 AF-P47102-F1-model_v1 (1).pdb title: 
    3556 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3557 (P47102) [more info...] 
    3558  
    3559 Chain information for AF-P47102-F1-model_v1 (1).pdb #25 
    3560 --- 
    3561 Chain | Description 
    3562 A | arf guanine-nucleotide exchange factor 1 
    3563  
    3564 
    3565 > hide #!8 models
    3566 
    3567 > show #!9 models
    3568 
    3569 > hide #!9 models
    3570 
    3571 > show #!8 models
    3572 
    3573 > matchmaker #24 to #1/B
    3574 
    3575 Parameters 
    3576 --- 
    3577 Chain pairing | bb 
    3578 Alignment algorithm | Needleman-Wunsch 
    3579 Similarity matrix | BLOSUM-62 
    3580 SS fraction | 0.3 
    3581 Gap open (HH/SS/other) | 18/18/6 
    3582 Gap extend | 1 
    3583 SS matrix |  |  | H | S | O 
    3584 ---|---|---|--- 
    3585 H | 6 | -9 | -6 
    3586 S |  | 6 | -6 
    3587 O |  |  | 4 
    3588 Iteration cutoff | 2 
    3589  
    3590 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    3591 with AF-P47102-F1-model_v1 (1).pdb, chain A (#24), sequence alignment score =
    3592 3579.8 
    3593 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    3594 5.699) 
    3595  
    3596 
    3597 > hide #24 models
    3598 
    3599 > hide #25 models
    3600 
    3601 > hide #!8 models
    3602 
    3603 > show #!2 models
    3604 
    3605 > hide #!2 models
    3606 
    3607 > show #4 models
    3608 
    3609 > show #23 models
    3610 
    3611 > show #22 models
    3612 
    3613 > matchmaker #22 to #4/A
    3614 
    3615 Parameters 
    3616 --- 
    3617 Chain pairing | bb 
    3618 Alignment algorithm | Needleman-Wunsch 
    3619 Similarity matrix | BLOSUM-62 
    3620 SS fraction | 0.3 
    3621 Gap open (HH/SS/other) | 18/18/6 
    3622 Gap extend | 1 
    3623 SS matrix |  |  | H | S | O 
    3624 ---|---|---|--- 
    3625 H | 6 | -9 | -6 
    3626 S |  | 6 | -6 
    3627 O |  |  | 4 
    3628 Iteration cutoff | 2 
    3629  
    3630 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#4)
    3631 with AF-P47102-F1-model_v1 (1).pdb, chain A (#22), sequence alignment score =
    3632 3215.1 
    3633 RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
    3634 10.861) 
    3635  
    3636 
    3637 > matchmaker #23 to #4/B
    3638 
    3639 Parameters 
    3640 --- 
    3641 Chain pairing | bb 
    3642 Alignment algorithm | Needleman-Wunsch 
    3643 Similarity matrix | BLOSUM-62 
    3644 SS fraction | 0.3 
    3645 Gap open (HH/SS/other) | 18/18/6 
    3646 Gap extend | 1 
    3647 SS matrix |  |  | H | S | O 
    3648 ---|---|---|--- 
    3649 H | 6 | -9 | -6 
    3650 S |  | 6 | -6 
    3651 O |  |  | 4 
    3652 Iteration cutoff | 2 
    3653  
    3654 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
    3655 with AF-P47102-F1-model_v1 (1).pdb, chain A (#23), sequence alignment score =
    3656 3284.5 
    3657 RMSD between 394 pruned atom pairs is 1.192 angstroms; (across all 1128 pairs:
    3658 11.128) 
    3659  
    3660 
    3661 > hide #23 models
    3662 
    3663 > hide #22 models
    3664 
    3665 > show #24 models
    3666 
    3667 > show #25 models
    3668 
    3669 > show #!8 models
    3670 
    3671 > hide #4 models
    3672 
    3673 > matchmaker #24 to #8/A
    3674 
    3675 Parameters 
    3676 --- 
    3677 Chain pairing | bb 
    3678 Alignment algorithm | Needleman-Wunsch 
    3679 Similarity matrix | BLOSUM-62 
    3680 SS fraction | 0.3 
    3681 Gap open (HH/SS/other) | 18/18/6 
    3682 Gap extend | 1 
    3683 SS matrix |  |  | H | S | O 
    3684 ---|---|---|--- 
    3685 H | 6 | -9 | -6 
    3686 S |  | 6 | -6 
    3687 O |  |  | 4 
    3688 Iteration cutoff | 2 
    3689  
    3690 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
    3691 AF-P47102-F1-model_v1 (1).pdb, chain A (#24), sequence alignment score =
    3692 3470.5 
    3693 RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
    3694 9.022) 
    3695  
    3696 
    3697 > matchmaker #25 to #8/C
    3698 
    3699 Parameters 
    3700 --- 
    3701 Chain pairing | bb 
    3702 Alignment algorithm | Needleman-Wunsch 
    3703 Similarity matrix | BLOSUM-62 
    3704 SS fraction | 0.3 
    3705 Gap open (HH/SS/other) | 18/18/6 
    3706 Gap extend | 1 
    3707 SS matrix |  |  | H | S | O 
    3708 ---|---|---|--- 
    3709 H | 6 | -9 | -6 
    3710 S |  | 6 | -6 
    3711 O |  |  | 4 
    3712 Iteration cutoff | 2 
    3713  
    3714 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
    3715 AF-P47102-F1-model_v1 (1).pdb, chain A (#25), sequence alignment score = 3462 
    3716 RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
    3717 9.117) 
    3718  
    3719 
    3720 > ui tool show "Show Sequence Viewer"
    3721 
    3722 > sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
    3723 
    3724 Alignment identifier is 1 
    3725 Drag select of 2 residues 
    3726 Seqview [ID: 1] region 7 chains [1-977] RMSD: 213.225 
    3727  
    3728 
    3729 > delete atoms (#24-25 & sel)
    3730 
    3731 > delete bonds (#24-25 & sel)
    3732 
    3733 Seqview [ID: 1] region 7 chains [999-1001] RMSD: 244.336 
    3734  
    3735 Seqview [ID: 1] region 7 chains [999-1408] RMSD: 263.648 
    3736  
    3737 
    3738 > delete atoms (#24-25 & sel)
    3739 
    3740 > delete bonds (#24-25 & sel)
    3741 
    3742 Drag select of 1 residues 
    3743 Seqview [ID: 1] region 7 chains [998-1030] RMSD: 280.618 
    3744  
    3745 Seqview [ID: 1] region 7 chains [978-998] RMSD: 221.446 
    3746  
    3747 
    3748 > color (#24-25 & sel) #55ffffff
    3749 
    3750 > color (#24-25 & sel) #ffaaffff
    3751 
    3752 > preset cartoons/nucleotides cylinders/stubs
    3753 
    3754 Changed 0 atom styles 
    3755 Preset expands to these ChimeraX commands:
    3756 
    3757    
    3758    
    3759     show nucleic
    3760     hide protein|solvent|H
    3761     surf hide
    3762     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    3763     cartoon
    3764     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    3765     cartoon style ~(nucleic|strand) x round
    3766     cartoon style (nucleic|strand) x rect
    3767     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    3768     cartoon style nucleic x round width 1.6 thick 1.6
    3769     nucleotides stubs
    3770 
    3771  
    3772 
    3773 > preset "overall look" publication
    3774 
    3775 Preset expands to these ChimeraX commands:
    3776 
    3777    
    3778    
    3779     set bg white
    3780     graphics silhouettes t
    3781 
    3782  
    3783 
    3784 > select clear
    3785 
    3786 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3787 > figures/lipids_slice.pdb
    3788 
    3789 > hide #25 models
    3790 
    3791 > hide #24 models
    3792 
    3793 > show #26#!8 surfaces
    3794 
    3795 > hide #!8 models
    3796 
    3797 > show #!8 models
    3798 
    3799 > hide #26#!8 surfaces
    3800 
    3801 > hide #!8 models
    3802 
    3803 > select #26
    3804 
    3805 313093 atoms, 317626 bonds, 3369 residues, 1 model selected 
    3806 
    3807 > show sel surfaces
    3808 
    3809 > select clear
    3810 
    3811 Drag select of lipids_slice.pdb_1X SES surface, lipids_slice.pdb_CX SES
    3812 surface, lipids_slice.pdb_SX SES surface, lipids_slice.pdb_EX SES surface,
    3813 lipids_slice.pdb_GX SES surface, 313093 atoms, 317626 bonds 
    3814 
    3815 > ~select #26
    3816 
    3817 5 models selected 
    3818 
    3819 > select #26
    3820 
    3821 313093 atoms, 317626 bonds, 3369 residues, 1 model selected 
    3822 
    3823 > color (#!26 & sel) #ffffffff
    3824 
    3825 > color (#!26 & sel) #ffaaffff
    3826 
    3827 > ~select #26
    3828 
    3829 5 models selected 
    3830 
    3831 > select #26
    3832 
    3833 313093 atoms, 317626 bonds, 3369 residues, 1 model selected 
    3834 
    3835 > hide sel surfaces
    3836 
    3837 > show sel surfaces
    3838 
    3839 > close #26
    3840 
    3841 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3842 > figures/lipids_slice.pdb
    3843 
    3844 > show #26 surfaces
    3845 
    3846 > hide #!26 models
    3847 
    3848 > show #23 models
    3849 
    3850 > show #22 models
    3851 
    3852 > show #21 models
    3853 
    3854 > show #20 models
    3855 
    3856 > show #24 models
    3857 
    3858 > show #25 models
    3859 
    3860 > hide #25 models
    3861 
    3862 > hide #24 models
    3863 
    3864 > hide #23 models
    3865 
    3866 > hide #22 models
    3867 
    3868 > hide #21 models
    3869 
    3870 > hide #20 models
    3871 
    3872 > show #20 models
    3873 
    3874 > show #21 models
    3875 
    3876 > show #22 models
    3877 
    3878 > show #23 models
    3879 
    3880 > show #24 models
    3881 
    3882 > show #25 models
    3883 
    3884 > hide #25 models
    3885 
    3886 > hide #24 models
    3887 
    3888 > hide #23 models
    3889 
    3890 > hide #22 models
    3891 
    3892 > hide #21 models
    3893 
    3894 > hide #20 models
    3895 
    3896 > show #1 models
    3897 
    3898 > hide #1 models
    3899 
    3900 > show #1 models
    3901 
    3902 > show #20 models
    3903 
    3904 > show #21 models
    3905 
    3906 > hide #21 models
    3907 
    3908 > show #22 models
    3909 
    3910 > hide #22 models
    3911 
    3912 > show #21 models
    3913 
    3914 > hide #21 models
    3915 
    3916 > show #24 models
    3917 
    3918 > hide #24 models
    3919 
    3920 > show #23 models
    3921 
    3922 > hide #23 models
    3923 
    3924 > show #22 models
    3925 
    3926 > show #23 models
    3927 
    3928 > hide #23 models
    3929 
    3930 > hide #22 models
    3931 
    3932 > hide #20 models
    3933 
    3934 > close #20-25
    3935 
    3936 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3937 > figures/AF-P47102-F1-model_v1.pdb
    3938 
    3939 AF-P47102-F1-model_v1.pdb title: 
    3940 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3941 (P47102) [more info...] 
    3942  
    3943 Chain information for AF-P47102-F1-model_v1.pdb #20 
    3944 --- 
    3945 Chain | Description 
    3946 A | arf guanine-nucleotide exchange factor 1 
    3947  
    3948 
    3949 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    3950 > figures/AF-P47102-F1-model_v1.pdb
    3951 
    3952 AF-P47102-F1-model_v1.pdb title: 
    3953 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    3954 (P47102) [more info...] 
    3955  
    3956 Chain information for AF-P47102-F1-model_v1.pdb #21 
    3957 --- 
    3958 Chain | Description 
    3959 A | arf guanine-nucleotide exchange factor 1 
    3960  
    3961 
    3962 > matchmaker #20 to #1/A
    3963 
    3964 Parameters 
    3965 --- 
    3966 Chain pairing | bb 
    3967 Alignment algorithm | Needleman-Wunsch 
    3968 Similarity matrix | BLOSUM-62 
    3969 SS fraction | 0.3 
    3970 Gap open (HH/SS/other) | 18/18/6 
    3971 Gap extend | 1 
    3972 SS matrix |  |  | H | S | O 
    3973 ---|---|---|--- 
    3974 H | 6 | -9 | -6 
    3975 S |  | 6 | -6 
    3976 O |  |  | 4 
    3977 Iteration cutoff | 2 
    3978  
    3979 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    3980 with AF-P47102-F1-model_v1.pdb, chain A (#20), sequence alignment score =
    3981 3608.2 
    3982 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    3983 5.511) 
    3984  
    3985 
    3986 > matchmaker #21 to #1/B
    3987 
    3988 Parameters 
    3989 --- 
    3990 Chain pairing | bb 
    3991 Alignment algorithm | Needleman-Wunsch 
    3992 Similarity matrix | BLOSUM-62 
    3993 SS fraction | 0.3 
    3994 Gap open (HH/SS/other) | 18/18/6 
    3995 Gap extend | 1 
    3996 SS matrix |  |  | H | S | O 
    3997 ---|---|---|--- 
    3998 H | 6 | -9 | -6 
    3999 S |  | 6 | -6 
    4000 O |  |  | 4 
    4001 Iteration cutoff | 2 
    4002  
    4003 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    4004 with AF-P47102-F1-model_v1.pdb, chain A (#21), sequence alignment score =
    4005 3579.8 
    4006 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    4007 5.699) 
    4008  
    4009 
    4010 > hide #1 models
    4011 
    4012 > hide #20 models
    4013 
    4014 > hide #21 models
    4015 
    4016 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    4017 > figures/AF-P47102-F1-model_v1.pdb
    4018 
    4019 AF-P47102-F1-model_v1.pdb title: 
    4020 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    4021 (P47102) [more info...] 
    4022  
    4023 Chain information for AF-P47102-F1-model_v1.pdb #22 
    4024 --- 
    4025 Chain | Description 
    4026 A | arf guanine-nucleotide exchange factor 1 
    4027  
    4028 
    4029 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    4030 > figures/AF-P47102-F1-model_v1.pdb
    4031 
    4032 AF-P47102-F1-model_v1.pdb title: 
    4033 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    4034 (P47102) [more info...] 
    4035  
    4036 Chain information for AF-P47102-F1-model_v1.pdb #23 
    4037 --- 
    4038 Chain | Description 
    4039 A | arf guanine-nucleotide exchange factor 1 
    4040  
    4041 
    4042 > show #4 models
    4043 
    4044 > matchmaker #22 to #1/A
    4045 
    4046 Parameters 
    4047 --- 
    4048 Chain pairing | bb 
    4049 Alignment algorithm | Needleman-Wunsch 
    4050 Similarity matrix | BLOSUM-62 
    4051 SS fraction | 0.3 
    4052 Gap open (HH/SS/other) | 18/18/6 
    4053 Gap extend | 1 
    4054 SS matrix |  |  | H | S | O 
    4055 ---|---|---|--- 
    4056 H | 6 | -9 | -6 
    4057 S |  | 6 | -6 
    4058 O |  |  | 4 
    4059 Iteration cutoff | 2 
    4060  
    4061 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    4062 with AF-P47102-F1-model_v1.pdb, chain A (#22), sequence alignment score =
    4063 3608.2 
    4064 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    4065 5.511) 
    4066  
    4067 
    4068 > matchmaker #22 to #4/A
    4069 
    4070 Parameters 
    4071 --- 
    4072 Chain pairing | bb 
    4073 Alignment algorithm | Needleman-Wunsch 
    4074 Similarity matrix | BLOSUM-62 
    4075 SS fraction | 0.3 
    4076 Gap open (HH/SS/other) | 18/18/6 
    4077 Gap extend | 1 
    4078 SS matrix |  |  | H | S | O 
    4079 ---|---|---|--- 
    4080 H | 6 | -9 | -6 
    4081 S |  | 6 | -6 
    4082 O |  |  | 4 
    4083 Iteration cutoff | 2 
    4084  
    4085 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#4)
    4086 with AF-P47102-F1-model_v1.pdb, chain A (#22), sequence alignment score =
    4087 3215.1 
    4088 RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
    4089 10.861) 
    4090  
    4091 
    4092 > matchmaker #23 to #4/B
    4093 
    4094 Parameters 
    4095 --- 
    4096 Chain pairing | bb 
    4097 Alignment algorithm | Needleman-Wunsch 
    4098 Similarity matrix | BLOSUM-62 
    4099 SS fraction | 0.3 
    4100 Gap open (HH/SS/other) | 18/18/6 
    4101 Gap extend | 1 
    4102 SS matrix |  |  | H | S | O 
    4103 ---|---|---|--- 
    4104 H | 6 | -9 | -6 
    4105 S |  | 6 | -6 
    4106 O |  |  | 4 
    4107 Iteration cutoff | 2 
    4108  
    4109 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
    4110 with AF-P47102-F1-model_v1.pdb, chain A (#23), sequence alignment score =
    4111 3284.5 
    4112 RMSD between 394 pruned atom pairs is 1.192 angstroms; (across all 1128 pairs:
    4113 11.128) 
    4114  
    4115 
    4116 > hide #22 models
    4117 
    4118 > hide #23 models
    4119 
    4120 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    4121 > figures/AF-P47102-F1-model_v1.pdb
    4122 
    4123 AF-P47102-F1-model_v1.pdb title: 
    4124 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    4125 (P47102) [more info...] 
    4126  
    4127 Chain information for AF-P47102-F1-model_v1.pdb #24 
    4128 --- 
    4129 Chain | Description 
    4130 A | arf guanine-nucleotide exchange factor 1 
    4131  
    4132 
    4133 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    4134 > figures/AF-P47102-F1-model_v1.pdb
    4135 
    4136 AF-P47102-F1-model_v1.pdb title: 
    4137 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    4138 (P47102) [more info...] 
    4139  
    4140 Chain information for AF-P47102-F1-model_v1.pdb #25 
    4141 --- 
    4142 Chain | Description 
    4143 A | arf guanine-nucleotide exchange factor 1 
    4144  
    4145 
    4146 > hide #4 models
    4147 
    4148 > show #!8 models
    4149 
    4150 > matchmaker #24 to #8/A
    4151 
    4152 Parameters 
    4153 --- 
    4154 Chain pairing | bb 
    4155 Alignment algorithm | Needleman-Wunsch 
    4156 Similarity matrix | BLOSUM-62 
    4157 SS fraction | 0.3 
    4158 Gap open (HH/SS/other) | 18/18/6 
    4159 Gap extend | 1 
    4160 SS matrix |  |  | H | S | O 
    4161 ---|---|---|--- 
    4162 H | 6 | -9 | -6 
    4163 S |  | 6 | -6 
    4164 O |  |  | 4 
    4165 Iteration cutoff | 2 
    4166  
    4167 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
    4168 AF-P47102-F1-model_v1.pdb, chain A (#24), sequence alignment score = 3470.5 
    4169 RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
    4170 9.022) 
    4171  
    4172 
    4173 > matchmaker #25 to #8/C
    4174 
    4175 Parameters 
    4176 --- 
    4177 Chain pairing | bb 
    4178 Alignment algorithm | Needleman-Wunsch 
    4179 Similarity matrix | BLOSUM-62 
    4180 SS fraction | 0.3 
    4181 Gap open (HH/SS/other) | 18/18/6 
    4182 Gap extend | 1 
    4183 SS matrix |  |  | H | S | O 
    4184 ---|---|---|--- 
    4185 H | 6 | -9 | -6 
    4186 S |  | 6 | -6 
    4187 O |  |  | 4 
    4188 Iteration cutoff | 2 
    4189  
    4190 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
    4191 AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3462 
    4192 RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
    4193 9.117) 
    4194  
    4195 
    4196 > hide #24 models
    4197 
    4198 > hide #25 models
    4199 
    4200 > ui tool show "Show Sequence Viewer"
    4201 
    4202 > sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
    4203 
    4204 Alignment identifier is 1 
    4205 
    4206 > show #23 models
    4207 
    4208 > hide #23 models
    4209 
    4210 > show #24 models
    4211 
    4212 > hide #24 models
    4213 
    4214 > show #23 models
    4215 
    4216 > hide #23 models
    4217 
    4218 > show #25 models
    4219 
    4220 Drag select of 2 residues 
    4221 
    4222 > select clear
    4223 
    4224 Drag select of 2 residues 
    4225 
    4226 > select clear
    4227 
    4228 > select #25/A:977
    4229 
    4230 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4231 Seqview [ID: 1] region 7 chains [978-999] RMSD: 225.702 
    4232  
    4233 Seqview [ID: 1] region 7 chains [1-977] RMSD: 184.260 
    4234  
    4235 
    4236 > show #24 models
    4237 
    4238 > hide #24 models
    4239 
    4240 > delete atoms (#25 & sel)
    4241 
    4242 > delete bonds (#25 & sel)
    4243 
    4244 Seqview [ID: 1] region 7 chains [1000-1408] RMSD: 238.000 
    4245  
    4246 
    4247 > delete atoms (#25 & sel)
    4248 
    4249 > delete bonds (#25 & sel)
    4250 
    4251 > hide #!8 models
    4252 
    4253 > show #!8 models
    4254 
    4255 > hide #!8 models
    4256 
    4257 > hide #25 models
    4258 
    4259 > show #25 models
    4260 
    4261 > show #24 models
    4262 
    4263 > show #23 models
    4264 
    4265 > show #22 models
    4266 
    4267 > show #21 models
    4268 
    4269 > hide #21 models
    4270 
    4271 > hide #22 models
    4272 
    4273 > hide #23 models
    4274 
    4275 > hide #24 models
    4276 
    4277 > hide #25 models
    4278 
    4279 > show #25 models
    4280 
    4281 > show #24 models
    4282 
    4283 > show #23 models
    4284 
    4285 > show #22 models
    4286 
    4287 > show #21 models
    4288 
    4289 > show #20 models
    4290 
    4291 > select #25
    4292 
    4293 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4294 Seqview [ID: 1] region 7 chains [1-977] RMSD: 198.926 
    4295  
    4296 
    4297 > delete atoms (#20-24 & sel)
    4298 
    4299 > delete bonds (#20-24 & sel)
    4300 
    4301 Seqview [ID: 1] region 7 chains [1031-1408] RMSD: 249.442 
    4302  
    4303 
    4304 > delete atoms (#20-24 & sel)
    4305 
    4306 > delete bonds (#20-24 & sel)
    4307 
    4308 Seqview [ID: 1] region 7 chains [1000-1031] RMSD: 217.674 
    4309  
    4310 
    4311 > delete atoms (#20-24 & sel)
    4312 
    4313 > delete bonds (#20-24 & sel)
    4314 
    4315 > select #10
    4316 
    4317 11218 atoms, 11405 bonds, 1408 residues, 1 model selected 
    4318 
    4319 > ~select #10
    4320 
    4321 Nothing selected 
    4322 
    4323 > select #20
    4324 
    4325 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4326 
    4327 > select #21
    4328 
    4329 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4330 
    4331 > select #22
    4332 
    4333 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4334 
    4335 > select #23
    4336 
    4337 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4338 
    4339 > select #20
    4340 
    4341 168 atoms, 170 bonds, 22 residues, 1 model selected 
    4342 Drag select of 132 residues 
    4343 
    4344 > color sel #ffffffff
    4345 
    4346 > color sel #ffaaffff
    4347 
    4348 > preset cartoons/nucleotides cylinders/stubs
    4349 
    4350 Changed 0 atom styles 
    4351 Preset expands to these ChimeraX commands:
    4352 
    4353    
    4354    
    4355     show nucleic
    4356     hide protein|solvent|H
    4357     surf hide
    4358     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    4359     cartoon
    4360     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    4361     cartoon style ~(nucleic|strand) x round
    4362     cartoon style (nucleic|strand) x rect
    4363     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    4364     cartoon style nucleic x round width 1.6 thick 1.6
    4365     nucleotides stubs
    4366 
    4367  
    4368 
    4369 > preset "overall look" publication
    4370 
    4371 Preset expands to these ChimeraX commands:
    4372 
    4373    
    4374    
    4375     set bg white
    4376     graphics silhouettes t
    4377 
    4378  
    4379 
    4380 > select clear
    4381 
    4382 > hide #25 models
    4383 
    4384 > hide #24 models
    4385 
    4386 > hide #23 models
    4387 
    4388 > hide #22 models
    4389 
    4390 > hide #21 models
    4391 
    4392 > hide #20 models
    4393 
    4394 > show #1 models
    4395 
    4396 > show #20 models
    4397 
    4398 > show #21 models
    4399 
    4400 > hide #21 models
    4401 
    4402 > hide #20 models
    4403 
    4404 > hide #1 models
    4405 
    4406 > show #!26 models
    4407 
    4408 > show #!26 surfaces
    4409 
    4410 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    4411 
    4412 > hide #!26 models
    4413 
    4414 > show #1 models
    4415 
    4416 > show #20 models
    4417 
    4418 > show #21 models
    4419 
    4420 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    4421 
    4422 > hide #20 models
    4423 
    4424 > hide #21 models
    4425 
    4426 > show #22 models
    4427 
    4428 > show #23 models
    4429 
    4430 > hide #1 models
    4431 
    4432 > show #4 models
    4433 
    4434 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    4435 
    4436 > hide #4 models
    4437 
    4438 > hide #22 models
    4439 
    4440 > hide #23 models
    4441 
    4442 > show #24 models
    4443 
    4444 > show #25 models
    4445 
    4446 > show #!8 models
    4447 
    4448 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    4449 
    4450 > show #!26 models
    4451 
    4452 > hide #!26 models
    4453 
    4454 > show #!26 models
    4455 
    4456 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    4457 
    4458 > hide #!26 models
    4459 
    4460 > hide #25 models
    4461 
    4462 > hide #24 models
    4463 
    4464 > hide #!8 models
    4465 
    4466 > show #!26 models
    4467 
    4468 > show #1 models
    4469 
    4470 > hide #1 models
    4471 
    4472 > save C:\Users\Arnold\Desktop\image4.png supersample 3
    4473 
    4474 > hide #!26 models
    4475 
    4476 > show #1 models
    4477 
    4478 > show #20 models
    4479 
    4480 > show #21 models
    4481 
    4482 > save C:\Users\Arnold\Desktop\image5.png supersample 3
    4483 
    4484 > show #!12 models
    4485 
    4486 > hide #!12 models
    4487 
    4488 > show #12.1 models
    4489 
    4490 > show #!17 models
    4491 
    4492 > hide #!17 models
    4493 
    4494 > show #17.1 models
    4495 
    4496 > hide #!17 models
    4497 
    4498 > hide #12.1 models
    4499 
    4500 > save C:\Users\Arnold\Desktop\image6.png supersample 3
    4501 
    4502 > show #12.1 models
    4503 
    4504 > show #!18 models
    4505 
    4506 > hide #!18 models
    4507 
    4508 > show #18.1 models
    4509 
    4510 > hide #18.1 models
    4511 
    4512 > show #!17 models
    4513 
    4514 > save C:\Users\Arnold\Desktop\image7.png supersample 3
    4515 
    4516 > hide #12.1 models
    4517 
    4518 > hide #!12 models
    4519 
    4520 > hide #!18 models
    4521 
    4522 > hide #17.1 models
    4523 
    4524 > hide #!17 models
    4525 
    4526 > hide #20 models
    4527 
    4528 > hide #21 models
    4529 
    4530 > show #22 models
    4531 
    4532 > show #23 models
    4533 
    4534 > hide #1 models
    4535 
    4536 > show #4 models
    4537 
    4538 > save C:\Users\Arnold\Desktop\image8.png supersample 3
    4539 
    4540 > hide #4 models
    4541 
    4542 > show #!8 models
    4543 
    4544 > hide #23 models
    4545 
    4546 > hide #22 models
    4547 
    4548 > show #24 models
    4549 
    4550 > show #25 models
    4551 
    4552 > save C:\Users\Arnold\Desktop\image9.png supersample 3
    4553 
    4554 > hide #25 models
    4555 
    4556 > hide #24 models
    4557 
    4558 > hide #!8 models
    4559 
    4560 > show #!14 models
    4561 
    4562 > save C:\Users\Arnold\Desktop\image10.png supersample 3
    4563 
    4564 > hide #!14 models
    4565 
    4566 > show #!15 models
    4567 
    4568 > show #15.15 models
    4569 
    4570 > save C:\Users\Arnold\Desktop\image11.png supersample 3
    4571 
    4572 > transparentBackground true
    4573 
    4574 Unknown command: transparentBackground true 
    4575 
    4576 > hide #15.15 models
    4577 
    4578 > hide #!15 models
    4579 
    4580 > show #!26 models
    4581 
    4582 > saved lipids.png transparentBackground true
    4583 
    4584 Unknown command: saved lipids.png transparentBackground true 
    4585 
    4586 > save lipids.png transparentBackground true supersample 3
    4587 
    4588 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    4589 > transparentBackground true supersample 3
    4590 
    4591 > hide #!26 models
    4592 
    4593 > show #1 models
    4594 
    4595 > show #20 models
    4596 
    4597 > show #21 models
    4598 
    4599 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    4600 > transparentBackground true supersample 3
    4601 
    4602 > show #!12 models
    4603 
    4604 > hide #!12 models
    4605 
    4606 > show #12.1 models
    4607 
    4608 > show #17.1 models
    4609 
    4610 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
    4611 > transparentBackground true supersample 3
    4612 
    4613 Cannot determine format for
    4614 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1' 
    4615 
    4616 > hide #17.1 models
    4617 
    4618 > hide #!17 models
    4619 
    4620 > hide #12.1 models
    4621 
    4622 > hide #!12 models
    4623 
    4624 > show #4 models
    4625 
    4626 > hide #1 models
    4627 
    4628 > show #22 models
    4629 
    4630 > show #23 models
    4631 
    4632 > hide #21 models
    4633 
    4634 > hide #20 models
    4635 
    4636 > hide #23 models
    4637 
    4638 > hide #22 models
    4639 
    4640 > hide #4 models
    4641 
    4642 > show #1 models
    4643 
    4644 > show #12.1 models
    4645 
    4646 > show #17.1 models
    4647 
    4648 > show #20 models
    4649 
    4650 > show #21 models
    4651 
    4652 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    4653 > arf1.png transparentBackground true supersample 3
    4654 
    4655 > hide #21 models
    4656 
    4657 > hide #20 models
    4658 
    4659 > show #22 models
    4660 
    4661 > show #23 models
    4662 
    4663 > hide #17.1 models
    4664 
    4665 > hide #!17 models
    4666 
    4667 > hide #12.1 models
    4668 
    4669 > hide #!12 models
    4670 
    4671 > show #4 models
    4672 
    4673 > hide #1 models
    4674 
    4675 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    4676 > transparentBackground true supersample 3
    4677 
    4678 > hide #4 models
    4679 
    4680 > show #!8 models
    4681 
    4682 > hide #23 models
    4683 
    4684 > hide #22 models
    4685 
    4686 > show #24 models
    4687 
    4688 > show #25 models
    4689 
    4690 > hide #!8 models
    4691 
    4692 > show #!8 models
    4693 
    4694 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
    4695 > transparentBackground true supersample 3
    4696 
    4697 > hide #24 models
    4698 
    4699 > hide #25 models
    4700 
    4701 > hide #!8 models
    4702 
    4703 > show #!14 models
    4704 
    4705 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
    4706 > transparentBackground true supersample 3
    4707 
    4708 Cannot determine format for
    4709 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp' 
    4710 
    4711 > show #15.15 models
    4712 
    4713 > hide #!14 models
    4714 
    4715 > select ::name="MYR"
    4716 
    4717 210 atoms, 205 bonds, 5 residues, 5 models selected 
    4718 
    4719 > hide sel & #15.15 atoms
    4720 
    4721 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    4722 > transparentBackground true supersample 3
    4723 
    4724 > hide #15.15 models
    4725 
    4726 > hide #!15 models
    4727 
    4728 > show #12.1 models
    4729 
    4730 > select #12
    4731 
    4732 2952 atoms, 2981 bonds, 182 residues, 2 models selected 
    4733 
    4734 > select #12.1
    4735 
    4736 2952 atoms, 2981 bonds, 182 residues, 1 model selected 
    4737 
    4738 > ~select #12.1
    4739 
    4740 Nothing selected 
    4741 
    4742 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    4743 > transparentBackground true supersample 3
    4744 
    4745 > hide #!12 models
    4746 
    4747 > show #1 models
    4748 
    4749 > show #20 models
    4750 
    4751 > show #21 models
    4752 
    4753 > hide #21 models
    4754 
    4755 > hide #20 models
    4756 
    4757 > hide #12.1 models
    4758 
    4759 > hide #1 models
    4760 
    4761 > show #!26 models
    4762 
    4763 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    4764 > transparentBackground true supersample 3
    4765 
    4766 > hide #!26 models
    4767 
    4768 > show #1 models
    4769 
    4770 > show #20 models
    4771 
    4772 > show #21 models
    4773 
    4774 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    4775 > transparentBackground true supersample 3
    4776 
    4777 > show #12.1 models
    4778 
    4779 > show #17.1 models
    4780 
    4781 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    4782 > arf1.png transparentBackground true supersample 3
    4783 
    4784 > hide #21 models
    4785 
    4786 > hide #20 models
    4787 
    4788 > hide #17.1 models
    4789 
    4790 > hide #!17 models
    4791 
    4792 > hide #12.1 models
    4793 
    4794 > hide #!12 models
    4795 
    4796 > hide #1 models
    4797 
    4798 > show #4 models
    4799 
    4800 > show #22 models
    4801 
    4802 > show #23 models
    4803 
    4804 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    4805 > transparentBackground true supersample 3
    4806 
    4807 > hide #22 models
    4808 
    4809 > hide #23 models
    4810 
    4811 > show #24 models
    4812 
    4813 > show #25 models
    4814 
    4815 > hide #4 models
    4816 
    4817 > show #!8 models
    4818 
    4819 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
    4820 > transparentBackground true supersample 3
    4821 
    4822 > hide #!8 models
    4823 
    4824 > hide #24 models
    4825 
    4826 > hide #25 models
    4827 
    4828 > show #12.1 models
    4829 
    4830 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    4831 > transparentBackground true supersample 3
    4832 
    4833 > hide #12.1 models
    4834 
    4835 > hide #!12 models
    4836 
    4837 > show #17.1 models
    4838 
    4839 > hide #17.1 models
    4840 
    4841 > hide #!17 models
    4842 
    4843 > show #!15 models
    4844 
    4845 > show #15.15 models
    4846 
    4847 > hide #!15 models
    4848 
    4849 > show #!14 models
    4850 
    4851 > hide #15.15 models
    4852 
    4853 > show #!15 models
    4854 
    4855 > show #15.15 models
    4856 
    4857 > hide #!14 models
    4858 
    4859 > hide #14.1 models
    4860 
    4861 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    4862 > transparentBackground true supersample 3
    4863 
    4864 > hide #15.15 models
    4865 
    4866 > hide #!15 models
    4867 
    4868 > show #1 models
    4869 
    4870 > show #20 models
    4871 
    4872 > show #21 models
    4873 
    4874 > show #!12 models
    4875 
    4876 > hide #!12 models
    4877 
    4878 > show #12.1 models
    4879 
    4880 > show #!15 models
    4881 
    4882 > hide #!15 models
    4883 
    4884 > show #15.15 models
    4885 
    4886 > hide #15.15 models
    4887 
    4888 > show #17.1 models
    4889 
    4890 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    4891 > arf1.png transparentBackground true supersample 3
    4892 
    4893 > hide #!17 models
    4894 
    4895 > hide #!15 models
    4896 
    4897 > hide #!12 models
    4898 
    4899 > hide #12.1 models
    4900 
    4901 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    4902 > side.png transparentBackground true supersample 3
    4903 
    4904 > show #12.1 models
    4905 
    4906 > show #!15 models
    4907 
    4908 > hide #!15 models
    4909 
    4910 > show #15.15 models
    4911 
    4912 > hide #15.15 models
    4913 
    4914 > hide #17.1 models
    4915 
    4916 > hide #!15 models
    4917 
    4918 > hide #!12 models
    4919 
    4920 > hide #12.1 models
    4921 
    4922 > show #12.1 models
    4923 
    4924 > show #14.1 models
    4925 
    4926 > hide #14.1 models
    4927 
    4928 > show #15.15 models
    4929 
    4930 > hide #15.15 models
    4931 
    4932 > show #17.1 models
    4933 
    4934 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    4935 > arf1-side.png transparentBackground true supersample 3
    4936 
    4937 > hide #!12 models
    4938 
    4939 > hide #12.1 models
    4940 
    4941 > hide #!14 models
    4942 
    4943 > hide #!15 models
    4944 
    4945 > hide #!17 models
    4946 
    4947 > hide #17.1 models
    4948 
    4949 > hide #20 models
    4950 
    4951 > hide #21 models
    4952 
    4953 > show #25 models
    4954 
    4955 > show #24 models
    4956 
    4957 > show #!8 models
    4958 
    4959 > hide #1 models
    4960 
    4961 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    4962 > side.png transparentBackground true supersample 3
    4963 
    4964 > hide #!8 models
    4965 
    4966 > hide #25 models
    4967 
    4968 > hide #24 models
    4969 
    4970 > show #!9 models
    4971 
    4972 > hide #!9 models
    4973 
    4974 > show #!8 models
    4975 
    4976 > show #24 models
    4977 
    4978 > show #25 models
    4979 
    4980 > hide #25 models
    4981 
    4982 > hide #24 models
    4983 
    4984 > show #21 models
    4985 
    4986 > show #20 models
    4987 
    4988 > hide #!8 models
    4989 
    4990 > show #!2 models
    4991 
    4992 > hide #!2 models
    4993 
    4994 > show #1 models
    4995 
    4996 > show #!2 models
    4997 
    4998 > hide #!2 models
    4999 
    5000 > show #!12 models
    5001 
    5002 > show #12.1 models
    5003 
    5004 > show #15.15 models
    5005 
    5006 > hide #15.15 models
    5007 
    5008 > show #!17 models
    5009 
    5010 > show #17.1 models
    5011 
    5012 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5013 > figures/2k5u.pdb
    5014 
    5015 2k5u.pdb title: 
    5016 Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
    5017 info...] 
    5018  
    5019 Chain information for 2k5u.pdb 
    5020 --- 
    5021 Chain | Description 
    5022 27.1/A | adp-ribosylation factor 1 
    5023 27.2/A 27.3/A 27.4/A 27.5/A 27.6/A 27.7/A 27.8/A 27.9/A 27.10/A 27.11/A
    5024 27.12/A 27.13/A 27.14/A 27.15/A 27.16/A | adp-ribosylation factor 1 
    5025  
    5026 
    5027 > hide #21 models
    5028 
    5029 > hide #20 models
    5030 
    5031 > hide #17.1 models
    5032 
    5033 > hide #!17 models
    5034 
    5035 > hide #!15 models
    5036 
    5037 > hide #12.1 models
    5038 
    5039 > hide #!12 models
    5040 
    5041 > hide #1 models
    5042 
    5043 > hide #!27 models
    5044 
    5045 > hide #27.1 models
    5046 
    5047 > hide #27.2 models
    5048 
    5049 > hide #27.3 models
    5050 
    5051 > hide #27.4 models
    5052 
    5053 > hide #27.5 models
    5054 
    5055 > hide #27.6 models
    5056 
    5057 > hide #27.7 models
    5058 
    5059 > hide #27.8 models
    5060 
    5061 > hide #27.9 models
    5062 
    5063 > hide #27.10 models
    5064 
    5065 > hide #27.11 models
    5066 
    5067 > hide #27.12 models
    5068 
    5069 > hide #27.13 models
    5070 
    5071 > hide #27.14 models
    5072 
    5073 > hide #27.15 models
    5074 
    5075 > hide #27.16 models
    5076 
    5077 > show #27.1 models
    5078 
    5079 > show #!2 models
    5080 
    5081 > hide #!2 models
    5082 
    5083 > show #1 models
    5084 
    5085 > show #!14 models
    5086 
    5087 > hide #!14 models
    5088 
    5089 > show #14.1 models
    5090 
    5091 > hide #14.1 models
    5092 
    5093 > show #15.15 models
    5094 
    5095 > hide #!15 models
    5096 
    5097 > hide #15.15 models
    5098 
    5099 > hide #!14 models
    5100 
    5101 > show #14.1 models
    5102 
    5103 > hide #14.1 models
    5104 
    5105 > hide #!14 models
    5106 
    5107 > show #12.1 models
    5108 
    5109 > hide #12.1 models
    5110 
    5111 > show #12.1 models
    5112 
    5113 > mmaker #27 to #12
    5114 
    5115 Parameters 
    5116 --- 
    5117 Chain pairing | bb 
    5118 Alignment algorithm | Needleman-Wunsch 
    5119 Similarity matrix | BLOSUM-62 
    5120 SS fraction | 0.3 
    5121 Gap open (HH/SS/other) | 18/18/6 
    5122 Gap extend | 1 
    5123 SS matrix |  |  | H | S | O 
    5124 ---|---|---|--- 
    5125 H | 6 | -9 | -6 
    5126 S |  | 6 | -6 
    5127 O |  |  | 4 
    5128 Iteration cutoff | 2 
    5129  
    5130 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.1), sequence
    5131 alignment score = 926 
    5132 RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
    5133 0.000) 
    5134  
    5135 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.2), sequence
    5136 alignment score = 903.3 
    5137 RMSD between 152 pruned atom pairs is 0.809 angstroms; (across all 180 pairs:
    5138 1.974) 
    5139  
    5140 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.3), sequence
    5141 alignment score = 907.5 
    5142 RMSD between 157 pruned atom pairs is 0.800 angstroms; (across all 180 pairs:
    5143 2.934) 
    5144  
    5145 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.4), sequence
    5146 alignment score = 903.9 
    5147 RMSD between 152 pruned atom pairs is 0.800 angstroms; (across all 180 pairs:
    5148 2.457) 
    5149  
    5150 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.5), sequence
    5151 alignment score = 910.5 
    5152 RMSD between 138 pruned atom pairs is 0.757 angstroms; (across all 180 pairs:
    5153 3.101) 
    5154  
    5155 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.6), sequence
    5156 alignment score = 909.3 
    5157 RMSD between 149 pruned atom pairs is 0.693 angstroms; (across all 180 pairs:
    5158 2.209) 
    5159  
    5160 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.7), sequence
    5161 alignment score = 911.7 
    5162 RMSD between 148 pruned atom pairs is 0.890 angstroms; (across all 180 pairs:
    5163 2.359) 
    5164  
    5165 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.8), sequence
    5166 alignment score = 913.5 
    5167 RMSD between 151 pruned atom pairs is 0.912 angstroms; (across all 180 pairs:
    5168 2.728) 
    5169  
    5170 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.9), sequence
    5171 alignment score = 914.1 
    5172 RMSD between 152 pruned atom pairs is 0.805 angstroms; (across all 180 pairs:
    5173 2.409) 
    5174  
    5175 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.10), sequence
    5176 alignment score = 899.7 
    5177 RMSD between 164 pruned atom pairs is 0.693 angstroms; (across all 180 pairs:
    5178 1.622) 
    5179  
    5180 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.11), sequence
    5181 alignment score = 911.1 
    5182 RMSD between 151 pruned atom pairs is 0.855 angstroms; (across all 180 pairs:
    5183 2.173) 
    5184  
    5185 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.12), sequence
    5186 alignment score = 914.1 
    5187 RMSD between 148 pruned atom pairs is 0.681 angstroms; (across all 180 pairs:
    5188 2.489) 
    5189  
    5190 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.13), sequence
    5191 alignment score = 926.7 
    5192 RMSD between 153 pruned atom pairs is 0.784 angstroms; (across all 180 pairs:
    5193 2.320) 
    5194  
    5195 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.14), sequence
    5196 alignment score = 910.5 
    5197 RMSD between 154 pruned atom pairs is 0.691 angstroms; (across all 180 pairs:
    5198 2.124) 
    5199  
    5200 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.15), sequence
    5201 alignment score = 892.5 
    5202 RMSD between 153 pruned atom pairs is 0.701 angstroms; (across all 180 pairs:
    5203 1.911) 
    5204  
    5205 Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.16), sequence
    5206 alignment score = 908.1 
    5207 RMSD between 153 pruned atom pairs is 0.770 angstroms; (across all 180 pairs:
    5208 2.227) 
    5209  
    5210 
    5211 > hide #12.1 models
    5212 
    5213 > hide #!12 models
    5214 
    5215 > hide #!27 models
    5216 
    5217 > hide #27.1 models
    5218 
    5219 > show #27.1 models
    5220 
    5221 > show #20 models
    5222 
    5223 > show #21 models
    5224 
    5225 > hide #27.1 models
    5226 
    5227 > show #27.2 models
    5228 
    5229 > hide #27.2 models
    5230 
    5231 > show #27.3 models
    5232 
    5233 > hide #27.3 models
    5234 
    5235 > show #27.4 models
    5236 
    5237 > hide #27.4 models
    5238 
    5239 > show #27.5 models
    5240 
    5241 > hide #27.5 models
    5242 
    5243 > show #27.6 models
    5244 
    5245 > hide #27.6 models
    5246 
    5247 > show #27.7 models
    5248 
    5249 > hide #27.7 models
    5250 
    5251 > show #27.8 models
    5252 
    5253 > hide #27.8 models
    5254 
    5255 > show #27.9 models
    5256 
    5257 > hide #27.9 models
    5258 
    5259 > show #27.10 models
    5260 
    5261 > hide #27.10 models
    5262 
    5263 > show #27.11 models
    5264 
    5265 > hide #27.11 models
    5266 
    5267 > show #27.12 models
    5268 
    5269 > hide #27.12 models
    5270 
    5271 > show #27.13 models
    5272 
    5273 > show #17.1 models
    5274 
    5275 > hide #17.1 models
    5276 
    5277 > hide #!17 models
    5278 
    5279 > show #12.1 models
    5280 
    5281 > hide #12.1 models
    5282 
    5283 > show #12.1 models
    5284 
    5285 > hide #12.1 models
    5286 
    5287 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5288 > figures/sample transparentBackground true supersample 3
    5289 
    5290 Cannot determine format for
    5291 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/sample' 
    5292 
    5293 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
    5294 > transparentBackground true supersample 3
    5295 
    5296 > hide #27.13 models
    5297 
    5298 > hide #!12 models
    5299 
    5300 > show #!2 models
    5301 
    5302 > hide #!2 models
    5303 
    5304 > show #!3 models
    5305 
    5306 > hide #21 models
    5307 
    5308 > hide #20 models
    5309 
    5310 > transparency #1,3#!27 80
    5311 
    5312 > transparency #1,3#!27 50
    5313 
    5314 > transparency #1,3#!27 0
    5315 
    5316 > hide #!27 models
    5317 
    5318 > hide #!3 models
    5319 
    5320 > hide #1 models
    5321 
    5322 > show #!7 models
    5323 
    5324 > hide #!7 models
    5325 
    5326 > show #!8 models
    5327 
    5328 > show #1 models
    5329 
    5330 > hide #1 models
    5331 
    5332 > show #1 models
    5333 
    5334 > hide #!8 models
    5335 
    5336 > show #!8 models
    5337 
    5338 > mmaker #8 to #1
    5339 
    5340 Parameters 
    5341 --- 
    5342 Chain pairing | bb 
    5343 Alignment algorithm | Needleman-Wunsch 
    5344 Similarity matrix | BLOSUM-62 
    5345 SS fraction | 0.3 
    5346 Gap open (HH/SS/other) | 18/18/6 
    5347 Gap extend | 1 
    5348 SS matrix |  |  | H | S | O 
    5349 ---|---|---|--- 
    5350 H | 6 | -9 | -6 
    5351 S |  | 6 | -6 
    5352 O |  |  | 4 
    5353 Iteration cutoff | 2 
    5354  
    5355 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    5356 with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
    5357 5451 
    5358 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    5359 8.396) 
    5360  
    5361 
    5362 > hide #!8 models
    5363 
    5364 > show #!8 models
    5365 
    5366 > hide #!8 models
    5367 
    5368 > hide #1 models
    5369 
    5370 > show #!8 models
    5371 
    5372 > undo
    5373 
    5374 > undo
    5375 
    5376 > undo
    5377 
    5378 > undo
    5379 
    5380 > undo
    5381 
    5382 > undo
    5383 
    5384 > undo
    5385 
    5386 > undo
    5387 
    5388 > undo
    5389 
    5390 > hide #!8 models
    5391 
    5392 > show #!8 models
    5393 
    5394 > hide #1 models
    5395 
    5396 > show #1 models
    5397 
    5398 > hide #!8 models
    5399 
    5400 > show #!8 models
    5401 
    5402 > hide #1 models
    5403 
    5404 > show #25 models
    5405 
    5406 > show #24 models
    5407 
    5408 > hide #24 models
    5409 
    5410 > hide #25 models
    5411 
    5412 > show #!9 models
    5413 
    5414 > select #9
    5415 
    5416 2 models selected 
    5417 
    5418 > ~select #9
    5419 
    5420 Nothing selected 
    5421 
    5422 > select #9
    5423 
    5424 2 models selected 
    5425 
    5426 > ~select #9
    5427 
    5428 Nothing selected 
    5429 
    5430 > ui tool show "Fit in Map"
    5431 
    5432 Fit molecule complex_dimer-FINAL-coot-7.pdb (#8) to map complex_dimer-
    5433 FINAL.ccp4 zone (#9) using 21258 atoms 
    5434 average map value = 18.77, steps = 168 
    5435 shifted from previous position = 7.66 
    5436 rotated from previous position = 14.8 degrees 
    5437 atoms outside contour = 11709, contour level = 19.427 
    5438  
    5439 Position of complex_dimer-FINAL-coot-7.pdb (#8) relative to complex_dimer-
    5440 FINAL.ccp4 zone (#9) coordinates: 
    5441 Matrix rotation and translation 
    5442 0.99999998 -0.00017475 -0.00004915 0.04741679 
    5443 0.00017475 0.99999998 -0.00000981 -0.05040213 
    5444 0.00004915 0.00000980 1.00000000 -0.01085846 
    5445 Axis 0.05393815 -0.27037831 0.96124203 
    5446 Axis point 279.56043468 269.54481820 0.00000000 
    5447 Rotation angle (degrees) 0.01041596 
    5448 Shift along axis 0.00574761 
    5449  
    5450 
    5451 > show #25 models
    5452 
    5453 > show #24 models
    5454 
    5455 > hide #24 models
    5456 
    5457 > hide #25 models
    5458 
    5459 > show #23 models
    5460 
    5461 > show #22 models
    5462 
    5463 > hide #22 models
    5464 
    5465 > hide #23 models
    5466 
    5467 > show #21 models
    5468 
    5469 > hide #21 models
    5470 
    5471 > show #25 models
    5472 
    5473 > show #24 models
    5474 
    5475 > show #4 models
    5476 
    5477 > hide #4 models
    5478 
    5479 > show #!5 models
    5480 
    5481 > hide #!5 models
    5482 
    5483 > close #25
    5484 
    5485 > close #24
    5486 
    5487 > hide #!9 models
    5488 
    5489 > hide #!8 models
    5490 
    5491 > show #!8 models
    5492 
    5493 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5494 > figures/AF-P47102-F1-model_v1.pdb
    5495 
    5496 AF-P47102-F1-model_v1.pdb title: 
    5497 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    5498 (P47102) [more info...] 
    5499  
    5500 Chain information for AF-P47102-F1-model_v1.pdb #24 
    5501 --- 
    5502 Chain | Description 
    5503 A | arf guanine-nucleotide exchange factor 1 
    5504  
    5505 
    5506 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5507 > figures/AF-P47102-F1-model_v1.pdb
    5508 
    5509 AF-P47102-F1-model_v1.pdb title: 
    5510 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    5511 (P47102) [more info...] 
    5512  
    5513 Chain information for AF-P47102-F1-model_v1.pdb #25 
    5514 --- 
    5515 Chain | Description 
    5516 A | arf guanine-nucleotide exchange factor 1 
    5517  
    5518 
    5519 > mmaker #24 #25 to #8
    5520 
    5521 Parameters 
    5522 --- 
    5523 Chain pairing | bb 
    5524 Alignment algorithm | Needleman-Wunsch 
    5525 Similarity matrix | BLOSUM-62 
    5526 SS fraction | 0.3 
    5527 Gap open (HH/SS/other) | 18/18/6 
    5528 Gap extend | 1 
    5529 SS matrix |  |  | H | S | O 
    5530 ---|---|---|--- 
    5531 H | 6 | -9 | -6 
    5532 S |  | 6 | -6 
    5533 O |  |  | 4 
    5534 Iteration cutoff | 2 
    5535  
    5536 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
    5537 AF-P47102-F1-model_v1.pdb, chain A (#24), sequence alignment score = 3470.5 
    5538 RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
    5539 9.022) 
    5540  
    5541 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
    5542 AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3470.5 
    5543 RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
    5544 9.022) 
    5545  
    5546 
    5547 > mmaker #25 to #8/C
    5548 
    5549 Parameters 
    5550 --- 
    5551 Chain pairing | bb 
    5552 Alignment algorithm | Needleman-Wunsch 
    5553 Similarity matrix | BLOSUM-62 
    5554 SS fraction | 0.3 
    5555 Gap open (HH/SS/other) | 18/18/6 
    5556 Gap extend | 1 
    5557 SS matrix |  |  | H | S | O 
    5558 ---|---|---|--- 
    5559 H | 6 | -9 | -6 
    5560 S |  | 6 | -6 
    5561 O |  |  | 4 
    5562 Iteration cutoff | 2 
    5563  
    5564 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
    5565 AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3462 
    5566 RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
    5567 9.117) 
    5568  
    5569 
    5570 > ui tool show "Show Sequence Viewer"
    5571 
    5572 > sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
    5573 
    5574 Alignment identifier is 1 
    5575 Drag select of 2 residues 
    5576 Seqview [ID: 1] region 7 chains [971-976] RMSD: 319.198 
    5577  
    5578 Seqview [ID: 1] region 7 chains [1-977] RMSD: 276.169 
    5579  
    5580 
    5581 > delete atoms (#24-25 & sel)
    5582 
    5583 > delete bonds (#24-25 & sel)
    5584 
    5585 Seqview [ID: 1] region 7 chains [985-993] RMSD: 233.627 
    5586  
    5587 Seqview [ID: 1] region 7 chains [994-1408] RMSD: 297.153 
    5588  
    5589 
    5590 > delete atoms (#24-25 & sel)
    5591 
    5592 > delete bonds (#24-25 & sel)
    5593 
    5594 > preset cartoons/nucleotides cylinders/stubs
    5595 
    5596 Changed 0 atom styles 
    5597 Preset expands to these ChimeraX commands:
    5598 
    5599    
    5600    
    5601     show nucleic
    5602     hide protein|solvent|H
    5603     surf hide
    5604     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5605     cartoon
    5606     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    5607     cartoon style ~(nucleic|strand) x round
    5608     cartoon style (nucleic|strand) x rect
    5609     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    5610     cartoon style nucleic x round width 1.6 thick 1.6
    5611     nucleotides stubs
    5612 
    5613  
    5614 
    5615 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
    5616 > transparentBackground true supersample 3
    5617 
    5618 > lighting soft
    5619 
    5620 > lighting simple
    5621 
    5622 > lighting soft
    5623 
    5624 > lighting full
    5625 
    5626 > lighting soft
    5627 
    5628 > lighting shadows true intensity 0.5
    5629 
    5630 > lighting shadows false
    5631 
    5632 > lighting shadows true
    5633 
    5634 > graphics silhouettes false
    5635 
    5636 > graphics silhouettes true
    5637 
    5638 > lighting soft
    5639 
    5640 > ui tool show "Side View"
    5641 
    5642 > ui tool show "Side View"
    5643 
    5644 > view orient
    5645 
    5646 > hide #25 models
    5647 
    5648 > hide #24 models
    5649 
    5650 > show #4 models
    5651 
    5652 > hide #4 models
    5653 
    5654 > show #1 models
    5655 
    5656 > hide #!8 models
    5657 
    5658 > show #!12 models
    5659 
    5660 > show #12.1 models
    5661 
    5662 > show #15.15 models
    5663 
    5664 > hide #15.15 models
    5665 
    5666 > show #18.1 models
    5667 
    5668 > hide #18.1 models
    5669 
    5670 > show #14.1 models
    5671 
    5672 > hide #14.1 models
    5673 
    5674 > show #15.15 models
    5675 
    5676 > hide #15.15 models
    5677 
    5678 > hide #!14 models
    5679 
    5680 > show #14.1 models
    5681 
    5682 > hide #14.1 models
    5683 
    5684 > hide #12.1 models
    5685 
    5686 > show #12.1 models
    5687 
    5688 > show #18.1 models
    5689 
    5690 > hide #18.1 models
    5691 
    5692 > hide #!18 models
    5693 
    5694 > show #17.1 models
    5695 
    5696 > show #20 models
    5697 
    5698 > show #21 models
    5699 
    5700 > hide #!17 models
    5701 
    5702 > select clear
    5703 
    5704 > select clear
    5705 
    5706 > hide #17.1 models
    5707 
    5708 > hide #!15 models
    5709 
    5710 > hide #!14 models
    5711 
    5712 > hide #12.1 models
    5713 
    5714 > show #18.1 models
    5715 
    5716 > hide #18.1 models
    5717 
    5718 > hide #!18 models
    5719 
    5720 > show #17.1 models
    5721 
    5722 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample
    5723 > transparentBackground true supersample 3
    5724 
    5725 Cannot determine format for
    5726 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample' 
    5727 
    5728 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample2.png
    5729 > transparentBackground true supersample 3
    5730 
    5731 > hide #17.1 models
    5732 
    5733 > hide #!17 models
    5734 
    5735 > hide #21 models
    5736 
    5737 > hide #20 models
    5738 
    5739 > show #24 models
    5740 
    5741 > show #25 models
    5742 
    5743 > hide #!12 models
    5744 
    5745 > hide #1 models
    5746 
    5747 > show #!5 models
    5748 
    5749 > hide #!5 models
    5750 
    5751 > show #!6 models
    5752 
    5753 > hide #!6 models
    5754 
    5755 > show #!7 models
    5756 
    5757 > hide #!7 models
    5758 
    5759 > show #!8 models
    5760 
    5761 > hide #!8 models
    5762 
    5763 > show #!8 models
    5764 
    5765 > hide #!8 models
    5766 
    5767 > hide #25 models
    5768 
    5769 > hide #24 models
    5770 
    5771 > show #!26 models
    5772 
    5773 > show #!26 surfaces
    5774 
    5775 > show #1 models
    5776 
    5777 > hide #1 models
    5778 
    5779 > show #1 models
    5780 
    5781 > hide #1 models
    5782 
    5783 > show #4 models
    5784 
    5785 > hide #4 models
    5786 
    5787 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    5788 > transparentBackground true supersample 3
    5789 
    5790 > hide #!26 models
    5791 
    5792 > show #1 models
    5793 
    5794 > ui tool show "Side View"
    5795 
    5796 > hide #1 models
    5797 
    5798 > show #!26 models
    5799 
    5800 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    5801 > transparentBackground true supersample 3
    5802 
    5803 > hide #!26 models
    5804 
    5805 > show #1 models
    5806 
    5807 > show #20 models
    5808 
    5809 > show #21 models
    5810 
    5811 > show #12.1 models
    5812 
    5813 > hide #12.1 models
    5814 
    5815 > show #17.1 models
    5816 
    5817 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
    5818 > transparentBackground true supersample 3
    5819 
    5820 Cannot determine format for
    5821 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1' 
    5822 
    5823 > hide #!17 models
    5824 
    5825 > hide #17.1 models
    5826 
    5827 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    5828 > transparentBackground true supersample 3
    5829 
    5830 > show #17.1 models
    5831 
    5832 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
    5833 > transparentBackground true supersample 3
    5834 
    5835 Cannot determine format for
    5836 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1' 
    5837 
    5838 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    5839 > arf1-.png transparentBackground true supersample 3
    5840 
    5841 > hide #!12 models
    5842 
    5843 > hide #!17 models
    5844 
    5845 > hide #17.1 models
    5846 
    5847 > hide #20 models
    5848 
    5849 > hide #21 models
    5850 
    5851 > show #22 models
    5852 
    5853 > show #23 models
    5854 
    5855 > hide #1 models
    5856 
    5857 > show #4 models
    5858 
    5859 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    5860 > transparentBackground true supersample 3
    5861 
    5862 > hide #4 models
    5863 
    5864 > hide #22 models
    5865 
    5866 > hide #23 models
    5867 
    5868 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5869 > figures/closed_dimer-FINAL.ccp4
    5870 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5871 > figures/complex_dimer-FINAL.ccp4
    5872 
    5873 Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
    5874 level 1.11, step 2, values float32 
    5875 
    5876 > close #28
    5877 
    5878 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5879 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    5880 
    5881 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #28 
    5882 --- 
    5883 Chain | Description 
    5884 A B | No description available 
    5885  
    5886 
    5887 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5888 > figures/complex_dimer-FINAL-coot-7.pdb
    5889 
    5890 Chain information for complex_dimer-FINAL-coot-7.pdb #29 
    5891 --- 
    5892 Chain | Description 
    5893 A C | No description available 
    5894 B | No description available 
    5895 D | No description available 
    5896  
    5897 
    5898 > select #28/B
    5899 
    5900 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    5901 
    5902 > delete atoms sel
    5903 
    5904 > delete bonds sel
    5905 
    5906 > select #29/D
    5907 
    5908 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    5909 
    5910 > delete atoms (#!29 & sel)
    5911 
    5912 > delete bonds (#!29 & sel)
    5913 
    5914 > select #29/B
    5915 
    5916 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    5917 
    5918 > delete atoms sel
    5919 
    5920 > delete bonds sel
    5921 
    5922 > select #29/A
    5923 
    5924 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected 
    5925 
    5926 > delete atoms (#!29 & sel)
    5927 
    5928 > delete bonds (#!29 & sel)
    5929 
    5930 > close #29
    5931 
    5932 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5933 > figures/complex_dimer-FINAL.ccp4
    5934 
    5935 Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
    5936 level 1.63, step 2, values float32 
    5937 
    5938 > close #29
    5939 
    5940 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5941 > figures/complex_dimer-FINAL.ccp4
    5942 
    5943 Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
    5944 level 1.63, step 2, values float32 
    5945 
    5946 > close #29
    5947 
    5948 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    5949 > figures/complex_dimer-FINAL-coot-7.pdb
    5950 
    5951 Chain information for complex_dimer-FINAL-coot-7.pdb #29 
    5952 --- 
    5953 Chain | Description 
    5954 A C | No description available 
    5955 B | No description available 
    5956 D | No description available 
    5957  
    5958 
    5959 > select #29/B
    5960 
    5961 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    5962 
    5963 > delete atoms sel
    5964 
    5965 > delete bonds sel
    5966 
    5967 > select #29/A
    5968 
    5969 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected 
    5970 
    5971 > delete atoms (#!29 & sel)
    5972 
    5973 > delete bonds (#!29 & sel)
    5974 
    5975 > show #1 models
    5976 
    5977 > mmaker #29 #1/B
    5978 
    5979 > matchmaker #29 #1/B
    5980 
    5981 Missing required "to" argument 
    5982 
    5983 > mmaker #29 to #1/B
    5984 
    5985 Parameters 
    5986 --- 
    5987 Chain pairing | bb 
    5988 Alignment algorithm | Needleman-Wunsch 
    5989 Similarity matrix | BLOSUM-62 
    5990 SS fraction | 0.3 
    5991 Gap open (HH/SS/other) | 18/18/6 
    5992 Gap extend | 1 
    5993 SS matrix |  |  | H | S | O 
    5994 ---|---|---|--- 
    5995 H | 6 | -9 | -6 
    5996 S |  | 6 | -6 
    5997 O |  |  | 4 
    5998 Iteration cutoff | 2 
    5999  
    6000 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    6001 with complex_dimer-FINAL-coot-7.pdb, chain C (#29), sequence alignment score =
    6002 5417.4 
    6003 RMSD between 739 pruned atom pairs is 1.151 angstroms; (across all 1153 pairs:
    6004 8.341) 
    6005  
    6006 
    6007 > show #20 models
    6008 
    6009 > show #21 models
    6010 
    6011 > color zone #29 #1
    6012 
    6013 Missing required "near" argument 
    6014 
    6015 > color zone #29 near #1
    6016 
    6017 > color zone #29 near #1 distance 3
    6018 
    6019 > ui tool show "Show Sequence Viewer"
    6020 
    6021 > sequence chain #29/C
    6022 
    6023 Alignment identifier is 29/C 
    6024 
    6025 > hide #1 models
    6026 
    6027 > color sel #f4e379ff
    6028 
    6029 Drag select of 1 residues 
    6030 
    6031 > select #29/C:799
    6032 
    6033 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6034 
    6035 > color sel #e1c4b2ff
    6036 
    6037 > ui tool show "Color Actions"
    6038 
    6039 > color sel #9ac2f5ff
    6040 
    6041 > select clear
    6042 
    6043 Drag select of 1 residues 
    6044 
    6045 > select clear
    6046 
    6047 > select #28/A:544
    6048 
    6049 20 atoms, 20 bonds, 1 residue, 1 model selected 
    6050 
    6051 > select clear
    6052 
    6053 > ui tool show "Show Sequence Viewer"
    6054 
    6055 > sequence chain #28/A
    6056 
    6057 Alignment identifier is 28/A 
    6058 Drag select of 1 residues 
    6059 Drag select of 1 residues 
    6060 
    6061 > color sel #f4e379ff
    6062 
    6063 > select #28/A:799
    6064 
    6065 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6066 
    6067 > select #28/A:799
    6068 
    6069 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6070 
    6071 > color sel #e1c4b2ff
    6072 
    6073 > color sel #9ac2f5ff
    6074 
    6075 > select clear
    6076 
    6077 > select #29/D
    6078 
    6079 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    6080 
    6081 > color (#!29 & sel) #7281dbff
    6082 
    6083 > select clear
    6084 
    6085 > show #!8 models
    6086 
    6087 > hide #!8 models
    6088 
    6089 > preset cartoons/nucleotides cylinders/stubs
    6090 
    6091 Changed 0 atom styles 
    6092 Preset expands to these ChimeraX commands:
    6093 
    6094    
    6095    
    6096     show nucleic
    6097     hide protein|solvent|H
    6098     surf hide
    6099     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    6100     cartoon
    6101     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    6102     cartoon style ~(nucleic|strand) x round
    6103     cartoon style (nucleic|strand) x rect
    6104     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    6105     cartoon style nucleic x round width 1.6 thick 1.6
    6106     nucleotides stubs
    6107 
    6108  
    6109 
    6110 > hide #!29 models
    6111 
    6112 > hide #28 models
    6113 
    6114 > hide #21 models
    6115 
    6116 > hide #20 models
    6117 
    6118 > show #!26 models
    6119 
    6120 > show #!26 surfaces
    6121 
    6122 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    6123 > transparentBackground true supersample 3
    6124 
    6125 > hide #!26 models
    6126 
    6127 > show #1 models
    6128 
    6129 > show #21 models
    6130 
    6131 > show #20 models
    6132 
    6133 > ui tool show "Side View"
    6134 
    6135 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    6136 > transparentBackground true supersample 3
    6137 
    6138 > hide #1 models
    6139 
    6140 > hide #21 models
    6141 
    6142 > hide #20 models
    6143 
    6144 > show #22 models
    6145 
    6146 > show #23 models
    6147 
    6148 > show #4 models
    6149 
    6150 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    6151 > transparentBackground true supersample 3
    6152 
    6153 > hide #4 models
    6154 
    6155 > hide #23 models
    6156 
    6157 > hide #22 models
    6158 
    6159 > show #25 models
    6160 
    6161 > show #24 models
    6162 
    6163 > show #28 models
    6164 
    6165 > show #!29 models
    6166 
    6167 > hide #25 models
    6168 
    6169 > hide #24 models
    6170 
    6171 > show #21 models
    6172 
    6173 > show #20 models
    6174 
    6175 > save
    6176 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    6177 > transparentBackground true supersample 3
    6178 
    6179 > hide #21 models
    6180 
    6181 > hide #20 models
    6182 
    6183 > hide #28 models
    6184 
    6185 > hide #!29 models
    6186 
    6187 > show #!12 models
    6188 
    6189 > show #12.1 models
    6190 
    6191 > hide #!12 models
    6192 
    6193 > show #!12 models
    6194 
    6195 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
    6196 > transparentBackground true supersample 3
    6197 
    6198 Cannot determine format for
    6199 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp' 
    6200 
    6201 > show #!15 models
    6202 
    6203 > show #15.15 models
    6204 
    6205 > hide #!12 models
    6206 
    6207 > hide #12.1 models
    6208 
    6209 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    6210 > transparentBackground true supersample 3
    6211 
    6212 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    6213 > transparentBackground true supersample 3
    6214 
    6215 > hide #15.15 models
    6216 
    6217 > hide #!15 models
    6218 
    6219 > show #14.1 models
    6220 
    6221 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    6222 > transparentBackground true supersample 3
    6223 
    6224 > hide #14.1 models
    6225 
    6226 > hide #!14 models
    6227 
    6228 > show #12.1 models
    6229 
    6230 > show #1 models
    6231 
    6232 > show #20 models
    6233 
    6234 > show #21 models
    6235 
    6236 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    6237 > arf1.png transparentBackground true supersample 3
    6238 
    6239 > hide #21 models
    6240 
    6241 > hide #20 models
    6242 
    6243 > show #20 models
    6244 
    6245 > show #21 models
    6246 
    6247 > hide #1 models
    6248 
    6249 > hide #!12 models
    6250 
    6251 > hide #12.1 models
    6252 
    6253 > show #28 models
    6254 
    6255 > show #!29 models
    6256 
    6257 > save
    6258 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    6259 > transparentBackground true supersample 3
    6260 
    6261 > hide #28 models
    6262 
    6263 > hide #!29 models
    6264 
    6265 > show #1 models
    6266 
    6267 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    6268 > side.png transparentBackground true supersample 3
    6269 
    6270 > hide #1 models
    6271 
    6272 > hide #21 models
    6273 
    6274 > hide #20 models
    6275 
    6276 > show #20 models
    6277 
    6278 > show #21 models
    6279 
    6280 > show #1 models
    6281 
    6282 > show #!12 models
    6283 
    6284 > hide #!12 models
    6285 
    6286 > show #!12 models
    6287 
    6288 > hide #!12 models
    6289 
    6290 > show #12.1 models
    6291 
    6292 > hide #12.1 models
    6293 
    6294 > show #18.1 models
    6295 
    6296 > hide #18.1 models
    6297 
    6298 > show #17.1 models
    6299 
    6300 > hide #!18 models
    6301 
    6302 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    6303 > arf1-side transparentBackground true supersample 3
    6304 
    6305 Cannot determine format for
    6306 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1-side' 
    6307 
    6308 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    6309 > arf1-side.png transparentBackground true supersample 3
    6310 
    6311 > hide #!17 models
    6312 
    6313 > hide #17.1 models
    6314 
    6315 > show #!27 models
    6316 
    6317 > hide #!27 models
    6318 
    6319 > show #28 models
    6320 
    6321 > show #!29 models
    6322 
    6323 > hide #21 models
    6324 
    6325 > show #21 models
    6326 
    6327 > hide #1 models
    6328 
    6329 > hide #!12 models
    6330 
    6331 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
    6332 > side.png transparentBackground true supersample 3
    6333 
    6334 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
    6335 > side.png transparentBackground true supersample 3
    6336 
    6337 > mmaker #4 #8 #28 #29 to #1 bring #22-25
    6338 
    6339 'bring' option can only be used when exactly one structure is being matched 
    6340 
    6341 > mmaker #4 to #1 bring #22-23
    6342 
    6343 Parameters 
    6344 --- 
    6345 Chain pairing | bb 
    6346 Alignment algorithm | Needleman-Wunsch 
    6347 Similarity matrix | BLOSUM-62 
    6348 SS fraction | 0.3 
    6349 Gap open (HH/SS/other) | 18/18/6 
    6350 Gap extend | 1 
    6351 SS matrix |  |  | H | S | O 
    6352 ---|---|---|--- 
    6353 H | 6 | -9 | -6 
    6354 S |  | 6 | -6 
    6355 O |  |  | 4 
    6356 Iteration cutoff | 2 
    6357  
    6358 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    6359 with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4),
    6360 sequence alignment score = 5250.9 
    6361 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    6362 10.353) 
    6363  
    6364 
    6365 > mmaker #8 to #1 bring #24-25
    6366 
    6367 Parameters 
    6368 --- 
    6369 Chain pairing | bb 
    6370 Alignment algorithm | Needleman-Wunsch 
    6371 Similarity matrix | BLOSUM-62 
    6372 SS fraction | 0.3 
    6373 Gap open (HH/SS/other) | 18/18/6 
    6374 Gap extend | 1 
    6375 SS matrix |  |  | H | S | O 
    6376 ---|---|---|--- 
    6377 H | 6 | -9 | -6 
    6378 S |  | 6 | -6 
    6379 O |  |  | 4 
    6380 Iteration cutoff | 2 
    6381  
    6382 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    6383 with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
    6384 5451 
    6385 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    6386 8.396) 
    6387  
    6388 
    6389 > hide #28 models
    6390 
    6391 > hide #!29 models
    6392 
    6393 > hide #21 models
    6394 
    6395 > hide #20 models
    6396 
    6397 > show #25 models
    6398 
    6399 > show #24 models
    6400 
    6401 > show #!8 models
    6402 
    6403 > show #1 models
    6404 
    6405 > hide #1 models
    6406 
    6407 > hide #25 models
    6408 
    6409 > hide #24 models
    6410 
    6411 > show #28 models
    6412 
    6413 > show #!29 models
    6414 
    6415 > hide #!8 models
    6416 
    6417 > hide #!29 models
    6418 
    6419 > show #!29 models
    6420 
    6421 > show #!15 models
    6422 
    6423 > show #15.15 models
    6424 
    6425 > hide #!15 models
    6426 
    6427 > hide #15.15 models
    6428 
    6429 > show #14.1 models
    6430 
    6431 > hide #14.1 models
    6432 
    6433 > hide #!14 models
    6434 
    6435 > show #15.15 models
    6436 
    6437 > mmaker #15 to #29/D
    6438 
    6439 Parameters 
    6440 --- 
    6441 Chain pairing | bb 
    6442 Alignment algorithm | Needleman-Wunsch 
    6443 Similarity matrix | BLOSUM-62 
    6444 SS fraction | 0.3 
    6445 Gap open (HH/SS/other) | 18/18/6 
    6446 Gap extend | 1 
    6447 SS matrix |  |  | H | S | O 
    6448 ---|---|---|--- 
    6449 H | 6 | -9 | -6 
    6450 S |  | 6 | -6 
    6451 O |  |  | 4 
    6452 Iteration cutoff | 2 
    6453  
    6454 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain D (#29) with 2ksq.pdb, chain
    6455 A (#15.15), sequence alignment score = 612.3 
    6456 RMSD between 105 pruned atom pairs is 1.288 angstroms; (across all 164 pairs:
    6457 4.121) 
    6458  
    6459 
    6460 > select #29/D
    6461 
    6462 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    6463 
    6464 > delete atoms (#!29 & sel)
    6465 
    6466 > delete bonds (#!29 & sel)
    6467 
    6468 > ui tool show "Show Sequence Viewer"
    6469 
    6470 > sequence chain #15.15/A
    6471 
    6472 Alignment identifier is 15.15/A 
    6473 
    6474 > color sel #aa0000ff
    6475 
    6476 > select clear
    6477 
    6478 > select clear
    6479 
    6480 > hide #15.15 models
    6481 
    6482 > hide #!15 models
    6483 
    6484 > show #1 models
    6485 
    6486 > hide #!29 models
    6487 
    6488 > hide #28 models
    6489 
    6490 > show #12.1 models
    6491 
    6492 > ui tool show "Show Sequence Viewer"
    6493 
    6494 > sequence chain #12.1/A
    6495 
    6496 Alignment identifier is 12.1/A 
    6497 
    6498 > color sel #ffffffff
    6499 
    6500 > color sel #aa0000ff
    6501 
    6502 > select clear
    6503 
    6504 > select clear
    6505 
    6506 > hide #!12 models
    6507 
    6508 > hide #12.1 models
    6509 
    6510 > show #20 models
    6511 
    6512 > show #21 models
    6513 
    6514 > hide #21 models
    6515 
    6516 > hide #20 models
    6517 
    6518 > hide #1 models
    6519 
    6520 > show #!26 models
    6521 
    6522 > ui tool show "Side View"
    6523 
    6524 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    6525 > transparentBackground true supersample 3
    6526 
    6527 > hide #!26 models
    6528 
    6529 > show #1 models
    6530 
    6531 > show #20 models
    6532 
    6533 > show #21 models
    6534 
    6535 > ui tool show "Side View"
    6536 
    6537 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    6538 > transparentBackground true supersample 3
    6539 
    6540 > show #12.1 models
    6541 
    6542 > show #28 models
    6543 
    6544 > show #!29 models
    6545 
    6546 > show #!27 models
    6547 
    6548 > hide #!27 models
    6549 
    6550 > show #15.15 models
    6551 
    6552 > hide #15.15 models
    6553 
    6554 > hide #!15 models
    6555 
    6556 > hide #!12 models
    6557 
    6558 > hide #12.1 models
    6559 
    6560 > show #17.1 models
    6561 
    6562 > ui tool show "Show Sequence Viewer"
    6563 
    6564 > sequence chain #17.1/A
    6565 
    6566 Alignment identifier is 17.1/A 
    6567 
    6568 > color sel #ffffffff
    6569 
    6570 > color sel #aa0000ff
    6571 
    6572 > select clear
    6573 
    6574 > hide #28 models
    6575 
    6576 > hide #!29 models
    6577 
    6578 > save
    6579 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-closed.png
    6580 > transparentBackground true supersample 3
    6581 
    6582 > hide #1 models
    6583 
    6584 > hide #21 models
    6585 
    6586 > hide #20 models
    6587 
    6588 > show #22 models
    6589 
    6590 > show #23 models
    6591 
    6592 > hide #17.1 models
    6593 
    6594 > hide #!17 models
    6595 
    6596 > show #4 models
    6597 
    6598 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    6599 > transparentBackground true supersample 3
    6600 
    6601 > hide #4 models
    6602 
    6603 > show #!29 models
    6604 
    6605 > show #28 models
    6606 
    6607 > show #20 models
    6608 
    6609 > hide #22 models
    6610 
    6611 > hide #23 models
    6612 
    6613 > show #21 models
    6614 
    6615 > show #15.15 models
    6616 
    6617 > save
    6618 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    6619 > transparentBackground true supersample 3
    6620 
    6621 > hide #28 models
    6622 
    6623 > hide #!29 models
    6624 
    6625 > hide #21 models
    6626 
    6627 > hide #20 models
    6628 
    6629 > select ::name="GTP"
    6630 
    6631 43 atoms, 45 bonds, 1 residue, 1 model selected 
    6632 
    6633 > color sel #55aa7fff
    6634 
    6635 > color sel byhetero
    6636 
    6637 > select clear
    6638 
    6639 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    6640 > transparentBackground true supersample 3
    6641 
    6642 > hide #15.15 models
    6643 
    6644 > hide #!15 models
    6645 
    6646 > show #17.1 models
    6647 
    6648 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    6649 > transparentBackground true supersample 3
    6650 
    6651 > hide #17.1 models
    6652 
    6653 > hide #!17 models
    6654 
    6655 > show #1 models
    6656 
    6657 > show #20 models
    6658 
    6659 > show #21 models
    6660 
    6661 > show #!26 models
    6662 
    6663 > hide #1,20-21#!26 surfaces
    6664 
    6665 > style #1,20-21#!26 stick
    6666 
    6667 Changed 353076 atom styles 
    6668 
    6669 > nucleotides #1,20-21#!26 atoms
    6670 
    6671 > style nucleic & #1,20-21#!26 stick
    6672 
    6673 Changed 0 atom styles 
    6674 
    6675 > select #1
    6676 
    6677 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    6678 
    6679 > select #4
    6680 
    6681 36826 atoms, 37112 bonds, 2258 residues, 1 model selected 
    6682 
    6683 > select #8
    6684 
    6685 21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected 
    6686 
    6687 > select #1
    6688 
    6689 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    6690 
    6691 > select #4
    6692 
    6693 36826 atoms, 37112 bonds, 2258 residues, 1 model selected 
    6694 
    6695 > select #1
    6696 
    6697 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    6698 
    6699 > hide #!26 models
    6700 
    6701 > show #!26 models
    6702 
    6703 > hide #21 models
    6704 
    6705 > hide #20 models
    6706 
    6707 > select clear
    6708 
    6709 > select #1
    6710 
    6711 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    6712 
    6713 > ~select #1
    6714 
    6715 Nothing selected 
    6716 
    6717 > select #1
    6718 
    6719 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    6720 
    6721 > select clear
    6722 
    6723 > hide #!26 models
    6724 
    6725 > show #!26 models
    6726 
    6727 > hide #!26 models
    6728 
    6729 > show #11 models
    6730 
    6731 > mmaker #11 to #1
    6732 
    6733 Parameters 
    6734 --- 
    6735 Chain pairing | bb 
    6736 Alignment algorithm | Needleman-Wunsch 
    6737 Similarity matrix | BLOSUM-62 
    6738 SS fraction | 0.3 
    6739 Gap open (HH/SS/other) | 18/18/6 
    6740 Gap extend | 1 
    6741 SS matrix |  |  | H | S | O 
    6742 ---|---|---|--- 
    6743 H | 6 | -9 | -6 
    6744 S |  | 6 | -6 
    6745 O |  |  | 4 
    6746 Iteration cutoff | 2 
    6747  
    6748 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    6749 with ger2.pdb, chain C (#11), sequence alignment score = 978.1 
    6750 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    6751 1.427) 
    6752  
    6753 
    6754 > show #15.15 models
    6755 
    6756 > hide #15.15 models
    6757 
    6758 > show #15.15 models
    6759 
    6760 > hide #15.15 models
    6761 
    6762 > show #15.15 models
    6763 
    6764 > hide #15.15 models
    6765 
    6766 > mmaker #15 to #13
    6767 
    6768 Parameters 
    6769 --- 
    6770 Chain pairing | bb 
    6771 Alignment algorithm | Needleman-Wunsch 
    6772 Similarity matrix | BLOSUM-62 
    6773 SS fraction | 0.3 
    6774 Gap open (HH/SS/other) | 18/18/6 
    6775 Gap extend | 1 
    6776 SS matrix |  |  | H | S | O 
    6777 ---|---|---|--- 
    6778 H | 6 | -9 | -6 
    6779 S |  | 6 | -6 
    6780 O |  |  | 4 
    6781 Iteration cutoff | 2 
    6782  
    6783 Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.15), sequence
    6784 alignment score = 656.7 
    6785 RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
    6786 3.660) 
    6787  
    6788 
    6789 > show #15.15 models
    6790 
    6791 > hide #!15 models
    6792 
    6793 > hide #15.15 models
    6794 
    6795 > show #15.15 models
    6796 
    6797 > show #13 models
    6798 
    6799 > hide #13 models
    6800 
    6801 > hide #11 models
    6802 
    6803 > mmaker #15 to #11
    6804 
    6805 Parameters 
    6806 --- 
    6807 Chain pairing | bb 
    6808 Alignment algorithm | Needleman-Wunsch 
    6809 Similarity matrix | BLOSUM-62 
    6810 SS fraction | 0.3 
    6811 Gap open (HH/SS/other) | 18/18/6 
    6812 Gap extend | 1 
    6813 SS matrix |  |  | H | S | O 
    6814 ---|---|---|--- 
    6815 H | 6 | -9 | -6 
    6816 S |  | 6 | -6 
    6817 O |  |  | 4 
    6818 Iteration cutoff | 2 
    6819  
    6820 Matchmaker ger2.pdb, chain A (#11) with 2ksq.pdb, chain A (#15.15), sequence
    6821 alignment score = 656.7 
    6822 RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
    6823 3.660) 
    6824  
    6825 
    6826 > mmaker #17 to #11
    6827 
    6828 Parameters 
    6829 --- 
    6830 Chain pairing | bb 
    6831 Alignment algorithm | Needleman-Wunsch 
    6832 Similarity matrix | BLOSUM-62 
    6833 SS fraction | 0.3 
    6834 Gap open (HH/SS/other) | 18/18/6 
    6835 Gap extend | 1 
    6836 SS matrix |  |  | H | S | O 
    6837 ---|---|---|--- 
    6838 H | 6 | -9 | -6 
    6839 S |  | 6 | -6 
    6840 O |  |  | 4 
    6841 Iteration cutoff | 2 
    6842  
    6843 Matchmaker ger2.pdb, chain A (#11) with 2k5u.pdb, chain A (#17.1), sequence
    6844 alignment score = 695 
    6845 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    6846 5.084) 
    6847  
    6848 
    6849 > show #17.1 models
    6850 
    6851 > hide #17.1 models
    6852 
    6853 > hide #!17 models
    6854 
    6855 > hide #15.15 models
    6856 
    6857 > hide #!15 models
    6858 
    6859 > hide #1 models
    6860 
    6861 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    6862 > figures/2ksq.pdb
    6863 
    6864 2ksq.pdb title: 
    6865 The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
    6866 info...] 
    6867  
    6868 Chain information for 2ksq.pdb 
    6869 --- 
    6870 Chain | Description 
    6871 30.1/A | adp-ribosylation factor 1 
    6872 30.2/A 30.3/A 30.4/A 30.5/A 30.6/A 30.7/A 30.8/A 30.9/A 30.10/A 30.11/A
    6873 30.12/A 30.13/A 30.14/A 30.15/A 30.16/A 30.17/A 30.18/A 30.19/A 30.20/A | adp-
    6874 ribosylation factor 1 
    6875  
    6876 
    6877 > hide #!30 models
    6878 
    6879 > hide #30.1 models
    6880 
    6881 > hide #30.2 models
    6882 
    6883 > hide #30.3 models
    6884 
    6885 > hide #30.4 models
    6886 
    6887 > hide #30.5 models
    6888 
    6889 > hide #30.7 models
    6890 
    6891 > hide #30.8 models
    6892 
    6893 > hide #30.6 models
    6894 
    6895 > hide #30.9 models
    6896 
    6897 > hide #30.10 models
    6898 
    6899 > hide #30.12 models
    6900 
    6901 > hide #30.13 models
    6902 
    6903 > hide #30.14 models
    6904 
    6905 > hide #30.11 models
    6906 
    6907 > hide #30.15 models
    6908 
    6909 > hide #30.16 models
    6910 
    6911 > hide #30.17 models
    6912 
    6913 > hide #30.18 models
    6914 
    6915 > hide #30.19 models
    6916 
    6917 > hide #30.20 models
    6918 
    6919 > show #30.1 models
    6920 
    6921 Drag select of 281 atoms, 180 residues, 258 bonds 
    6922 
    6923 > hide sel atoms
    6924 
    6925 > select clear
    6926 
    6927 > select clear
    6928 
    6929 > hide #!30 models
    6930 
    6931 > hide #30.1 models
    6932 
    6933 > show #30.1 models
    6934 
    6935 > show #30.2 models
    6936 
    6937 > hide #30.2 models
    6938 
    6939 > show #30.3 models
    6940 
    6941 > show #30.4 models
    6942 
    6943 > hide #30.3 models
    6944 
    6945 > hide #30.4 models
    6946 
    6947 > show #30.5 models
    6948 
    6949 > hide #30.1 models
    6950 
    6951 > hide #!30 models
    6952 
    6953 > show #!30 models
    6954 
    6955 > hide #!30 models
    6956 
    6957 > hide #30.5 models
    6958 
    6959 > show #30.5 models
    6960 
    6961 Drag select of 265 atoms, 180 residues, 243 bonds 
    6962 
    6963 > hide sel atoms
    6964 
    6965 > select clear
    6966 
    6967 > select clear
    6968 
    6969 > show #30.6 models
    6970 
    6971 > hide #30.6 models
    6972 
    6973 > show #30.8 models
    6974 
    6975 > hide #30.8 models
    6976 
    6977 > show #30.9 models
    6978 
    6979 > hide #30.9 models
    6980 
    6981 > show #30.10 models
    6982 
    6983 > hide #30.10 models
    6984 
    6985 > show #30.11 models
    6986 
    6987 > hide #30.11 models
    6988 
    6989 > show #30.12 models
    6990 
    6991 > hide #30.12 models
    6992 
    6993 > show #30.13 models
    6994 
    6995 > hide #30.13 models
    6996 
    6997 > show #30.14 models
    6998 
    6999 > hide #30.5 models
    7000 
    7001 Drag select of 269 atoms, 180 residues, 248 bonds 
    7002 
    7003 > hide sel atoms
    7004 
    7005 > select clear
    7006 
    7007 > select clear
    7008 
    7009 > close #30.1-13
    7010 
    7011 > close #30.15-20
    7012 
    7013 > preset cartoons/nucleotides cylinders/stubs
    7014 
    7015 Changed 0 atom styles 
    7016 Preset expands to these ChimeraX commands:
    7017 
    7018    
    7019    
    7020     show nucleic
    7021     hide protein|solvent|H
    7022     surf hide
    7023     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7024     cartoon
    7025     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7026     cartoon style ~(nucleic|strand) x round
    7027     cartoon style (nucleic|strand) x rect
    7028     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    7029     cartoon style nucleic x round width 1.6 thick 1.6
    7030     nucleotides stubs
    7031 
    7032  
    7033 
    7034 > ui tool show "Show Sequence Viewer"
    7035 
    7036 > sequence chain #30.14/A
    7037 
    7038 Alignment identifier is 30.14/A 
    7039 
    7040 > color sel #aa0000ff
    7041 
    7042 > select clear
    7043 
    7044 > show #1 models
    7045 
    7046 > hide #!30 models
    7047 
    7048 > show #!29 models
    7049 
    7050 > show #28 models
    7051 
    7052 > show #20 models
    7053 
    7054 > show #21 models
    7055 
    7056 > show #22 models
    7057 
    7058 > show #23 models
    7059 
    7060 > show #24 models
    7061 
    7062 > show #25 models
    7063 
    7064 > mmaker #29 to #1 bring #20-25
    7065 
    7066 Parameters 
    7067 --- 
    7068 Chain pairing | bb 
    7069 Alignment algorithm | Needleman-Wunsch 
    7070 Similarity matrix | BLOSUM-62 
    7071 SS fraction | 0.3 
    7072 Gap open (HH/SS/other) | 18/18/6 
    7073 Gap extend | 1 
    7074 SS matrix |  |  | H | S | O 
    7075 ---|---|---|--- 
    7076 H | 6 | -9 | -6 
    7077 S |  | 6 | -6 
    7078 O |  |  | 4 
    7079 Iteration cutoff | 2 
    7080  
    7081 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    7082 with complex_dimer-FINAL-coot-7.pdb, chain C (#29), sequence alignment score =
    7083 5449.8 
    7084 RMSD between 719 pruned atom pairs is 1.188 angstroms; (across all 1153 pairs:
    7085 8.380) 
    7086  
    7087 
    7088 > hide #25 models
    7089 
    7090 > hide #24 models
    7091 
    7092 > hide #23 models
    7093 
    7094 > hide #22 models
    7095 
    7096 > hide #21 models
    7097 
    7098 > hide #20 models
    7099 
    7100 > mmaker #28 to #1/B
    7101 
    7102 Parameters 
    7103 --- 
    7104 Chain pairing | bb 
    7105 Alignment algorithm | Needleman-Wunsch 
    7106 Similarity matrix | BLOSUM-62 
    7107 SS fraction | 0.3 
    7108 Gap open (HH/SS/other) | 18/18/6 
    7109 Gap extend | 1 
    7110 SS matrix |  |  | H | S | O 
    7111 ---|---|---|--- 
    7112 H | 6 | -9 | -6 
    7113 S |  | 6 | -6 
    7114 O |  |  | 4 
    7115 Iteration cutoff | 2 
    7116  
    7117 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    7118 with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#28),
    7119 sequence alignment score = 6081.2 
    7120 RMSD between 1222 pruned atom pairs is 0.340 angstroms; (across all 1222
    7121 pairs: 0.340) 
    7122  
    7123 
    7124 > hide #30.14 models
    7125 
    7126 > hide #!29 models
    7127 
    7128 > hide #28 models
    7129 
    7130 > show #!29 models
    7131 
    7132 > show #28 models
    7133 
    7134 > hide #1 models
    7135 
    7136 > show #4 models
    7137 
    7138 > mmaker #4 to #1
    7139 
    7140 Parameters 
    7141 --- 
    7142 Chain pairing | bb 
    7143 Alignment algorithm | Needleman-Wunsch 
    7144 Similarity matrix | BLOSUM-62 
    7145 SS fraction | 0.3 
    7146 Gap open (HH/SS/other) | 18/18/6 
    7147 Gap extend | 1 
    7148 SS matrix |  |  | H | S | O 
    7149 ---|---|---|--- 
    7150 H | 6 | -9 | -6 
    7151 S |  | 6 | -6 
    7152 O |  |  | 4 
    7153 Iteration cutoff | 2 
    7154  
    7155 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    7156 with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4),
    7157 sequence alignment score = 5250.9 
    7158 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    7159 10.353) 
    7160  
    7161 
    7162 > hide #4 models
    7163 
    7164 > show #11 models
    7165 
    7166 > mmaker #11 to #29
    7167 
    7168 Parameters 
    7169 --- 
    7170 Chain pairing | bb 
    7171 Alignment algorithm | Needleman-Wunsch 
    7172 Similarity matrix | BLOSUM-62 
    7173 SS fraction | 0.3 
    7174 Gap open (HH/SS/other) | 18/18/6 
    7175 Gap extend | 1 
    7176 SS matrix |  |  | H | S | O 
    7177 ---|---|---|--- 
    7178 H | 6 | -9 | -6 
    7179 S |  | 6 | -6 
    7180 O |  |  | 4 
    7181 Iteration cutoff | 2 
    7182  
    7183 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#29) with ger2.pdb, chain
    7184 C (#11), sequence alignment score = 1028.5 
    7185 RMSD between 196 pruned atom pairs is 0.965 angstroms; (across all 201 pairs:
    7186 1.024) 
    7187  
    7188 
    7189 > mmaker #30 to #11
    7190 
    7191 Parameters 
    7192 --- 
    7193 Chain pairing | bb 
    7194 Alignment algorithm | Needleman-Wunsch 
    7195 Similarity matrix | BLOSUM-62 
    7196 SS fraction | 0.3 
    7197 Gap open (HH/SS/other) | 18/18/6 
    7198 Gap extend | 1 
    7199 SS matrix |  |  | H | S | O 
    7200 ---|---|---|--- 
    7201 H | 6 | -9 | -6 
    7202 S |  | 6 | -6 
    7203 O |  |  | 4 
    7204 Iteration cutoff | 2 
    7205  
    7206 Matchmaker ger2.pdb, chain A (#11) with 2ksq.pdb, chain A (#30.14), sequence
    7207 alignment score = 663.9 
    7208 RMSD between 108 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    7209 3.655) 
    7210  
    7211 
    7212 > show #!30 models
    7213 
    7214 > show #30.14 models
    7215 
    7216 > hide #30.14 models
    7217 
    7218 > hide #!30 models
    7219 
    7220 > hide #!29 models
    7221 
    7222 > hide #28 models
    7223 
    7224 > hide #11 models
    7225 
    7226 > show #!26 models
    7227 
    7228 > show #1 models
    7229 
    7230 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    7231 > figures/2ksq.pdb
    7232 
    7233 2ksq.pdb title: 
    7234 The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
    7235 info...] 
    7236  
    7237 Chain information for 2ksq.pdb 
    7238 --- 
    7239 Chain | Description 
    7240 31.1/A | adp-ribosylation factor 1 
    7241 31.2/A 31.3/A 31.4/A 31.5/A 31.6/A 31.7/A 31.8/A 31.9/A 31.10/A 31.11/A
    7242 31.12/A 31.13/A 31.14/A 31.15/A 31.16/A 31.17/A 31.18/A 31.19/A 31.20/A | adp-
    7243 ribosylation factor 1 
    7244  
    7245 
    7246 > hide #!31 models
    7247 
    7248 > select #26
    7249 
    7250 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7251 
    7252 > ~select #26
    7253 
    7254 5 models selected 
    7255 
    7256 > select #26
    7257 
    7258 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7259 
    7260 > ~select #26
    7261 
    7262 5 models selected 
    7263 
    7264 > select #26
    7265 
    7266 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7267 
    7268 > show sel surfaces
    7269 
    7270 > ~select #26
    7271 
    7272 5 models selected 
    7273 
    7274 > select #26
    7275 
    7276 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7277 
    7278 > ~select #26
    7279 
    7280 Nothing selected 
    7281 
    7282 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    7283 > figures/figures.cxs
    7284 
    7285 > hide #1 models
    7286 
    7287 > show #1 models
    7288 
    7289 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    7290 > transparentBackground true supersample 3
    7291 
    7292 > hide #1 models
    7293 
    7294 > show #1 models
    7295 
    7296 > hide #1 models
    7297 
    7298 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    7299 > transparentBackground true supersample 3
    7300 
    7301 > hide #!26 models
    7302 
    7303 > show #1 models
    7304 
    7305 > show #20 models
    7306 
    7307 > show #21 models
    7308 
    7309 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    7310 > transparentBackground true supersample 3
    7311 
    7312 > hide #21 models
    7313 
    7314 > show #21 models
    7315 
    7316 > show #!27 models
    7317 
    7318 > hide #!27 models
    7319 
    7320 > show #!30 models
    7321 
    7322 > hide #!30 models
    7323 
    7324 > show #!31 models
    7325 
    7326 > hide #!31 models
    7327 
    7328 > hide #21 models
    7329 
    7330 > show #21 models
    7331 
    7332 > show #12.1 models
    7333 
    7334 > hide #12.1 models
    7335 
    7336 > show #14.1 models
    7337 
    7338 > hide #14.1 models
    7339 
    7340 > show #15.15 models
    7341 
    7342 > hide #15.15 models
    7343 
    7344 > show #17.1 models
    7345 
    7346 > save
    7347 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-closed.png
    7348 > transparentBackground true supersample 3
    7349 
    7350 > hide #!14 models
    7351 
    7352 > hide #!12 models
    7353 
    7354 > hide #!15 models
    7355 
    7356 > hide #!17 models
    7357 
    7358 > hide #17.1 models
    7359 
    7360 > show #4 models
    7361 
    7362 > show #22 models
    7363 
    7364 > show #23 models
    7365 
    7366 > hide #21 models
    7367 
    7368 > hide #20 models
    7369 
    7370 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    7371 > transparentBackground true supersample 3
    7372 
    7373 > hide #23 models
    7374 
    7375 > hide #22 models
    7376 
    7377 > show #28 models
    7378 
    7379 > show #!29 models
    7380 
    7381 > hide #1 models
    7382 
    7383 > hide #4 models
    7384 
    7385 > show #4 models
    7386 
    7387 > hide #!29 models
    7388 
    7389 > hide #28 models
    7390 
    7391 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    7392 > transparentBackground true supersample 3
    7393 
    7394 > hide #4 models
    7395 
    7396 > show #!29 models
    7397 
    7398 > show #28 models
    7399 
    7400 > show #30.14 models
    7401 
    7402 > show #20 models
    7403 
    7404 > show #21 models
    7405 
    7406 > hide #!30 models
    7407 
    7408 > hide #30.14 models
    7409 
    7410 > show #!30 models
    7411 
    7412 > show #30.14 models
    7413 
    7414 > mmaker #31 to #30
    7415 
    7416 Parameters 
    7417 --- 
    7418 Chain pairing | bb 
    7419 Alignment algorithm | Needleman-Wunsch 
    7420 Similarity matrix | BLOSUM-62 
    7421 SS fraction | 0.3 
    7422 Gap open (HH/SS/other) | 18/18/6 
    7423 Gap extend | 1 
    7424 SS matrix |  |  | H | S | O 
    7425 ---|---|---|--- 
    7426 H | 6 | -9 | -6 
    7427 S |  | 6 | -6 
    7428 O |  |  | 4 
    7429 Iteration cutoff | 2 
    7430  
    7431 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.1), sequence
    7432 alignment score = 925.2 
    7433 RMSD between 162 pruned atom pairs is 0.566 angstroms; (across all 180 pairs:
    7434 1.892) 
    7435  
    7436 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.2), sequence
    7437 alignment score = 929.4 
    7438 RMSD between 162 pruned atom pairs is 0.637 angstroms; (across all 180 pairs:
    7439 3.198) 
    7440  
    7441 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.3), sequence
    7442 alignment score = 922.8 
    7443 RMSD between 159 pruned atom pairs is 0.505 angstroms; (across all 180 pairs:
    7444 4.009) 
    7445  
    7446 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.4), sequence
    7447 alignment score = 928.8 
    7448 RMSD between 165 pruned atom pairs is 0.588 angstroms; (across all 180 pairs:
    7449 2.079) 
    7450  
    7451 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.5), sequence
    7452 alignment score = 913.8 
    7453 RMSD between 162 pruned atom pairs is 0.570 angstroms; (across all 180 pairs:
    7454 2.622) 
    7455  
    7456 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.6), sequence
    7457 alignment score = 909 
    7458 RMSD between 159 pruned atom pairs is 0.598 angstroms; (across all 180 pairs:
    7459 3.348) 
    7460  
    7461 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.7), sequence
    7462 alignment score = 914.4 
    7463 RMSD between 160 pruned atom pairs is 0.771 angstroms; (across all 180 pairs:
    7464 3.467) 
    7465  
    7466 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.8), sequence
    7467 alignment score = 939 
    7468 RMSD between 162 pruned atom pairs is 0.601 angstroms; (across all 180 pairs:
    7469 2.232) 
    7470  
    7471 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.9), sequence
    7472 alignment score = 913.2 
    7473 RMSD between 160 pruned atom pairs is 0.657 angstroms; (across all 180 pairs:
    7474 3.047) 
    7475  
    7476 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.10),
    7477 sequence alignment score = 916.8 
    7478 RMSD between 165 pruned atom pairs is 0.623 angstroms; (across all 180 pairs:
    7479 2.568) 
    7480  
    7481 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.11),
    7482 sequence alignment score = 906 
    7483 RMSD between 160 pruned atom pairs is 0.571 angstroms; (across all 180 pairs:
    7484 2.803) 
    7485  
    7486 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.12),
    7487 sequence alignment score = 939 
    7488 RMSD between 161 pruned atom pairs is 0.537 angstroms; (across all 180 pairs:
    7489 3.640) 
    7490  
    7491 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.13),
    7492 sequence alignment score = 922.2 
    7493 RMSD between 162 pruned atom pairs is 0.631 angstroms; (across all 180 pairs:
    7494 3.208) 
    7495  
    7496 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.14),
    7497 sequence alignment score = 945.6 
    7498 RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
    7499 0.000) 
    7500  
    7501 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.15),
    7502 sequence alignment score = 931.8 
    7503 RMSD between 163 pruned atom pairs is 0.597 angstroms; (across all 180 pairs:
    7504 3.138) 
    7505  
    7506 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.16),
    7507 sequence alignment score = 901.2 
    7508 RMSD between 160 pruned atom pairs is 0.600 angstroms; (across all 180 pairs:
    7509 2.591) 
    7510  
    7511 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.17),
    7512 sequence alignment score = 916.8 
    7513 RMSD between 159 pruned atom pairs is 0.585 angstroms; (across all 180 pairs:
    7514 2.919) 
    7515  
    7516 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.18),
    7517 sequence alignment score = 931.2 
    7518 RMSD between 160 pruned atom pairs is 0.569 angstroms; (across all 180 pairs:
    7519 2.533) 
    7520  
    7521 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.19),
    7522 sequence alignment score = 922.2 
    7523 RMSD between 160 pruned atom pairs is 0.558 angstroms; (across all 180 pairs:
    7524 2.973) 
    7525  
    7526 Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.20),
    7527 sequence alignment score = 928.8 
    7528 RMSD between 161 pruned atom pairs is 0.530 angstroms; (across all 180 pairs:
    7529 3.897) 
    7530  
    7531 
    7532 > show #!31 models
    7533 
    7534 > hide #!30 models
    7535 
    7536 > hide #30.14 models
    7537 
    7538 > hide #!31 models
    7539 
    7540 > hide #31.1 models
    7541 
    7542 > hide #31.2 models
    7543 
    7544 > hide #31.3 models
    7545 
    7546 > hide #31.4 models
    7547 
    7548 > hide #31.5 models
    7549 
    7550 > hide #31.6 models
    7551 
    7552 > hide #31.7 models
    7553 
    7554 > hide #31.8 models
    7555 
    7556 > hide #31.9 models
    7557 
    7558 > hide #31.10 models
    7559 
    7560 > hide #31.11 models
    7561 
    7562 > hide #31.12 models
    7563 
    7564 > hide #31.13 models
    7565 
    7566 > hide #31.14 models
    7567 
    7568 > hide #31.15 models
    7569 
    7570 > hide #31.16 models
    7571 
    7572 > hide #31.17 models
    7573 
    7574 > hide #31.18 models
    7575 
    7576 > hide #31.19 models
    7577 
    7578 > hide #31.20 models
    7579 
    7580 > show #31.1 models
    7581 
    7582 > hide #31.1 models
    7583 
    7584 > show #31.2 models
    7585 
    7586 > hide #31.2 models
    7587 
    7588 > show #31.3 models
    7589 
    7590 > hide #31.3 models
    7591 
    7592 > show #31.4 models
    7593 
    7594 > hide #31.4 models
    7595 
    7596 > show #31.5 models
    7597 
    7598 > hide #31.5 models
    7599 
    7600 > show #31.6 models
    7601 
    7602 > hide #31.6 models
    7603 
    7604 > show #31.5 models
    7605 
    7606 > show #31.7 models
    7607 
    7608 > hide #31.5 models
    7609 
    7610 > close #31.1-6
    7611 
    7612 > close #31.8-20
    7613 
    7614 > select #31.7
    7615 
    7616 3045 atoms, 3079 bonds, 187 residues, 1 model selected 
    7617 
    7618 > hide sel atoms
    7619 
    7620 > preset cartoons/nucleotides cylinders/stubs
    7621 
    7622 Changed 0 atom styles 
    7623 Preset expands to these ChimeraX commands:
    7624 
    7625    
    7626    
    7627     show nucleic
    7628     hide protein|solvent|H
    7629     surf hide
    7630     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7631     cartoon
    7632     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7633     cartoon style ~(nucleic|strand) x round
    7634     cartoon style (nucleic|strand) x rect
    7635     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    7636     cartoon style nucleic x round width 1.6 thick 1.6
    7637     nucleotides stubs
    7638 
    7639  
    7640 
    7641 > color sel #7281dbff
    7642 
    7643 > select clear
    7644 
    7645 > select ::name="GTP"
    7646 
    7647 129 atoms, 135 bonds, 3 residues, 3 models selected 
    7648 
    7649 > color (#31.7 & sel) #55aa00ff
    7650 
    7651 > select ::name="GTP"
    7652 
    7653 129 atoms, 135 bonds, 3 residues, 3 models selected 
    7654 
    7655 > show sel & #31.7 atoms
    7656 
    7657 > color sel & #31.7 byhetero
    7658 
    7659 > select clear
    7660 
    7661 > ui tool show "Show Sequence Viewer"
    7662 
    7663 > sequence chain #31.7/A
    7664 
    7665 Alignment identifier is 31.7/A 
    7666 
    7667 > color sel #aa0000ff
    7668 
    7669 > select clear
    7670 
    7671 > select clear
    7672 
    7673 > hide #20 models
    7674 
    7675 > hide #21 models
    7676 
    7677 > hide #28 models
    7678 
    7679 > hide #!29 models
    7680 
    7681 > hide #!31 models
    7682 
    7683 > hide #31.7 models
    7684 
    7685 > show #!26 models
    7686 
    7687 > show #!26 surfaces
    7688 
    7689 > show #1 models
    7690 
    7691 > hide #1 models
    7692 
    7693 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    7694 > transparentBackground true supersample 3
    7695 
    7696 > hide #!26 surfaces
    7697 
    7698 > show #1 models
    7699 
    7700 > hide #!26 models
    7701 
    7702 > show #20 models
    7703 
    7704 > show #21 models
    7705 
    7706 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    7707 > transparentBackground true supersample 3
    7708 
    7709 > show #17.1 models
    7710 
    7711 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    7712 > arf1.png transparentBackground true supersample 3
    7713 
    7714 > hide #20 models
    7715 
    7716 > show #22 models
    7717 
    7718 > show #23 models
    7719 
    7720 > hide #21 models
    7721 
    7722 > hide #17.1 models
    7723 
    7724 > hide #!17 models
    7725 
    7726 > show #4 models
    7727 
    7728 > hide #1 models
    7729 
    7730 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    7731 > transparentBackground true supersample 3
    7732 
    7733 > hide #4 models
    7734 
    7735 > hide #23 models
    7736 
    7737 > hide #22 models
    7738 
    7739 > show #!29 models
    7740 
    7741 > show #28 models
    7742 
    7743 > show #20 models
    7744 
    7745 > show #21 models
    7746 
    7747 > show #!31 models
    7748 
    7749 > show #31.7 models
    7750 
    7751 > save
    7752 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    7753 > transparentBackground true supersample 3
    7754 
    7755 > hide #!31 models
    7756 
    7757 > hide #31.7 models
    7758 
    7759 > show #31.7 models
    7760 
    7761 > hide #!29 models
    7762 
    7763 > hide #28 models
    7764 
    7765 > hide #21 models
    7766 
    7767 > hide #20 models
    7768 
    7769 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp
    7770 > transparentBackground true supersample 3
    7771 
    7772 Cannot determine format for
    7773 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp' 
    7774 
    7775 > hide #!31 models
    7776 
    7777 > hide #31.7 models
    7778 
    7779 > show #15.15 models
    7780 
    7781 > hide #15.15 models
    7782 
    7783 > hide #!15 models
    7784 
    7785 > show #17.1 models
    7786 
    7787 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
    7788 > transparentBackground true supersample 3
    7789 
    7790 Cannot determine format for
    7791 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp' 
    7792 
    7793 > hide #17.1 models
    7794 
    7795 > hide #!17 models
    7796 
    7797 > show #31.7 models
    7798 
    7799 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    7800 > transparentBackground true supersample 3
    7801 
    7802 > hide #!31 models
    7803 
    7804 > hide #31.7 models
    7805 
    7806 > show #17.1 models
    7807 
    7808 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    7809 > transparentBackground true supersample 3
    7810 
    7811 > hide #17.1 models
    7812 
    7813 > hide #!17 models
    7814 
    7815 > show #31.7 models
    7816 
    7817 > select ::name="GTP"
    7818 
    7819 129 atoms, 135 bonds, 3 residues, 3 models selected 
    7820 
    7821 > hide sel & #31.7 surfaces
    7822 
    7823 > hide sel & #31.7 atoms
    7824 
    7825 > hide #31.7 models
    7826 
    7827 > hide #!31 models
    7828 
    7829 > show #!26 models
    7830 
    7831 > show #1 models
    7832 
    7833 > select #26
    7834 
    7835 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7836 
    7837 > select clear
    7838 
    7839 > show #20 models
    7840 
    7841 > show #21 models
    7842 
    7843 > select #26
    7844 
    7845 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7846 
    7847 > show #31.7 models
    7848 
    7849 > ~select #26
    7850 
    7851 5 models selected 
    7852 
    7853 > hide #31.7 models
    7854 
    7855 > hide #!31 models
    7856 
    7857 > select #26
    7858 
    7859 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7860 
    7861 > hide #!26 models
    7862 
    7863 > show #!26 models
    7864 
    7865 > hide #!26 models
    7866 
    7867 > show #!26 models
    7868 
    7869 > ~select #26
    7870 
    7871 5 models selected 
    7872 
    7873 > select #26
    7874 
    7875 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7876 
    7877 > show sel surfaces
    7878 
    7879 > select clear
    7880 
    7881 > ~select #26
    7882 
    7883 Nothing selected 
    7884 
    7885 > select #26
    7886 
    7887 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    7888 
    7889 > ~select #26
    7890 
    7891 5 models selected 
    7892 
    7893 > hide #1 models
    7894 
    7895 > hide #20 models
    7896 
    7897 > hide #21 models
    7898 
    7899 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    7900 > transparentBackground true supersample 3
    7901 
    7902 > hide #!26 models
    7903 
    7904 > show #1 models
    7905 
    7906 > show #20 models
    7907 
    7908 > show #21 models
    7909 
    7910 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    7911 > transparentBackground true supersample 3
    7912 
    7913 > show #15.15 models
    7914 
    7915 > hide #15.15 models
    7916 
    7917 > show #17.1 models
    7918 
    7919 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    7920 > arf1.png transparentBackground true supersample 3
    7921 
    7922 > hide #17.1 models
    7923 
    7924 > hide #!17 models
    7925 
    7926 > show #18.1 models
    7927 
    7928 > hide #18.1 models
    7929 
    7930 > hide #!18 models
    7931 
    7932 > hide #20 models
    7933 
    7934 > hide #21 models
    7935 
    7936 > hide #!15 models
    7937 
    7938 > hide #1 models
    7939 
    7940 > show #4 models
    7941 
    7942 > show #22 models
    7943 
    7944 > show #23 models
    7945 
    7946 > hide #23 models
    7947 
    7948 > show #21 models
    7949 
    7950 > hide #21 models
    7951 
    7952 > show #23 models
    7953 
    7954 > hide #22 models
    7955 
    7956 > show #21 models
    7957 
    7958 > hide #21 models
    7959 
    7960 > show #20 models
    7961 
    7962 > hide #23 models
    7963 
    7964 > hide #20 models
    7965 
    7966 > show #25 models
    7967 
    7968 > hide #25 models
    7969 
    7970 > show #24 models
    7971 
    7972 > show #23 models
    7973 
    7974 > hide #23 models
    7975 
    7976 > show #22 models
    7977 
    7978 > hide #22 models
    7979 
    7980 > show #21 models
    7981 
    7982 > show #22 models
    7983 
    7984 > show #23 models
    7985 
    7986 > hide #24 models
    7987 
    7988 > hide #23 models
    7989 
    7990 > show #23 models
    7991 
    7992 > hide #22 models
    7993 
    7994 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    7995 > transparentBackground true supersample 3
    7996 
    7997 > hide #23 models
    7998 
    7999 > hide #21 models
    8000 
    8001 > show #20 models
    8002 
    8003 > show #21 models
    8004 
    8005 > hide #4 models
    8006 
    8007 > show #1 models
    8008 
    8009 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    8010 > transparentBackground true supersample 3
    8011 
    8012 > hide #1 models
    8013 
    8014 > show #1 models
    8015 
    8016 > show #!9 models
    8017 
    8018 > hide #!9 models
    8019 
    8020 > show #18.1 models
    8021 
    8022 > hide #18.1 models
    8023 
    8024 > show #17.1 models
    8025 
    8026 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8027 > arf1.png transparentBackground true supersample 3
    8028 
    8029 > hide #!18 models
    8030 
    8031 > hide #!17 models
    8032 
    8033 > show #!31 models
    8034 
    8035 > hide #!31 models
    8036 
    8037 > show #31.7 models
    8038 
    8039 > show #!29 models
    8040 
    8041 > show #28 models
    8042 
    8043 > hide #1 models
    8044 
    8045 > save
    8046 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    8047 > transparentBackground true supersample 3
    8048 
    8049 > hide #31.7 models
    8050 
    8051 > hide #!31 models
    8052 
    8053 > hide #!29 models
    8054 
    8055 > hide #28 models
    8056 
    8057 > show #4 models
    8058 
    8059 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    8060 > transparentBackground true supersample 3
    8061 
    8062 > hide #4 models
    8063 
    8064 > hide #21 models
    8065 
    8066 > hide #20 models
    8067 
    8068 > show #31.7 models
    8069 
    8070 > select ::name="GTP"
    8071 
    8072 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8073 
    8074 > show sel & #31.7 atoms
    8075 
    8076 > select clear
    8077 
    8078 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    8079 > transparentBackground true supersample 3
    8080 
    8081 > hide #31.7 models
    8082 
    8083 > hide #!31 models
    8084 
    8085 > show #!18 models
    8086 
    8087 > hide #!18 models
    8088 
    8089 > show #18.1 models
    8090 
    8091 > show #19 models
    8092 
    8093 > hide #19 models
    8094 
    8095 > hide #18.1 models
    8096 
    8097 > hide #!18 models
    8098 
    8099 > hide #17.1 models
    8100 
    8101 > show #!17 models
    8102 
    8103 > show #17.1 models
    8104 
    8105 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    8106 > transparentBackground true supersample 3
    8107 
    8108 > show #1 models
    8109 
    8110 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    8111 > figures/figures.cxs includeMaps true
    8112 
    8113 > show #20 models
    8114 
    8115 > show #21 models
    8116 
    8117 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
    8118 > transparentBackground true supersample 3
    8119 
    8120 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
    8121 > transparentBackground true supersample 3
    8122 
    8123 > hide #!17 models
    8124 
    8125 > hide #17.1 models
    8126 
    8127 > show #!17 models
    8128 
    8129 > show #!26 models
    8130 
    8131 > select #26
    8132 
    8133 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    8134 
    8135 > hide sel surfaces
    8136 
    8137 > hide #1 models
    8138 
    8139 > hide #20 models
    8140 
    8141 > hide #21 models
    8142 
    8143 > hide #!17 models
    8144 
    8145 > show sel surfaces
    8146 
    8147 > select clear
    8148 
    8149 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    8150 > transparentBackground true supersample 3
    8151 
    8152 > hide #!26 models
    8153 
    8154 > show #1 models
    8155 
    8156 > show #20 models
    8157 
    8158 > show #21 models
    8159 
    8160 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    8161 > transparentBackground true supersample 3
    8162 
    8163 > show #17.1 models
    8164 
    8165 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8166 > arf1.png transparentBackground true supersample 3
    8167 
    8168 > show #28 models
    8169 
    8170 > show #!29 models
    8171 
    8172 > hide #1 models
    8173 
    8174 > hide #17.1 models
    8175 
    8176 > hide #!17 models
    8177 
    8178 > show #31.7 models
    8179 
    8180 > save
    8181 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activiation.png
    8182 > transparentBackground true supersample 3
    8183 
    8184 > hide #31.7 models
    8185 
    8186 > hide #!31 models
    8187 
    8188 > hide #!29 models
    8189 
    8190 > hide #28 models
    8191 
    8192 > show #4 models
    8193 
    8194 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    8195 > transparentBackground true supersample 3
    8196 
    8197 > hide #4 models
    8198 
    8199 > hide #21 models
    8200 
    8201 > hide #20 models
    8202 
    8203 > show #31.7 models
    8204 
    8205 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    8206 > transparentBackground true supersample 3
    8207 
    8208 > hide #31.7 models
    8209 
    8210 > hide #!31 models
    8211 
    8212 > show #17.1 models
    8213 
    8214 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    8215 > transparentBackground true supersample 3
    8216 
    8217 > show #31.7 models
    8218 
    8219 > hide #17.1 models
    8220 
    8221 > hide #!17 models
    8222 
    8223 > select ::name="GTP"
    8224 
    8225 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8226 
    8227 > hide sel & #31.7 atoms
    8228 
    8229 > show #20 models
    8230 
    8231 > show #21 models
    8232 
    8233 > select clear
    8234 
    8235 > show #!29 models
    8236 
    8237 > show #28 models
    8238 
    8239 > save
    8240 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activiation.png
    8241 > transparentBackground true supersample 3
    8242 
    8243 > hide #21 models
    8244 
    8245 > hide #20 models
    8246 
    8247 > hide #28 models
    8248 
    8249 > hide #!29 models
    8250 
    8251 > hide #!31 models
    8252 
    8253 > hide #31.7 models
    8254 
    8255 > show #!26 models
    8256 
    8257 > select #26
    8258 
    8259 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    8260 
    8261 > hide sel surfaces
    8262 
    8263 > ~select #26
    8264 
    8265 5 models selected 
    8266 
    8267 > show #!26 surfaces
    8268 
    8269 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    8270 > transparentBackground true supersample 3
    8271 
    8272 > hide #!26 models
    8273 
    8274 > show #1 models
    8275 
    8276 > show #20 models
    8277 
    8278 > show #21 models
    8279 
    8280 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    8281 > transparentBackground true supersample 3
    8282 
    8283 > show #17.1 models
    8284 
    8285 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8286 > arf1.png transparentBackground true supersample 3
    8287 
    8288 > show #31.7 models
    8289 
    8290 > show #!29 models
    8291 
    8292 > show #28 models
    8293 
    8294 > hide #17.1 models
    8295 
    8296 > hide #!17 models
    8297 
    8298 > hide #1 models
    8299 
    8300 > save
    8301 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    8302 > transparentBackground true supersample 3
    8303 
    8304 > hide #!29 models
    8305 
    8306 > hide #28 models
    8307 
    8308 > hide #!31 models
    8309 
    8310 > hide #31.7 models
    8311 
    8312 > show #!2 models
    8313 
    8314 > hide #!2 models
    8315 
    8316 > show #4 models
    8317 
    8318 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    8319 > transparentBackground true supersample 3
    8320 
    8321 > hide #4 models
    8322 
    8323 > hide #21 models
    8324 
    8325 > hide #20 models
    8326 
    8327 > show #31.7 models
    8328 
    8329 > select ::name="GTP"
    8330 
    8331 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8332 
    8333 > show sel & #31.7 atoms
    8334 
    8335 > select clear
    8336 
    8337 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    8338 > transparentBackground true supersample 3
    8339 
    8340 > hide #31.7 models
    8341 
    8342 > hide #!31 models
    8343 
    8344 > show #!30 models
    8345 
    8346 > hide #!30 models
    8347 
    8348 > show #17.1 models
    8349 
    8350 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    8351 > transparentBackground true supersample 3
    8352 
    8353 > hide #!17 models
    8354 
    8355 > hide #17.1 models
    8356 
    8357 > show #!26 models
    8358 
    8359 > hide #!26 surfaces
    8360 
    8361 > select #26
    8362 
    8363 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    8364 
    8365 > ~select #26
    8366 
    8367 5 models selected 
    8368 
    8369 > show #!26 surfaces
    8370 
    8371 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    8372 > transparentBackground true supersample 3
    8373 
    8374 > hide #!26 models
    8375 
    8376 > show #1 models
    8377 
    8378 > show #20 models
    8379 
    8380 > show #21 models
    8381 
    8382 > hide #21 models
    8383 
    8384 > hide #20 models
    8385 
    8386 > hide #1 models
    8387 
    8388 > show #!26 models
    8389 
    8390 > hide #!26 surfaces
    8391 
    8392 > show #!26 surfaces
    8393 
    8394 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
    8395 > transparentBackground true supersample 3
    8396 
    8397 > hide #!26 models
    8398 
    8399 > show #20 models
    8400 
    8401 > show #21 models
    8402 
    8403 > show #1 models
    8404 
    8405 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
    8406 > transparentBackground true supersample 3
    8407 
    8408 > hide #1 models
    8409 
    8410 > show #1 models
    8411 
    8412 > show #12.1 models
    8413 
    8414 > hide #12.1 models
    8415 
    8416 > show #14.1 models
    8417 
    8418 > hide #14.1 models
    8419 
    8420 > show #17.1 models
    8421 
    8422 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8423 > arf1.png transparentBackground true supersample 3
    8424 
    8425 > hide #!14 models
    8426 
    8427 > hide #!12 models
    8428 
    8429 > hide #!17 models
    8430 
    8431 > hide #17.1 models
    8432 
    8433 > hide #1 models
    8434 
    8435 > show #28 models
    8436 
    8437 > show #!29 models
    8438 
    8439 > show #31.7 models
    8440 
    8441 > select ::name="GTP"
    8442 
    8443 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8444 
    8445 > hide sel & #31.7 atoms
    8446 
    8447 > save
    8448 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
    8449 > transparentBackground true supersample 3
    8450 
    8451 > show sel & #31.7 atoms
    8452 
    8453 > hide #31.7 models
    8454 
    8455 > hide #!31 models
    8456 
    8457 > hide #!29 models
    8458 
    8459 > hide #28 models
    8460 
    8461 > select #30
    8462 
    8463 3045 atoms, 3079 bonds, 187 residues, 2 models selected 
    8464 
    8465 > select #30.14
    8466 
    8467 3045 atoms, 3079 bonds, 187 residues, 1 model selected 
    8468 
    8469 > select #31
    8470 
    8471 3045 atoms, 3079 bonds, 187 residues, 2 models selected 
    8472 
    8473 > ~select #31.7
    8474 
    8475 1 model selected 
    8476 
    8477 > select #30.14
    8478 
    8479 3045 atoms, 3079 bonds, 187 residues, 1 model selected 
    8480 
    8481 > select #31
    8482 
    8483 3045 atoms, 3079 bonds, 187 residues, 2 models selected 
    8484 
    8485 > ~select #31
    8486 
    8487 Nothing selected 
    8488 
    8489 > hide #21 models
    8490 
    8491 > show #21 models
    8492 
    8493 > show #4 models
    8494 
    8495 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
    8496 > transparentBackground true supersample 3
    8497 
    8498 > hide #4 models
    8499 
    8500 > hide #21 models
    8501 
    8502 > hide #20 models
    8503 
    8504 > show #!30 models
    8505 
    8506 > show #30.14 models
    8507 
    8508 > hide #!30 models
    8509 
    8510 > hide #30.14 models
    8511 
    8512 > show #!31 models
    8513 
    8514 > show #31.7 models
    8515 
    8516 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
    8517 > transparentBackground true supersample 3
    8518 
    8519 > hide #!31 models
    8520 
    8521 > hide #31.7 models
    8522 
    8523 > show #!27 models
    8524 
    8525 > hide #!27 models
    8526 
    8527 > show #17.1 models
    8528 
    8529 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
    8530 > transparentBackground true supersample 3
    8531 
    8532 > hide #17.1 models
    8533 
    8534 > hide #!17 models
    8535 
    8536 > show #1 models
    8537 
    8538 > show #20 models
    8539 
    8540 > show #21 models
    8541 
    8542 > hide #21 models
    8543 
    8544 > hide #20 models
    8545 
    8546 > hide #1 models
    8547 
    8548 > show #!26 models
    8549 
    8550 > hide #!26 models
    8551 
    8552 > show #!26 models
    8553 
    8554 > hide #!26 surfaces
    8555 
    8556 > show #!26 surfaces
    8557 
    8558 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids-
    8559 > side.png transparentBackground true supersample 3
    8560 
    8561 > hide #!26 models
    8562 
    8563 > show #1 models
    8564 
    8565 > show #20 models
    8566 
    8567 > show #21 models
    8568 
    8569 > show #!17 models
    8570 
    8571 > show #17.1 models
    8572 
    8573 > hide #17.1 models
    8574 
    8575 > hide #!17 models
    8576 
    8577 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8578 > side.png transparentBackground true supersample 3
    8579 
    8580 > show #17.1 models
    8581 
    8582 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8583 > arf1-side.png transparentBackground true supersample 3
    8584 
    8585 > hide #17.1 models
    8586 
    8587 > hide #!17 models
    8588 
    8589 > show #!31 models
    8590 
    8591 > show #31.7 models
    8592 
    8593 > hide #!31 models
    8594 
    8595 > show #!31 models
    8596 
    8597 > show #!29 models
    8598 
    8599 > show #28 models
    8600 
    8601 > hide #1 models
    8602 
    8603 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
    8604 > side.png transparentBackground true supersample 3
    8605 
    8606 > hide #!29 models
    8607 
    8608 > hide #28 models
    8609 
    8610 > hide #!31 models
    8611 
    8612 > hide #31.7 models
    8613 
    8614 > show #!31 models
    8615 
    8616 > show #31.7 models
    8617 
    8618 > show #!29 models
    8619 
    8620 > show #28 models
    8621 
    8622 > select ::name="GTP"
    8623 
    8624 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8625 
    8626 > hide sel & #31.7 surfaces
    8627 
    8628 > hide sel & #31.7 atoms
    8629 
    8630 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
    8631 > side.png transparentBackground true supersample 3
    8632 
    8633 > hide #!29 models
    8634 
    8635 > hide #28 models
    8636 
    8637 > hide #21 models
    8638 
    8639 > hide #20 models
    8640 
    8641 > show sel & #31.7 atoms
    8642 
    8643 > select clear
    8644 
    8645 > show #1 models
    8646 
    8647 > hide #1 models
    8648 
    8649 > hide #!31 models
    8650 
    8651 > hide #31.7 models
    8652 
    8653 > show #1 models
    8654 
    8655 > show #20 models
    8656 
    8657 > show #21 models
    8658 
    8659 > ui tool show "Side View"
    8660 
    8661 > show #!26 models
    8662 
    8663 > hide #1,20-21#!26 surfaces
    8664 
    8665 > select #1
    8666 
    8667 39647 atoms, 39961 bonds, 2444 residues, 1 model selected 
    8668 
    8669 > undo
    8670 
    8671 > select #21
    8672 
    8673 168 atoms, 170 bonds, 22 residues, 1 model selected 
    8674 
    8675 > select #20
    8676 
    8677 168 atoms, 170 bonds, 22 residues, 1 model selected 
    8678 
    8679 > select #21
    8680 
    8681 168 atoms, 170 bonds, 22 residues, 1 model selected 
    8682 
    8683 > ~select #21
    8684 
    8685 Nothing selected 
    8686 
    8687 > hide #21 models
    8688 
    8689 > hide #20 models
    8690 
    8691 > show #21 models
    8692 
    8693 > show #20 models
    8694 
    8695 > select #26
    8696 
    8697 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    8698 
    8699 > hide #1 models
    8700 
    8701 > hide #20 models
    8702 
    8703 > hide #21 models
    8704 
    8705 > ~select #26
    8706 
    8707 5 models selected 
    8708 
    8709 > select #26
    8710 
    8711 313093 atoms, 317626 bonds, 3369 residues, 6 models selected 
    8712 
    8713 > show sel surfaces
    8714 
    8715 > select clear
    8716 
    8717 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids-
    8718 > side.png transparentBackground true supersample 3
    8719 
    8720 > hide #!26 models
    8721 
    8722 > show #1 models
    8723 
    8724 > show #20 models
    8725 
    8726 > show #21 models
    8727 
    8728 > show #17.1 models
    8729 
    8730 > hide #17.1 models
    8731 
    8732 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8733 > side.png transparentBackground true supersample 3
    8734 
    8735 > show #17.1 models
    8736 
    8737 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    8738 > arf1-side.png transparentBackground true supersample 3
    8739 
    8740 > hide #17.1 models
    8741 
    8742 > hide #!17 models
    8743 
    8744 > hide #1 models
    8745 
    8746 > show #28 models
    8747 
    8748 > show #!29 models
    8749 
    8750 > show #30.14 models
    8751 
    8752 > hide #30.14 models
    8753 
    8754 > show #17.1 models
    8755 
    8756 > hide #!17 models
    8757 
    8758 > hide #17.1 models
    8759 
    8760 > show #!31 models
    8761 
    8762 > show #31.7 models
    8763 
    8764 > select ::name="GTP"
    8765 
    8766 129 atoms, 135 bonds, 3 residues, 3 models selected 
    8767 
    8768 > hide sel & #31.7 atoms
    8769 
    8770 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
    8771 > side.png transparentBackground true supersample 3
    8772 
    8773 > show sel & #31.7 atoms
    8774 
    8775 > select clear
    8776 
    8777 > hide #21 models
    8778 
    8779 > hide #20 models
    8780 
    8781 > hide #28 models
    8782 
    8783 > hide #!29 models
    8784 
    8785 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp-
    8786 > side.png transparentBackground true supersample 3
    8787 
    8788 > hide #!30 models
    8789 
    8790 > hide #!31 models
    8791 
    8792 > hide #31.7 models
    8793 
    8794 > show #17.1 models
    8795 
    8796 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp-
    8797 > side.png transparentBackground true supersample 3
    8798 
    8799 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    8800 > figures/figures.cxs includeMaps true
    8801 
    8802 > toolshed show
    8803 
    8804 > help help:user/tools/toolbar.html
    8805 
    8806 > hide #17.1 models
    8807 
    8808 > hide #!17 models
    8809 
    8810 > show #1 models
    8811 
    8812 > open C:/Users/Arnold/Downloads/io.mc
    8813 
    8814 Unrecognized file suffix '.mc' 
    8815 
    8816 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    8817 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    8818 
    8819 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32 
    8820 --- 
    8821 Chain | Description 
    8822 A B | No description available 
    8823  
    8824 
    8825 > hide #1 models
    8826 
    8827 > select #32/A
    8828 
    8829 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    8830 
    8831 > color sel #9ac2f5ff
    8832 
    8833 > select #32/B
    8834 
    8835 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    8836 
    8837 > color sel #f4e379ff
    8838 
    8839 > select clear
    8840 
    8841 > lighting soft
    8842 
    8843 Drag select of 8 residues 
    8844 
    8845 > show sel atoms
    8846 
    8847 > color sel byhetero
    8848 
    8849 > select clear
    8850 
    8851 Drag select of 1 atoms, 6 residues 
    8852 
    8853 > show sel atoms
    8854 
    8855 > color sel byhetero
    8856 
    8857 > select clear
    8858 
    8859 > hbonds #32
    8860 
    8861 3464 hydrogen bonds found 
    8862 
    8863 > ~hbonds
    8864 
    8865 > ui mousemode right distance
    8866 
    8867 > ui mousemode right distance
    8868 
    8869 > distance #32/B:17@HZ2 #32/A:413@OG1
    8870 
    8871 Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/B
    8872 LYS 17 HZ2 and /A THR 413 OG1: 2.776Å 
    8873 
    8874 > distance #32/B:17@HZ3 #32/A:414@OG1
    8875 
    8876 Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/B
    8877 LYS 17 HZ3 and /A THR 414 OG1: 3.117Å 
    8878 
    8879 > ui mousemode right translate
    8880 
    8881 > ui mousemode right "rotate selected models"
    8882 
    8883 > ui mousemode right "translate selected models"
    8884 
    8885 > select #33
    8886 
    8887 2 pseudobonds, 2 models selected 
    8888 
    8889 > ~select #33
    8890 
    8891 Nothing selected 
    8892 
    8893 > hide #33.1 models
    8894 
    8895 > ui mousemode right distance
    8896 
    8897 > distance #32/A:410@HE21 #32/B:21@OD1
    8898 
    8899 Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/A
    8900 GLN 410 HE21 and /B ASN 21 OD1: 3.052Å 
    8901 
    8902 > show #33.1 models
    8903 
    8904 > hide #33.1 models
    8905 
    8906 Drag select of 4 residues 
    8907 
    8908 > show sel atoms
    8909 
    8910 > color sel byhetero
    8911 
    8912 > select clear
    8913 
    8914 > select clear
    8915 
    8916 Drag select of 2 residues 
    8917 
    8918 > show sel atoms
    8919 
    8920 > color sel byhetero
    8921 
    8922 > select clear
    8923 
    8924 > select clear
    8925 
    8926 > select clear
    8927 
    8928 > ui mousemode right distance
    8929 
    8930 > distance #32/A:406@HE21 #32/B:24@OG1
    8931 
    8932 Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/A
    8933 GLN 406 HE21 and /B THR 24 OG1: 3.960Å 
    8934 
    8935 > show #33.1 models
    8936 
    8937 > hide #33.1 models
    8938 
    8939 > hide #32 models
    8940 
    8941 > show #32 models
    8942 
    8943 > hide #!33 models
    8944 
    8945 > select #32
    8946 
    8947 39644 atoms, 39958 bonds, 4 pseudobonds, 2444 residues, 2 models selected 
    8948 
    8949 > coulombic sel
    8950 
    8951 The following heavy (non-hydrogen) atoms are missing, which may result in
    8952 inaccurate electrostatics: closed_dimer-FINAL-
    8953 coot-3_real_space_refined_206.pdb #32/A SER 1417 OXT and closed_dimer-FINAL-
    8954 coot-3_real_space_refined_206.pdb #32/B SER 1417 OXT 
    8955 
    8956 > show #10 models
    8957 
    8958 > select #10
    8959 
    8960 11218 atoms, 11405 bonds, 1408 residues, 1 model selected 
    8961 
    8962 > mmaker #10 to #32
    8963 
    8964 Parameters 
    8965 --- 
    8966 Chain pairing | bb 
    8967 Alignment algorithm | Needleman-Wunsch 
    8968 Similarity matrix | BLOSUM-62 
    8969 SS fraction | 0.3 
    8970 Gap open (HH/SS/other) | 18/18/6 
    8971 Gap extend | 1 
    8972 SS matrix |  |  | H | S | O 
    8973 ---|---|---|--- 
    8974 H | 6 | -9 | -6 
    8975 S |  | 6 | -6 
    8976 O |  |  | 4 
    8977 Iteration cutoff | 2 
    8978  
    8979 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#32)
    8980 with AF-P47102-F1-model_v1.pdb, chain A (#10), sequence alignment score =
    8981 3608.2 
    8982 RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
    8983 5.511) 
    8984  
    8985 
    8986 > mlp sel
    8987 
    8988 Map values for surface "AF-P47102-F1-model_v1.pdb_A SES surface": minimum
    8989 -30.22, mean -5.341, maximum 24.77 
    8990 
    8991 > coulombic sel
    8992 
    8993 > select clear
    8994 
    8995 > hide #!32 models
    8996 
    8997 > hide #!10 models
    8998 
    8999 > show #!32 models
    9000 
    9001 > ui tool show "Side View"
    9002 
    9003 > save
    9004 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/electrostatics.png
    9005 > transparentBackground true supersample 3
    9006 
    9007 > hide #!32 models
    9008 
    9009 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    9010 > gea1.pdb
    9011 
    9012 AF-gea1.pdb title: 
    9013 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
    9014 (P47102) [more info...] 
    9015  
    9016 Chain information for AF-gea1.pdb #34 
    9017 --- 
    9018 Chain | Description 
    9019 A | arf guanine-nucleotide exchange factor 1 
    9020  
    9021 
    9022 > hide #34 models
    9023 
    9024 > show #34 models
    9025 
    9026 > ui tool show "Side View"
    9027 
    9028 > show #1 models
    9029 
    9030 > view
    9031 
    9032 > hide #1 models
    9033 
    9034 > coulombic #34
    9035 
    9036 > show #!32 models
    9037 
    9038 > hide #!32 models
    9039 
    9040 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    9041 > gea2.pdb
    9042 
    9043 AF-gea2.pdb title: 
    9044 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    9045 (P39993) [more info...] 
    9046  
    9047 Chain information for AF-gea2.pdb #35 
    9048 --- 
    9049 Chain | Description 
    9050 A | arf guanine-nucleotide exchange factor 2 
    9051  
    9052 
    9053 > mmaker #35 to #34
    9054 
    9055 Parameters 
    9056 --- 
    9057 Chain pairing | bb 
    9058 Alignment algorithm | Needleman-Wunsch 
    9059 Similarity matrix | BLOSUM-62 
    9060 SS fraction | 0.3 
    9061 Gap open (HH/SS/other) | 18/18/6 
    9062 Gap extend | 1 
    9063 SS matrix |  |  | H | S | O 
    9064 ---|---|---|--- 
    9065 H | 6 | -9 | -6 
    9066 S |  | 6 | -6 
    9067 O |  |  | 4 
    9068 Iteration cutoff | 2 
    9069  
    9070 Matchmaker AF-gea1.pdb, chain A (#34) with AF-gea2.pdb, chain A (#35),
    9071 sequence alignment score = 4404 
    9072 RMSD between 910 pruned atom pairs is 1.051 angstroms; (across all 1388 pairs:
    9073 5.497) 
    9074  
    9075 
    9076 > hide #!34 models
    9077 
    9078 > coulombic #35
    9079 
    9080 > show #!34 models
    9081 
    9082 > select #34
    9083 
    9084 11218 atoms, 11405 bonds, 1408 residues, 1 model selected 
    9085 
    9086 > ui mousemode right "translate selected models"
    9087 
    9088 > mlp sel
    9089 
    9090 Map values for surface "AF-gea1.pdb_A SES surface": minimum -30.35, mean
    9091 -5.339, maximum 24.96 
    9092 
    9093 > select #35
    9094 
    9095 11659 atoms, 11853 bonds, 1459 residues, 1 model selected 
    9096 
    9097 > ~select #35
    9098 
    9099 1 model selected 
    9100 
    9101 > select #34
    9102 
    9103 11218 atoms, 11405 bonds, 1408 residues, 1 model selected 
    9104 
    9105 > ~select #34
    9106 
    9107 1 model selected 
    9108 
    9109 > select #35
    9110 
    9111 11659 atoms, 11853 bonds, 1459 residues, 1 model selected 
    9112 
    9113 > mlp sel
    9114 
    9115 Map values for surface "AF-gea2.pdb_A SES surface": minimum -32.32, mean
    9116 -5.657, maximum 27.63 
    9117 
    9118 > show #!2 models
    9119 
    9120 > hide #!2 models
    9121 
    9122 > show #1 models
    9123 
    9124 > mmaker #35 to #1/A
    9125 
    9126 Parameters 
    9127 --- 
    9128 Chain pairing | bb 
    9129 Alignment algorithm | Needleman-Wunsch 
    9130 Similarity matrix | BLOSUM-62 
    9131 SS fraction | 0.3 
    9132 Gap open (HH/SS/other) | 18/18/6 
    9133 Gap extend | 1 
    9134 SS matrix |  |  | H | S | O 
    9135 ---|---|---|--- 
    9136 H | 6 | -9 | -6 
    9137 S |  | 6 | -6 
    9138 O |  |  | 4 
    9139 Iteration cutoff | 2 
    9140  
    9141 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    9142 with AF-gea2.pdb, chain A (#35), sequence alignment score = 5664 
    9143 RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
    9144 2.486) 
    9145  
    9146 
    9147 > mmaker #34 to #1/B
    9148 
    9149 Parameters 
    9150 --- 
    9151 Chain pairing | bb 
    9152 Alignment algorithm | Needleman-Wunsch 
    9153 Similarity matrix | BLOSUM-62 
    9154 SS fraction | 0.3 
    9155 Gap open (HH/SS/other) | 18/18/6 
    9156 Gap extend | 1 
    9157 SS matrix |  |  | H | S | O 
    9158 ---|---|---|--- 
    9159 H | 6 | -9 | -6 
    9160 S |  | 6 | -6 
    9161 O |  |  | 4 
    9162 Iteration cutoff | 2 
    9163  
    9164 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
    9165 with AF-gea1.pdb, chain A (#34), sequence alignment score = 3579.8 
    9166 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    9167 5.699) 
    9168  
    9169 
    9170 > select clear
    9171 
    9172 > select #35
    9173 
    9174 11659 atoms, 11853 bonds, 1459 residues, 1 model selected 
    9175 
    9176 > hide sel surfaces
    9177 
    9178 > hide #1 models
    9179 
    9180 > mlp sel
    9181 
    9182 Map values for surface "AF-gea2.pdb_A SES surface": minimum -32.33, mean
    9183 -5.655, maximum 27.08 
    9184 
    9185 > select #35/A:265@OE1
    9186 
    9187 1 atom, 1 residue, 1 model selected 
    9188 
    9189 > select clear
    9190 
    9191 > hide #!34-35 surfaces
    9192 
    9193 Drag select of 171 residues 
    9194 
    9195 > show sel atoms
    9196 
    9197 > select clear
    9198 
    9199 > select clear
    9200 
    9201 Drag select of 205 atoms, 275 residues, 168 bonds 
    9202 
    9203 > show sel atoms
    9204 
    9205 > select clear
    9206 
    9207 > select clear
    9208 
    9209 > select #34/A:216
    9210 
    9211 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9212 Drag select of 2 residues 
    9213 
    9214 > show sel atoms
    9215 
    9216 > show sel atoms
    9217 
    9218 > select clear
    9219 
    9220 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    9221 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    9222 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    9223 > figures/complex_dimer-FINAL-coot-7.pdb
    9224 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    9225 > figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
    9226 
    9227 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #36 
    9228 --- 
    9229 Chain | Description 
    9230 A B | No description available 
    9231  
    9232 Chain information for complex_dimer-FINAL-coot-7.pdb #37 
    9233 --- 
    9234 Chain | Description 
    9235 A C | No description available 
    9236 B | No description available 
    9237 D | No description available 
    9238  
    9239 Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #38 
    9240 --- 
    9241 Chain | Description 
    9242 A B | No description available 
    9243  
    9244 
    9245 > hide #!34 models
    9246 
    9247 > mmaker #36-38 to #35
    9248 
    9249 Parameters 
    9250 --- 
    9251 Chain pairing | bb 
    9252 Alignment algorithm | Needleman-Wunsch 
    9253 Similarity matrix | BLOSUM-62 
    9254 SS fraction | 0.3 
    9255 Gap open (HH/SS/other) | 18/18/6 
    9256 Gap extend | 1 
    9257 SS matrix |  |  | H | S | O 
    9258 ---|---|---|--- 
    9259 H | 6 | -9 | -6 
    9260 S |  | 6 | -6 
    9261 O |  |  | 4 
    9262 Iteration cutoff | 2 
    9263  
    9264 Matchmaker AF-gea2.pdb, chain A (#35) with closed_dimer-FINAL-
    9265 coot-3_real_space_refined_206.pdb, chain A (#36), sequence alignment score =
    9266 5664 
    9267 RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
    9268 2.486) 
    9269  
    9270 Matchmaker AF-gea2.pdb, chain A (#35) with complex_dimer-FINAL-coot-7.pdb,
    9271 chain C (#37), sequence alignment score = 5320.4 
    9272 RMSD between 689 pruned atom pairs is 1.128 angstroms; (across all 1159 pairs:
    9273 7.511) 
    9274  
    9275 Matchmaker AF-gea2.pdb, chain A (#35) with open_dimer-FINAL-
    9276 coot-5_real_space_refined_208.pdb, chain B (#38), sequence alignment score =
    9277 5053.9 
    9278 RMSD between 662 pruned atom pairs is 1.268 angstroms; (across all 1129 pairs:
    9279 9.186) 
    9280  
    9281 
    9282 > hide #!37 models
    9283 
    9284 > hide #36 models
    9285 
    9286 > hide #!35 models
    9287 
    9288 > hide #38 models
    9289 
    9290 > show #36 models
    9291 
    9292 > show #38 models
    9293 
    9294 > show #!37 models
    9295 
    9296 > hide #36 models
    9297 
    9298 > hide #!37 models
    9299 
    9300 > hide #38 models
    9301 
    9302 > show #36 models
    9303 
    9304 > hide #36 models
    9305 
    9306 > show #!37 models
    9307 
    9308 > hide #!37 models
    9309 
    9310 > show #38 models
    9311 
    9312 > hide #38 models
    9313 
    9314 > show #!37 models
    9315 
    9316 > hide #!37 models
    9317 
    9318 > show #36 models
    9319 
    9320 > show #38 models
    9321 
    9322 > morph #36,38
    9323 
    9324 Computed 21 frame morph #39 
    9325 
    9326 > coordset #39 1,21
    9327 
    9328 > movie record
    9329 
    9330 > movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
    9331 
    9332 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9333  
    9334 
    9335 > hide #!39 models
    9336 
    9337 > show #36 models
    9338 
    9339 > show #38 models
    9340 
    9341 > matchmaker #36 to #38
    9342 
    9343 Parameters 
    9344 --- 
    9345 Chain pairing | bb 
    9346 Alignment algorithm | Needleman-Wunsch 
    9347 Similarity matrix | BLOSUM-62 
    9348 SS fraction | 0.3 
    9349 Gap open (HH/SS/other) | 18/18/6 
    9350 Gap extend | 1 
    9351 SS matrix |  |  | H | S | O 
    9352 ---|---|---|--- 
    9353 H | 6 | -9 | -6 
    9354 S |  | 6 | -6 
    9355 O |  |  | 4 
    9356 Iteration cutoff | 2 
    9357  
    9358 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38)
    9359 with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36),
    9360 sequence alignment score = 5250.9 
    9361 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    9362 10.353) 
    9363  
    9364 
    9365 > matchmaker #38 to #36
    9366 
    9367 Parameters 
    9368 --- 
    9369 Chain pairing | bb 
    9370 Alignment algorithm | Needleman-Wunsch 
    9371 Similarity matrix | BLOSUM-62 
    9372 SS fraction | 0.3 
    9373 Gap open (HH/SS/other) | 18/18/6 
    9374 Gap extend | 1 
    9375 SS matrix |  |  | H | S | O 
    9376 ---|---|---|--- 
    9377 H | 6 | -9 | -6 
    9378 S |  | 6 | -6 
    9379 O |  |  | 4 
    9380 Iteration cutoff | 2 
    9381  
    9382 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36)
    9383 with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38),
    9384 sequence alignment score = 5250.9 
    9385 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    9386 10.353) 
    9387  
    9388 
    9389 > select #38
    9390 
    9391 36826 atoms, 37112 bonds, 2258 residues, 1 model selected 
    9392 
    9393 > ~select #38
    9394 
    9395 Nothing selected 
    9396 
    9397 > matchmaker #38 to #36
    9398 
    9399 Parameters 
    9400 --- 
    9401 Chain pairing | bb 
    9402 Alignment algorithm | Needleman-Wunsch 
    9403 Similarity matrix | BLOSUM-62 
    9404 SS fraction | 0.3 
    9405 Gap open (HH/SS/other) | 18/18/6 
    9406 Gap extend | 1 
    9407 SS matrix |  |  | H | S | O 
    9408 ---|---|---|--- 
    9409 H | 6 | -9 | -6 
    9410 S |  | 6 | -6 
    9411 O |  |  | 4 
    9412 Iteration cutoff | 2 
    9413  
    9414 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36)
    9415 with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38),
    9416 sequence alignment score = 5250.9 
    9417 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    9418 10.353) 
    9419  
    9420 
    9421 > select #38
    9422 
    9423 36826 atoms, 37112 bonds, 2258 residues, 1 model selected 
    9424 
    9425 > select clear
    9426 
    9427 > mmaker #36 to #38
    9428 
    9429 Parameters 
    9430 --- 
    9431 Chain pairing | bb 
    9432 Alignment algorithm | Needleman-Wunsch 
    9433 Similarity matrix | BLOSUM-62 
    9434 SS fraction | 0.3 
    9435 Gap open (HH/SS/other) | 18/18/6 
    9436 Gap extend | 1 
    9437 SS matrix |  |  | H | S | O 
    9438 ---|---|---|--- 
    9439 H | 6 | -9 | -6 
    9440 S |  | 6 | -6 
    9441 O |  |  | 4 
    9442 Iteration cutoff | 2 
    9443  
    9444 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38)
    9445 with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36),
    9446 sequence alignment score = 5250.9 
    9447 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    9448 10.353) 
    9449  
    9450 
    9451 > morph #36,38
    9452 
    9453 Computed 21 frame morph #40 
    9454 
    9455 > coordset #40 1,21
    9456 
    9457 > coordset #40 1,21
    9458 
    9459 > morph #36,38 method linear
    9460 
    9461 Computed 21 frame morph #41 
    9462 
    9463 > coordset #41 1,21
    9464 
    9465 > movie record
    9466 
    9467 > movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
    9468 
    9469 Error processing trigger "new frame": 
    9470 Movie encoding failed because no images were recorded. 
    9471 
    9472 > hide #!41 models
    9473 
    9474 > close #39-41
    9475 
    9476 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    9477 > figures/figures.cxs includeMaps true
    9478 
    9479 opened ChimeraX session 
    9480 
    9481 > show #1 models
    9482 
    9483 > hide #1 models
    9484 
    9485 > show #1 models
    9486 
    9487 > ui mousemode right distance
    9488 
    9489 > ui mousemode right "tape measure"
    9490 
    9491 > show #!2 models
    9492 
    9493 > hide #!2 models
    9494 
    9495 > show #!3 models
    9496 
    9497 > hide #1 models
    9498 
    9499 > ui mousemode right "tape measure"
    9500 
    9501 > ui mousemode right "tape measure"
    9502 
    9503 > ui mousemode right "tape measure"
    9504 
    9505 > ui mousemode right "tape measure"
    9506 
    9507 > ui mousemode right "tape measure"
    9508 
    9509 > show #1 models
    9510 
    9511 > ui mousemode right "tape measure"
    9512 
    9513 > ui mousemode right "tape measure"
    9514 
    9515 > ui mousemode right "tape measure"
    9516 
    9517 > hide #1 models
    9518 
    9519 > hide #!3 models
    9520 
    9521 > show #!35 models
    9522 
    9523 > show #!2 models
    9524 
    9525 > hide #!2 models
    9526 
    9527 > show #1 models
    9528 
    9529 > show #28 models
    9530 
    9531 > hide #1 models
    9532 
    9533 > select #28
    9534 
    9535 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    9536 
    9537 > preset cartoons/nucleotides ribbons/slabs
    9538 
    9539 Changed 0 atom styles 
    9540 Preset expands to these ChimeraX commands:
    9541 
    9542    
    9543    
    9544     show nucleic
    9545     hide protein|solvent|H
    9546     surf hide
    9547     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    9548     cartoon
    9549     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    9550     cartoon style ~(nucleic|strand) x round
    9551     cartoon style (nucleic|strand) x rect
    9552     nucleotides tube/slab shape box
    9553 
    9554  
    9555 
    9556 > select clear
    9557 
    9558 > mmaker #35 to #28
    9559 
    9560 Parameters 
    9561 --- 
    9562 Chain pairing | bb 
    9563 Alignment algorithm | Needleman-Wunsch 
    9564 Similarity matrix | BLOSUM-62 
    9565 SS fraction | 0.3 
    9566 Gap open (HH/SS/other) | 18/18/6 
    9567 Gap extend | 1 
    9568 SS matrix |  |  | H | S | O 
    9569 ---|---|---|--- 
    9570 H | 6 | -9 | -6 
    9571 S |  | 6 | -6 
    9572 O |  |  | 4 
    9573 Iteration cutoff | 2 
    9574  
    9575 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#28)
    9576 with AF-gea2.pdb, chain A (#35), sequence alignment score = 5664 
    9577 RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
    9578 2.486) 
    9579  
    9580 
    9581 > ui tool show "Show Sequence Viewer"
    9582 
    9583 > sequence chain #35/A
    9584 
    9585 Alignment identifier is 35/A 
    9586 Drag select of 3 residues 
    9587 
    9588 > show sel atoms
    9589 
    9590 > color sel byhetero
    9591 
    9592 > show sel atoms
    9593 
    9594 > color sel byhetero
    9595 
    9596 > select clear
    9597 
    9598 Drag select of 1 residues 
    9599 
    9600 > show sel atoms
    9601 
    9602 > select clear
    9603 
    9604 > save
    9605 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction
    9606 > transparentBackground true supersample 3
    9607 
    9608 Cannot determine format for
    9609 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction' 
    9610 
    9611 > save
    9612 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction.png
    9613 > transparentBackground true supersample 3
    9614 
    9615 > hide #!35 models
    9616 
    9617 > hide #28 models
    9618 
    9619 > show #1 models
    9620 
    9621 > preset cartoons/nucleotides cylinders/stubs
    9622 
    9623 Changed 0 atom styles 
    9624 Preset expands to these ChimeraX commands:
    9625 
    9626    
    9627    
    9628     show nucleic
    9629     hide protein|solvent|H
    9630     surf hide
    9631     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    9632     cartoon
    9633     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    9634     cartoon style ~(nucleic|strand) x round
    9635     cartoon style (nucleic|strand) x rect
    9636     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    9637     cartoon style nucleic x round width 1.6 thick 1.6
    9638     nucleotides stubs
    9639 
    9640  
    9641 
    9642 > turn #1
    9643 
    9644 Expected an axis vector or a keyword 
    9645 
    9646 > view orient
    9647 
    9648 > view orient
    9649 
    9650 > view orient
    9651 
    9652 > view orient
    9653 
    9654 > view orient
    9655 
    9656 > turn #1 x
    9657 
    9658 Expected an axis vector or a keyword 
    9659 
    9660 > turn #1 x 90
    9661 
    9662 Expected an axis vector or a keyword 
    9663 
    9664 > turn x 90 #1
    9665 
    9666 Expected 'forever' or an integer >= 1 or a keyword 
    9667 
    9668 > turn #1
    9669 
    9670 Expected an axis vector or a keyword 
    9671 
    9672 > turn #1
    9673 
    9674 Expected an axis vector or a keyword 
    9675 
    9676 > turn models #1
    9677 
    9678 > view orient
    9679 
    9680 > view orient
    9681 
    9682 > turn models #1
    9683 
    9684 > turn models #1
    9685 
    9686 > turn models #1
    9687 
    9688 > view orient
    9689 
    9690 > turn z 90 60 models #1
    9691 
    9692 > turn z 1-90 60 model #1
    9693 
    9694 Expected a number or a keyword 
    9695 
    9696 > turn z 1 90
    9697 
    9698 > star; turn z 1 90
    9699 
    9700 Unknown command: movie star; turn z 1 90 
    9701 
    9702 > start; turn z 1 90
    9703 
    9704 Unknown command: movie start; turn z 1 90 
    9705 
    9706 > ; turn z 1 90
    9707 
    9708 Incomplete command: movie 
    9709 
    9710 > movie record
    9711 
    9712 > turn z 1 90
    9713 
    9714 > view orient
    9715 
    9716 > turn x 0 45
    9717 
    9718 > movie stop
    9719 
    9720 > turn x 0 45
    9721 
    9722 > turn x 0 45
    9723 
    9724 > turn x 0 45
    9725 
    9726 > turn z 1 90
    9727 
    9728 > turn z 1 90
    9729 
    9730 > roll
    9731 
    9732 > top
    9733 
    9734 Unknown command: top 
    9735 
    9736 > stop
    9737 
    9738 > view orient
    9739 
    9740 > view orient
    9741 
    9742 > turn x 1-90
    9743 
    9744 Expected a number or a keyword 
    9745 
    9746 > turn x 1 90
    9747 
    9748 > turn x 1 90
    9749 
    9750 > turn x 1 90
    9751 
    9752 > turn x 1 90
    9753 
    9754 > turn x 90-1
    9755 
    9756 Expected a number or a keyword 
    9757 
    9758 > turn x 90 1
    9759 
    9760 > turn x
    9761 
    9762 > turn x
    9763 
    9764 > turn x
    9765 
    9766 > turn x -90 -1
    9767 
    9768 Missing or invalid "frames" argument: Must be greater than or equal to 1 
    9769 
    9770 > turn x 270 360
    9771 
    9772 > turn x 1 90
    9773 
    9774 > turn x 1 90
    9775 
    9776 > turn x 1 90
    9777 
    9778 > turn x 1 90
    9779 
    9780 > turn x 1 90
    9781 
    9782 > turn x 1 90
    9783 
    9784 > turn x 1 90
    9785 
    9786 > turn x 1 90
    9787 
    9788 > turn x 1 90
    9789 
    9790 > turn x 1 90
    9791 
    9792 > turn x 1 90
    9793 
    9794 > turn x 1 90
    9795 
    9796 > turn x 1 180
    9797 
    9798 > turn x 1 270
    9799 
    9800 > turn x -1 270
    9801 
    9802 > turn x
    9803 
    9804 > turn x
    9805 
    9806 > turn x -1 90
    9807 
    9808 > turn x -1 90
    9809 
    9810 > wait
    9811 
    9812 > turn y 1 90
    9813 
    9814 > turn x -1 90
    9815 
    9816 > wait
    9817 
    9818 > turn y 1 90
    9819 
    9820 > turn x -1 90
    9821 
    9822 > wait
    9823 
    9824 > turn y 1 90
    9825 
    9826 > turn x
    9827 
    9828 > turn x -1 90
    9829 
    9830 > wait
    9831 
    9832 > turn y 1 360
    9833 
    9834 > view orient
    9835 
    9836 > turn x -1 90
    9837 
    9838 > wait
    9839 
    9840 > turn y 1 180
    9841 
    9842 > view orient
    9843 
    9844 > star; turn x -1 90; wait; turn y 1 180
    9845 
    9846 Unknown command: movie star; turn x -1 90; wait; turn y 1 180 
    9847 
    9848 > movie record
    9849 
    9850 > turn x -1 90
    9851 
    9852 > wait
    9853 
    9854 > turn y 1 180
    9855 
    9856 > movie encode C:\Users\Arnold/Desktop
    9857 
    9858 Unrecognized movie file suffix Desktop, use *.webm, *.avi, *.mov, *.mp4,
    9859 *.wmv, *.ogv 
    9860 
    9861 > movie encode C:\Users\Arnold/Desktop/movie.mp4
    9862 
    9863 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9864  
    9865 
    9866 > view orient
    9867 
    9868 > view orient
    9869 
    9870 > movie record
    9871 
    9872 > turn x -1 90
    9873 
    9874 > wait
    9875 
    9876 > turn y 1 180
    9877 
    9878 > movie encode C:\Users\Arnold/Desktop/movie.mp4
    9879 
    9880 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9881  
    9882 
    9883 > movie record
    9884 
    9885 > wait 3
    9886 
    9887 > turn x -1 90
    9888 
    9889 > wait
    9890 
    9891 > turn y 1 180
    9892 
    9893 > movie encode C:\Users\Arnold/Desktop/movie.mp4
    9894 
    9895 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9896  
    9897 
    9898 > movie record
    9899 
    9900 > wait 3
    9901 
    9902 > turn x -1 90
    9903 
    9904 > wait
    9905 
    9906 > turn y 1 180
    9907 
    9908 > wait
    9909 
    9910 > movie encode C:\Users\Arnold/Desktop/movie.mp4
    9911 
    9912 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9913  
    9914 
    9915 > view orient
    9916 
    9917 > movie record
    9918 
    9919 > wait
    9920 
    9921 wait requires a frame count argument unless motion is in progress 
    9922 
    9923 > wait 20
    9924 
    9925 > turn x -1 90
    9926 
    9927 > wait
    9928 
    9929 > turn y 1 180
    9930 
    9931 > wait
    9932 
    9933 > movie encode C:\Users\Arnold/Desktop/movie.mp4
    9934 
    9935 Movie saved to C:\Users\Arnold/Desktop/movie.mp4 
    9936  
    9937 
    9938 > view orient
    9939 
    9940 > hide #1 models
    9941 
    9942 > show #4 models
    9943 
    9944 > movie record
    9945 
    9946 > wait
    9947 
    9948 wait requires a frame count argument unless motion is in progress 
    9949 
    9950 > wait 20
    9951 
    9952 > turn x -1 90
    9953 
    9954 > wait
    9955 
    9956 > turn y 1 180
    9957 
    9958 > wait
    9959 
    9960 > movie encode C:\Users\Arnold/Desktop/Gea2Open.mp4
    9961 
    9962 Movie saved to C:\Users\Arnold/Desktop/Gea2Open.mp4 
    9963  
    9964 
    9965 > hide #4 models
    9966 
    9967 > show #!8 models
    9968 
    9969 > mmaker #8 to #1
    9970 
    9971 Parameters 
    9972 --- 
    9973 Chain pairing | bb 
    9974 Alignment algorithm | Needleman-Wunsch 
    9975 Similarity matrix | BLOSUM-62 
    9976 SS fraction | 0.3 
    9977 Gap open (HH/SS/other) | 18/18/6 
    9978 Gap extend | 1 
    9979 SS matrix |  |  | H | S | O 
    9980 ---|---|---|--- 
    9981 H | 6 | -9 | -6 
    9982 S |  | 6 | -6 
    9983 O |  |  | 4 
    9984 Iteration cutoff | 2 
    9985  
    9986 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    9987 with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
    9988 5451 
    9989 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    9990 8.396) 
    9991  
    9992 
    9993 > view orient
    9994 
    9995 > movie record
    9996 
    9997 > wait
    9998 
    9999 wait requires a frame count argument unless motion is in progress 
    10000 
    10001 > wait 20
    10002 
    10003 > turn x -1 90
    10004 
    10005 > wait
    10006 
    10007 > turn y 1 180
    10008 
    10009 > wait
    10010 
    10011 > movie encode C:\Users\Arnold/Desktop/Gea2Complex.mp4
    10012 
    10013 Movie saved to C:\Users\Arnold/Desktop/Gea2Complex.mp4 
    10014  
    10015 
    10016 > show #16 models
    10017 
    10018 > hide #16 models
    10019 
    10020 > hide #!8 models
    10021 
    10022 > show #1 models
    10023 
    10024 > show #16 models
    10025 
    10026 > mmaker #16 to #1
    10027 
    10028 Parameters 
    10029 --- 
    10030 Chain pairing | bb 
    10031 Alignment algorithm | Needleman-Wunsch 
    10032 Similarity matrix | BLOSUM-62 
    10033 SS fraction | 0.3 
    10034 Gap open (HH/SS/other) | 18/18/6 
    10035 Gap extend | 1 
    10036 SS matrix |  |  | H | S | O 
    10037 ---|---|---|--- 
    10038 H | 6 | -9 | -6 
    10039 S |  | 6 | -6 
    10040 O |  |  | 4 
    10041 Iteration cutoff | 2 
    10042  
    10043 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    10044 with ger2.pdb, chain C (#16), sequence alignment score = 978.1 
    10045 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    10046 1.427) 
    10047  
    10048 
    10049 > show #!8 models
    10050 
    10051 > hide #16 models
    10052 
    10053 > hide #!8 models
    10054 
    10055 > show #!8 models
    10056 
    10057 > hide #1 models
    10058 
    10059 > show #1 models
    10060 
    10061 > hide #!8 models
    10062 
    10063 > show #16 models
    10064 
    10065 > select #16/A
    10066 
    10067 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10068 
    10069 > select #16/C
    10070 
    10071 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10072 
    10073 > hide sel target a
    10074 
    10075 > hide sel cartoons
    10076 
    10077 > hide #16 models
    10078 
    10079 > select #16
    10080 
    10081 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    10082 
    10083 > show #16 models
    10084 
    10085 > ~select #16
    10086 
    10087 Nothing selected 
    10088 
    10089 > hide #1 models
    10090 
    10091 > show #1 models
    10092 
    10093 > show #!8 models
    10094 
    10095 > hide #1 models
    10096 
    10097 > show #1 models
    10098 
    10099 > hide #!8 models
    10100 
    10101 > show #!8 models
    10102 
    10103 > hide #!8 models
    10104 
    10105 > show #!8 models
    10106 
    10107 > hide #1 models
    10108 
    10109 > hide #16 models
    10110 
    10111 > hide #!8 models
    10112 
    10113 > show #1 models
    10114 
    10115 > hide #1 models
    10116 
    10117 > show #!2 models
    10118 
    10119 > hide #!2 models
    10120 
    10121 > show #4 models
    10122 
    10123 > show #16 models
    10124 
    10125 > mmaker #16 to #4
    10126 
    10127 Parameters 
    10128 --- 
    10129 Chain pairing | bb 
    10130 Alignment algorithm | Needleman-Wunsch 
    10131 Similarity matrix | BLOSUM-62 
    10132 SS fraction | 0.3 
    10133 Gap open (HH/SS/other) | 18/18/6 
    10134 Gap extend | 1 
    10135 SS matrix |  |  | H | S | O 
    10136 ---|---|---|--- 
    10137 H | 6 | -9 | -6 
    10138 S |  | 6 | -6 
    10139 O |  |  | 4 
    10140 Iteration cutoff | 2 
    10141  
    10142 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
    10143 with ger2.pdb, chain C (#16), sequence alignment score = 1010.5 
    10144 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    10145 1.454) 
    10146  
    10147 
    10148 > hide #4 models
    10149 
    10150 > hide #16 models
    10151 
    10152 > show #1 models
    10153 
    10154 > hide #1 models
    10155 
    10156 > show #!8 models
    10157 
    10158 > show #!29 models
    10159 
    10160 > hide #!29 models
    10161 
    10162 > show #!29 models
    10163 
    10164 > show #28 models
    10165 
    10166 > hide #!8 models
    10167 
    10168 > hide #!29 models
    10169 
    10170 > hide #28 models
    10171 
    10172 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    10173 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    10174 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    10175 > figures/complex_dimer-FINAL-coot-7.pdb
    10176 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    10177 > figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
    10178 
    10179 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #39 
    10180 --- 
    10181 Chain | Description 
    10182 A B | No description available 
    10183  
    10184 Chain information for complex_dimer-FINAL-coot-7.pdb #40 
    10185 --- 
    10186 Chain | Description 
    10187 A C | No description available 
    10188 B | No description available 
    10189 D | No description available 
    10190  
    10191 Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #41 
    10192 --- 
    10193 Chain | Description 
    10194 A B | No description available 
    10195  
    10196 
    10197 > mmaker #40-41 to #39
    10198 
    10199 Parameters 
    10200 --- 
    10201 Chain pairing | bb 
    10202 Alignment algorithm | Needleman-Wunsch 
    10203 Similarity matrix | BLOSUM-62 
    10204 SS fraction | 0.3 
    10205 Gap open (HH/SS/other) | 18/18/6 
    10206 Gap extend | 1 
    10207 SS matrix |  |  | H | S | O 
    10208 ---|---|---|--- 
    10209 H | 6 | -9 | -6 
    10210 S |  | 6 | -6 
    10211 O |  |  | 4 
    10212 Iteration cutoff | 2 
    10213  
    10214 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    10215 with complex_dimer-FINAL-coot-7.pdb, chain A (#40), sequence alignment score =
    10216 5451 
    10217 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    10218 8.396) 
    10219  
    10220 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    10221 with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41),
    10222 sequence alignment score = 5250.9 
    10223 RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
    10224 10.353) 
    10225  
    10226 
    10227 > hide #39 models
    10228 
    10229 > hide #!40 models
    10230 
    10231 > hide #41 models
    10232 
    10233 > show #39 models
    10234 
    10235 > ui tool show "Show Sequence Viewer"
    10236 
    10237 > sequence chain #8/C
    10238 
    10239 Alignment identifier is 8/C 
    10240 
    10241 > sequence chain #8/A
    10242 
    10243 Alignment identifier is 8/A 
    10244 
    10245 > show #1 models
    10246 
    10247 > hide #1 models
    10248 
    10249 > select clear
    10250 
    10251 Drag select of 2 residues 
    10252 
    10253 > ui tool show "Show Sequence Viewer"
    10254 
    10255 > ui tool show "Show Sequence Viewer"
    10256 
    10257 > ui tool show "Color Actions"
    10258 
    10259 > ui tool show "Show Sequence Viewer"
    10260 
    10261 > sequence chain #39/A
    10262 
    10263 Alignment identifier is 39/A 
    10264 
    10265 > sequence chain #39/B
    10266 
    10267 Alignment identifier is 39/B 
    10268 Drag select of 3 residues 
    10269 
    10270 > color sel #f5e4deff
    10271 
    10272 > color sel #f8e266ff
    10273 
    10274 > color sel #8fc3faff
    10275 
    10276 > color sel #f8e266ff
    10277 
    10278 > color sel #e7c3afff
    10279 
    10280 > select clear
    10281 
    10282 > color sel #f5e4deff
    10283 
    10284 > color sel #e7c3afff
    10285 
    10286 > select clear
    10287 
    10288 > color sel #8fc3faff
    10289 
    10290 > color sel #2e79abff
    10291 
    10292 > color sel #8fc3faff
    10293 
    10294 > select clear
    10295 
    10296 > preset cartoons/nucleotides ribbons/slabs
    10297 
    10298 Changed 0 atom styles 
    10299 Preset expands to these ChimeraX commands:
    10300 
    10301    
    10302    
    10303     show nucleic
    10304     hide protein|solvent|H
    10305     surf hide
    10306     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    10307     cartoon
    10308     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    10309     cartoon style ~(nucleic|strand) x round
    10310     cartoon style (nucleic|strand) x rect
    10311     nucleotides tube/slab shape box
    10312 
    10313  
    10314 
    10315 > preset cartoons/nucleotides cylinders/stubs
    10316 
    10317 Changed 0 atom styles 
    10318 Preset expands to these ChimeraX commands:
    10319 
    10320    
    10321    
    10322     show nucleic
    10323     hide protein|solvent|H
    10324     surf hide
    10325     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    10326     cartoon
    10327     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    10328     cartoon style ~(nucleic|strand) x round
    10329     cartoon style (nucleic|strand) x rect
    10330     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    10331     cartoon style nucleic x round width 1.6 thick 1.6
    10332     nucleotides stubs
    10333 
    10334  
    10335 
    10336 > show #!40 models
    10337 
    10338 > hide #39 models
    10339 
    10340 > ui tool show "Show Sequence Viewer"
    10341 
    10342 > sequence chain #40/A
    10343 
    10344 Alignment identifier is 40/A 
    10345 
    10346 > sequence chain #40/C
    10347 
    10348 Alignment identifier is 40/C 
    10349 
    10350 > select #40/C:545
    10351 
    10352 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10353 
    10354 > color sel #f8e266ff
    10355 
    10356 > color sel #8fc3faff
    10357 
    10358 > color sel #f8e266ff
    10359 
    10360 > select #40/C:780
    10361 
    10362 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10363 
    10364 > color sel #e7c3afff
    10365 
    10366 > color sel #2e79abff
    10367 
    10368 > color sel #e7c3afff
    10369 
    10370 > color sel #8fc3faff
    10371 
    10372 > color sel #2e79abff
    10373 
    10374 > color sel #8fc3faff
    10375 
    10376 > color sel #2e79abff
    10377 
    10378 > color sel #8fc3faff
    10379 
    10380 > select clear
    10381 
    10382 > select #40/B
    10383 
    10384 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10385 
    10386 > show #!8 models
    10387 
    10388 > hide #!40 models
    10389 
    10390 > select #8/B
    10391 
    10392 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10393 
    10394 > select clear
    10395 
    10396 > select #40/B
    10397 
    10398 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10399 
    10400 > color #8 #ffffffff
    10401 
    10402 > undo
    10403 
    10404 > select #40
    10405 
    10406 21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected 
    10407 
    10408 > ~select #40
    10409 
    10410 Nothing selected 
    10411 
    10412 > select #40/B
    10413 
    10414 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10415 
    10416 > show #!40 models
    10417 
    10418 > color sel #f5e4deff
    10419 
    10420 > color sel #31358cff
    10421 
    10422 > color sel #f0f0f0ff
    10423 
    10424 > color sel #ffffffff
    10425 
    10426 > color sel #000000ff
    10427 
    10428 > color sel #889affff
    10429 
    10430 > color sel #5a66adff
    10431 
    10432 > color sel #6471c1ff
    10433 
    10434 > color sel #7b8cedff
    10435 
    10436 > color sel #6c7acfff
    10437 
    10438 > color sel #7282dcff
    10439 
    10440 > color sel #8192f9ff
    10441 
    10442 > color sel #889affff
    10443 
    10444 > color sel #7887e6ff
    10445 
    10446 > color sel #8192f9ff
    10447 
    10448 > color sel #8293f9ff
    10449 
    10450 > color sel #ffffffff
    10451 
    10452 > color sel #889affff
    10453 
    10454 > select clear
    10455 
    10456 > hide #!8 models
    10457 
    10458 > lighting soft
    10459 
    10460 > select #40/D
    10461 
    10462 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    10463 
    10464 > color (#!40 & sel) #ffffffff
    10465 
    10466 > color (#!40 & sel) #889affff
    10467 
    10468 > select clear
    10469 
    10470 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    10471 
    10472 Chain information for ger2.pdb #42 
    10473 --- 
    10474 Chain | Description 
    10475 A | No description available 
    10476 C | No description available 
    10477  
    10478 
    10479 > hide #42 models
    10480 
    10481 > hide #!40 models
    10482 
    10483 > show #39 models
    10484 
    10485 > mmaker #42 to #39
    10486 
    10487 Parameters 
    10488 --- 
    10489 Chain pairing | bb 
    10490 Alignment algorithm | Needleman-Wunsch 
    10491 Similarity matrix | BLOSUM-62 
    10492 SS fraction | 0.3 
    10493 Gap open (HH/SS/other) | 18/18/6 
    10494 Gap extend | 1 
    10495 SS matrix |  |  | H | S | O 
    10496 ---|---|---|--- 
    10497 H | 6 | -9 | -6 
    10498 S |  | 6 | -6 
    10499 O |  |  | 4 
    10500 Iteration cutoff | 2 
    10501  
    10502 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    10503 with ger2.pdb, chain C (#42), sequence alignment score = 978.1 
    10504 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    10505 1.427) 
    10506  
    10507 
    10508 > show #42 models
    10509 
    10510 > select #42/C
    10511 
    10512 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10513 
    10514 > hide sel cartoons
    10515 
    10516 > select #42/A
    10517 
    10518 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10519 
    10520 > color sel #e7c3afff
    10521 
    10522 > color sel #889affff
    10523 
    10524 > select clear
    10525 
    10526 > select #42
    10527 
    10528 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    10529 
    10530 > preset cartoons/nucleotides cylinders/stubs
    10531 
    10532 Changed 0 atom styles 
    10533 Preset expands to these ChimeraX commands:
    10534 
    10535    
    10536    
    10537     show nucleic
    10538     hide protein|solvent|H
    10539     surf hide
    10540     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    10541     cartoon
    10542     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    10543     cartoon style ~(nucleic|strand) x round
    10544     cartoon style (nucleic|strand) x rect
    10545     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    10546     cartoon style nucleic x round width 1.6 thick 1.6
    10547     nucleotides stubs
    10548 
    10549  
    10550 
    10551 > select #42/A
    10552 
    10553 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10554 
    10555 > select #42/C
    10556 
    10557 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10558 
    10559 > hide sel cartoons
    10560 
    10561 > select #42/A
    10562 
    10563 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10564 
    10565 > color sel #ffffffff
    10566 
    10567 > color sel #889affff
    10568 
    10569 > color sel #889cffff
    10570 
    10571 > color sel #8497f7ff
    10572 
    10573 > color sel #8396f5ff
    10574 
    10575 > color sel #8295f4ff
    10576 
    10577 > color sel #8295f3ff
    10578 
    10579 > color sel #7e90ecff
    10580 
    10581 > color sel #7d90ebff
    10582 
    10583 > color sel #7c8ee8ff
    10584 
    10585 > color sel #788ae1ff
    10586 
    10587 > select clear
    10588 
    10589 > ui tool show "Side View"
    10590 
    10591 > ui tool show "Show Sequence Viewer"
    10592 
    10593 > sequence chain #42/A
    10594 
    10595 Alignment identifier is 42/A 
    10596 
    10597 > select #6
    10598 
    10599 2 models selected 
    10600 
    10601 > undo
    10602 
    10603 > undo
    10604 
    10605 > hide #39 models
    10606 
    10607 > show #4 models
    10608 
    10609 > hide #!6 models
    10610 
    10611 > hide #4 models
    10612 
    10613 > show #39 models
    10614 
    10615 Drag select of 2 residues 
    10616 
    10617 > color sel #ffffffff
    10618 
    10619 > color sel #ff0000ff
    10620 
    10621 > color sel #aa55ffff
    10622 
    10623 > color sel #00aaffff
    10624 
    10625 > color sel #ff5500ff
    10626 
    10627 > color sel #ff0000ff
    10628 
    10629 > color sel #aa0000ff
    10630 
    10631 > show sel atoms
    10632 
    10633 > color sel byhetero
    10634 
    10635 > select clear
    10636 
    10637 > ui tool show "Show Sequence Viewer"
    10638 
    10639 > sequence chain #39/A
    10640 
    10641 Alignment identifier is 39/A 
    10642 Drag select of 1 residues 
    10643 Drag select of 2 residues 
    10644 
    10645 > show sel atoms
    10646 
    10647 > color sel byhetero
    10648 
    10649 > color sel #ffff7fff
    10650 
    10651 > color sel #ffff00ff
    10652 
    10653 > color sel #aaff7fff
    10654 
    10655 > color sel #ff5500ff
    10656 
    10657 > color sel #ff557fff
    10658 
    10659 > color sel #55557fff
    10660 
    10661 > color sel #555500ff
    10662 
    10663 > color sel #ff0000ff
    10664 
    10665 > color sel #550000ff
    10666 
    10667 > color sel #55007fff
    10668 
    10669 > color sel byhetero
    10670 
    10671 > select clear
    10672 
    10673 > select #42/A
    10674 
    10675 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10676 
    10677 > color sel #788ae1ff
    10678 
    10679 > hide sel atoms
    10680 
    10681 > hide sel atoms
    10682 
    10683 > color sel red
    10684 
    10685 > color sel #ff0000ff
    10686 
    10687 > color sel #aa0000ff
    10688 
    10689 > color sel #aa007fff
    10690 
    10691 > color sel #ff007fff
    10692 
    10693 > color sel #550000ff
    10694 
    10695 > color sel #aa0000ff
    10696 
    10697 > select clear
    10698 
    10699 > select #42/C
    10700 
    10701 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10702 
    10703 > show sel cartoons
    10704 
    10705 > hide sel cartoons
    10706 
    10707 > show sel cartoons
    10708 
    10709 > select clear
    10710 
    10711 > select #42/C:201
    10712 
    10713 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10714 
    10715 > ui tool show "Show Sequence Viewer"
    10716 
    10717 > sequence chain #42/C
    10718 
    10719 Alignment identifier is 42/C 
    10720 
    10721 > color sel #e7c3afff
    10722 
    10723 > color sel #aa0000ff
    10724 
    10725 > hide sel cartoons
    10726 
    10727 > show #!40 models
    10728 
    10729 > hide #39 models
    10730 
    10731 > hide #42 models
    10732 
    10733 > ui tool show "Show Sequence Viewer"
    10734 
    10735 > sequence chain #8/B
    10736 
    10737 Alignment identifier is 8/B 
    10738 
    10739 No statusbar messages will be shown due to inadequate OpenGL 
    10740 
    10741 > ui tool show "Show Sequence Viewer"
    10742 
    10743 > sequence chain #40/A
    10744 
    10745 Alignment identifier is 40/A 
    10746 
    10747 > color sel #005500ff
    10748 
    10749 > color sel #aa0000ff
    10750 
    10751 > undo
    10752 
    10753 > undo
    10754 
    10755 Drag select of 1 residues 
    10756 
    10757 > select clear
    10758 
    10759 > select clear
    10760 
    10761 Drag select of 1 residues 
    10762 
    10763 > color sel #005500ff
    10764 
    10765 > color sel #aa0000ff
    10766 
    10767 > hide #!40 models
    10768 
    10769 > show #41 models
    10770 
    10771 > show #!40 models
    10772 
    10773 > hide #!40 models
    10774 
    10775 > ui tool show "Show Sequence Viewer"
    10776 
    10777 > sequence chain #41/A
    10778 
    10779 Alignment identifier is 41/A 
    10780 
    10781 > ui tool show "Show Sequence Viewer"
    10782 
    10783 > sequence chain #41/B
    10784 
    10785 Alignment identifier is 41/B 
    10786 Drag select of 1 residues 
    10787 
    10788 > color sel #f8e266ff
    10789 
    10790 > color sel #8fc3faff
    10791 
    10792 > color sel #f8e266ff
    10793 
    10794 Drag select of 1 residues 
    10795 
    10796 > color sel #e7c3afff
    10797 
    10798 > color sel #aa0000ff
    10799 
    10800 Drag select of 1 residues 
    10801 
    10802 > color sel #8fc3faff
    10803 
    10804 > select clear
    10805 
    10806 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    10807 
    10808 Chain information for ger2.pdb #43 
    10809 --- 
    10810 Chain | Description 
    10811 A | No description available 
    10812 C | No description available 
    10813  
    10814 
    10815 > mmaker #43 #41
    10816 
    10817 > matchmaker #43 #41
    10818 
    10819 Missing required "to" argument 
    10820 
    10821 > mmaker #43 to #41
    10822 
    10823 Parameters 
    10824 --- 
    10825 Chain pairing | bb 
    10826 Alignment algorithm | Needleman-Wunsch 
    10827 Similarity matrix | BLOSUM-62 
    10828 SS fraction | 0.3 
    10829 Gap open (HH/SS/other) | 18/18/6 
    10830 Gap extend | 1 
    10831 SS matrix |  |  | H | S | O 
    10832 ---|---|---|--- 
    10833 H | 6 | -9 | -6 
    10834 S |  | 6 | -6 
    10835 O |  |  | 4 
    10836 Iteration cutoff | 2 
    10837  
    10838 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
    10839 with ger2.pdb, chain C (#43), sequence alignment score = 1010.5 
    10840 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    10841 1.454) 
    10842  
    10843 
    10844 > preset cartoons/nucleotides cylinders/stubs
    10845 
    10846 Changed 0 atom styles 
    10847 Preset expands to these ChimeraX commands:
    10848 
    10849    
    10850    
    10851     show nucleic
    10852     hide protein|solvent|H
    10853     surf hide
    10854     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    10855     cartoon
    10856     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    10857     cartoon style ~(nucleic|strand) x round
    10858     cartoon style (nucleic|strand) x rect
    10859     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    10860     cartoon style nucleic x round width 1.6 thick 1.6
    10861     nucleotides stubs
    10862 
    10863  
    10864 
    10865 > select #43/A
    10866 
    10867 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    10868 
    10869 > color sel #788ae1ff
    10870 
    10871 > select #43/C
    10872 
    10873 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10874 
    10875 > hide sel cartoons
    10876 
    10877 > show #42 models
    10878 
    10879 > hide #41 models
    10880 
    10881 > show #41 models
    10882 
    10883 > hide #42 models
    10884 
    10885 > hide #43 models
    10886 
    10887 > show #!40 models
    10888 
    10889 > hide #41 models
    10890 
    10891 > hide #!40 models
    10892 
    10893 > show #!6 models
    10894 
    10895 > hide #!6 models
    10896 
    10897 > show #!5 models
    10898 
    10899 > hide #!5 models
    10900 
    10901 > show #4 models
    10902 
    10903 > show #11 models
    10904 
    10905 > hide #11 models
    10906 
    10907 > show #13 models
    10908 
    10909 > hide #13 models
    10910 
    10911 > show #16 models
    10912 
    10913 > hide #16 models
    10914 
    10915 > hide #4 models
    10916 
    10917 > show #42 models
    10918 
    10919 > hide #42 models
    10920 
    10921 > show #43 models
    10922 
    10923 > hide #43 models
    10924 
    10925 > show #42 models
    10926 
    10927 > show #39 models
    10928 
    10929 > select #42/C
    10930 
    10931 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    10932 
    10933 > hide sel surfaces
    10934 
    10935 > hide sel cartoons
    10936 
    10937 > select clear
    10938 
    10939 > show #!37 models
    10940 
    10941 > hide #!37 models
    10942 
    10943 > hide #39 models
    10944 
    10945 > hide #42 models
    10946 
    10947 > show #!40 models
    10948 
    10949 > hide #!40 models
    10950 
    10951 > show #36 models
    10952 
    10953 > show #42 models
    10954 
    10955 > hide #42 models
    10956 
    10957 > show #43 models
    10958 
    10959 > show #42 models
    10960 
    10961 > hide #43 models
    10962 
    10963 > hide #36 models
    10964 
    10965 > show #39 models
    10966 
    10967 > hide #39 models
    10968 
    10969 > show #!37 models
    10970 
    10971 > hide #42 models
    10972 
    10973 > show #!40 models
    10974 
    10975 > hide #!37 models
    10976 
    10977 > hide #!40 models
    10978 
    10979 > show #39 models
    10980 
    10981 > show #!40 models
    10982 
    10983 > show #41 models
    10984 
    10985 > hide #41 models
    10986 
    10987 > hide #!40 models
    10988 
    10989 > hide #39 models
    10990 
    10991 > show #39 models
    10992 
    10993 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-closed
    10994 > transparentBackground true supersample 3
    10995 
    10996 Cannot determine format for
    10997 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-closed' 
    10998 
    10999 > show #42 models
    11000 
    11001 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11002 > closed.png transparentBackground true supersample 3
    11003 
    11004 > hide #39 models
    11005 
    11006 > hide #42 models
    11007 
    11008 > show #43 models
    11009 
    11010 > show #38 models
    11011 
    11012 > hide #43 models
    11013 
    11014 > hide #38 models
    11015 
    11016 > show #41 models
    11017 
    11018 > show #43 models
    11019 
    11020 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11021 > open.png transparentBackground true supersample 3
    11022 
    11023 > hide #41 models
    11024 
    11025 > hide #43 models
    11026 
    11027 > show #!40 models
    11028 
    11029 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11030 > complex.png transparentBackground true supersample 3
    11031 
    11032 > hide #!40 models
    11033 
    11034 > show #!40 models
    11035 
    11036 > hide #!40 models
    11037 
    11038 > show #1 models
    11039 
    11040 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/closed.png
    11041 > transparentBackground true supersample 3
    11042 
    11043 > hide #1 models
    11044 
    11045 > show #39 models
    11046 
    11047 > hide #39 models
    11048 
    11049 > show #41 models
    11050 
    11051 > show #43 models
    11052 
    11053 > hide #41 models
    11054 
    11055 > hide #43 models
    11056 
    11057 > show #39 models
    11058 
    11059 > show #42 models
    11060 
    11061 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11062 > open.png transparentBackground true supersample 3
    11063 
    11064 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11065 > closed.png transparentBackground true supersample 3
    11066 
    11067 > hide #39 models
    11068 
    11069 > hide #42 models
    11070 
    11071 > show #!40 models
    11072 
    11073 > hide #!40 models
    11074 
    11075 > show #39 models
    11076 
    11077 > show #42 models
    11078 
    11079 > show #!40 models
    11080 
    11081 > hide #!40 models
    11082 
    11083 > show #!40 models
    11084 
    11085 > hide #39 models
    11086 
    11087 > hide #!40 models
    11088 
    11089 > show #!40 models
    11090 
    11091 > hide #42 models
    11092 
    11093 > hide #!40 models
    11094 
    11095 > show #39 models
    11096 
    11097 > show #42 models
    11098 
    11099 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11100 > closed.png transparentBackground true supersample 3
    11101 
    11102 > hide #42 models
    11103 
    11104 > hide #39 models
    11105 
    11106 > show #!40 models
    11107 
    11108 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11109 > complex.png transparentBackground true supersample 3
    11110 
    11111 > hide #!40 models
    11112 
    11113 > show #41 models
    11114 
    11115 > show #43 models
    11116 
    11117 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
    11118 > open.png transparentBackground true supersample 3
    11119 
    11120 > hide #43 models
    11121 
    11122 > show #42 models
    11123 
    11124 > hide #41 models
    11125 
    11126 > hide #42 models
    11127 
    11128 > show #39 models
    11129 
    11130 > show #42 models
    11131 
    11132 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash.png
    11133 > transparentBackground true supersample 3
    11134 
    11135 > show #1 models
    11136 
    11137 > hide #39 models
    11138 
    11139 > hide #42 models
    11140 
    11141 > show #!29 models
    11142 
    11143 > show #28 models
    11144 
    11145 > hide #1 models
    11146 
    11147 > show #!7 models
    11148 
    11149 > hide #!7 models
    11150 
    11151 > show #!8 models
    11152 
    11153 > hide #!8 models
    11154 
    11155 > show #!9 models
    11156 
    11157 > hide #!9 models
    11158 
    11159 > hide #!29 models
    11160 
    11161 > hide #28 models
    11162 
    11163 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11164 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    11165 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11166 > figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
    11167 
    11168 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #44 
    11169 --- 
    11170 Chain | Description 
    11171 A B | No description available 
    11172  
    11173 Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #45 
    11174 --- 
    11175 Chain | Description 
    11176 A B | No description available 
    11177  
    11178 
    11179 > select #44/A
    11180 
    11181 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    11182 
    11183 > delete atoms sel
    11184 
    11185 > delete bonds sel
    11186 
    11187 > select #45/B
    11188 
    11189 18413 atoms, 18556 bonds, 1129 residues, 1 model selected 
    11190 
    11191 > delete atoms sel
    11192 
    11193 > delete bonds sel
    11194 
    11195 > ui tool show "Show Sequence Viewer"
    11196 
    11197 > sequence chain #44/B
    11198 
    11199 Alignment identifier is 44/B 
    11200 
    11201 > select #45/A:554
    11202 
    11203 18 atoms, 17 bonds, 1 residue, 1 model selected 
    11204 
    11205 > select #44/B:814
    11206 
    11207 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11208 
    11209 > select clear
    11210 
    11211 Drag select of 2 residues 
    11212 
    11213 > color sel #f8e266ff
    11214 
    11215 > select #44/B:799
    11216 
    11217 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11218 
    11219 > color sel #e7c3afff
    11220 
    11221 > color sel #8fc3faff
    11222 
    11223 > select clear
    11224 
    11225 > ui tool show "Show Sequence Viewer"
    11226 
    11227 > sequence chain #45/A
    11228 
    11229 Alignment identifier is 45/A 
    11230 
    11231 > color sel #f8e266ff
    11232 
    11233 > color sel #e7c3afff
    11234 
    11235 > color sel #8fc3faff
    11236 
    11237 > select clear
    11238 
    11239 > select #45/A:545
    11240 
    11241 7 atoms, 6 bonds, 1 residue, 1 model selected 
    11242 
    11243 > color sel #f8e266ff
    11244 
    11245 > select clear
    11246 
    11247 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    11248 > gea2.pdb
    11249 
    11250 AF-gea2.pdb title: 
    11251 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    11252 (P39993) [more info...] 
    11253  
    11254 Chain information for AF-gea2.pdb #46 
    11255 --- 
    11256 Chain | Description 
    11257 A | arf guanine-nucleotide exchange factor 2 
    11258  
    11259 
    11260 > mmaker #46 to #44
    11261 
    11262 Parameters 
    11263 --- 
    11264 Chain pairing | bb 
    11265 Alignment algorithm | Needleman-Wunsch 
    11266 Similarity matrix | BLOSUM-62 
    11267 SS fraction | 0.3 
    11268 Gap open (HH/SS/other) | 18/18/6 
    11269 Gap extend | 1 
    11270 SS matrix |  |  | H | S | O 
    11271 ---|---|---|--- 
    11272 H | 6 | -9 | -6 
    11273 S |  | 6 | -6 
    11274 O |  |  | 4 
    11275 Iteration cutoff | 2 
    11276  
    11277 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#44)
    11278 with AF-gea2.pdb, chain A (#46), sequence alignment score = 5628 
    11279 RMSD between 756 pruned atom pairs is 1.152 angstroms; (across all 1222 pairs:
    11280 2.471) 
    11281  
    11282 
    11283 > ui tool show "Show Sequence Viewer"
    11284 
    11285 > sequence chain #46/A
    11286 
    11287 Alignment identifier is 46/A 
    11288 Drag select of 8 residues 
    11289 
    11290 > delete atoms sel
    11291 
    11292 > delete bonds sel
    11293 
    11294 > delete atoms sel
    11295 
    11296 > delete bonds sel
    11297 
    11298 > color sel #ffaaffff
    11299 
    11300 > select clear
    11301 
    11302 > select clear
    11303 
    11304 > mmaker #34 to #45
    11305 
    11306 Parameters 
    11307 --- 
    11308 Chain pairing | bb 
    11309 Alignment algorithm | Needleman-Wunsch 
    11310 Similarity matrix | BLOSUM-62 
    11311 SS fraction | 0.3 
    11312 Gap open (HH/SS/other) | 18/18/6 
    11313 Gap extend | 1 
    11314 SS matrix |  |  | H | S | O 
    11315 ---|---|---|--- 
    11316 H | 6 | -9 | -6 
    11317 S |  | 6 | -6 
    11318 O |  |  | 4 
    11319 Iteration cutoff | 2 
    11320  
    11321 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
    11322 with AF-gea1.pdb, chain A (#34), sequence alignment score = 3215.1 
    11323 RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
    11324 10.861) 
    11325  
    11326 
    11327 > show #!34 models
    11328 
    11329 > hide #!34 models
    11330 
    11331 > mmaker #34 to #44
    11332 
    11333 Parameters 
    11334 --- 
    11335 Chain pairing | bb 
    11336 Alignment algorithm | Needleman-Wunsch 
    11337 Similarity matrix | BLOSUM-62 
    11338 SS fraction | 0.3 
    11339 Gap open (HH/SS/other) | 18/18/6 
    11340 Gap extend | 1 
    11341 SS matrix |  |  | H | S | O 
    11342 ---|---|---|--- 
    11343 H | 6 | -9 | -6 
    11344 S |  | 6 | -6 
    11345 O |  |  | 4 
    11346 Iteration cutoff | 2 
    11347  
    11348 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#44)
    11349 with AF-gea1.pdb, chain A (#34), sequence alignment score = 3579.8 
    11350 RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
    11351 5.699) 
    11352  
    11353 
    11354 > show #!34 models
    11355 
    11356 > hide #!34 models
    11357 
    11358 > color sel #55ffffff
    11359 
    11360 > color sel #ffaaffff
    11361 
    11362 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    11363 > gea2.pdb
    11364 
    11365 AF-gea2.pdb title: 
    11366 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    11367 (P39993) [more info...] 
    11368  
    11369 Chain information for AF-gea2.pdb #47 
    11370 --- 
    11371 Chain | Description 
    11372 A | arf guanine-nucleotide exchange factor 2 
    11373  
    11374 
    11375 > mmaker #47 to #45
    11376 
    11377 Parameters 
    11378 --- 
    11379 Chain pairing | bb 
    11380 Alignment algorithm | Needleman-Wunsch 
    11381 Similarity matrix | BLOSUM-62 
    11382 SS fraction | 0.3 
    11383 Gap open (HH/SS/other) | 18/18/6 
    11384 Gap extend | 1 
    11385 SS matrix |  |  | H | S | O 
    11386 ---|---|---|--- 
    11387 H | 6 | -9 | -6 
    11388 S |  | 6 | -6 
    11389 O |  |  | 4 
    11390 Iteration cutoff | 2 
    11391  
    11392 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
    11393 with AF-gea2.pdb, chain A (#47), sequence alignment score = 4981.5 
    11394 RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
    11395 9.500) 
    11396  
    11397 
    11398 > ui tool show "Show Sequence Viewer"
    11399 
    11400 > sequence chain #47/A
    11401 
    11402 Alignment identifier is 47/A 
    11403 Drag select of 12 residues 
    11404 
    11405 > delete atoms sel
    11406 
    11407 > delete bonds sel
    11408 
    11409 > delete atoms sel
    11410 
    11411 > delete bonds sel
    11412 
    11413 > color sel #55ffffff
    11414 
    11415 > color sel #ffaaffff
    11416 
    11417 > preset cartoons/nucleotides cylinders/stubs
    11418 
    11419 Changed 0 atom styles 
    11420 Preset expands to these ChimeraX commands:
    11421 
    11422    
    11423    
    11424     show nucleic
    11425     hide protein|solvent|H
    11426     surf hide
    11427     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    11428     cartoon
    11429     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    11430     cartoon style ~(nucleic|strand) x round
    11431     cartoon style (nucleic|strand) x rect
    11432     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    11433     cartoon style nucleic x round width 1.6 thick 1.6
    11434     nucleotides stubs
    11435 
    11436  
    11437 
    11438 > select clear
    11439 
    11440 > color #44-47 #55ffffff
    11441 
    11442 > color #44-47 #ffaaffff
    11443 
    11444 > undo
    11445 
    11446 > undo
    11447 
    11448 > hide #47 models
    11449 
    11450 > show #47 models
    11451 
    11452 > close #47
    11453 
    11454 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    11455 > gea2.pdb
    11456 
    11457 AF-gea2.pdb title: 
    11458 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    11459 (P39993) [more info...] 
    11460  
    11461 Chain information for AF-gea2.pdb #47 
    11462 --- 
    11463 Chain | Description 
    11464 A | arf guanine-nucleotide exchange factor 2 
    11465  
    11466 
    11467 > mmaker #47 to #45
    11468 
    11469 Parameters 
    11470 --- 
    11471 Chain pairing | bb 
    11472 Alignment algorithm | Needleman-Wunsch 
    11473 Similarity matrix | BLOSUM-62 
    11474 SS fraction | 0.3 
    11475 Gap open (HH/SS/other) | 18/18/6 
    11476 Gap extend | 1 
    11477 SS matrix |  |  | H | S | O 
    11478 ---|---|---|--- 
    11479 H | 6 | -9 | -6 
    11480 S |  | 6 | -6 
    11481 O |  |  | 4 
    11482 Iteration cutoff | 2 
    11483  
    11484 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
    11485 with AF-gea2.pdb, chain A (#47), sequence alignment score = 4981.5 
    11486 RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
    11487 9.500) 
    11488  
    11489 
    11490 > ui tool show "Show Sequence Viewer"
    11491 
    11492 > sequence chain #47/A
    11493 
    11494 Alignment identifier is 47/A 
    11495 
    11496 > delete atoms sel
    11497 
    11498 > delete bonds sel
    11499 
    11500 > delete atoms sel
    11501 
    11502 > delete bonds sel
    11503 
    11504 > preset cartoons/nucleotides cylinders/stubs
    11505 
    11506 Changed 0 atom styles 
    11507 Preset expands to these ChimeraX commands:
    11508 
    11509    
    11510    
    11511     show nucleic
    11512     hide protein|solvent|H
    11513     surf hide
    11514     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    11515     cartoon
    11516     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    11517     cartoon style ~(nucleic|strand) x round
    11518     cartoon style (nucleic|strand) x rect
    11519     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    11520     cartoon style nucleic x round width 1.6 thick 1.6
    11521     nucleotides stubs
    11522 
    11523  
    11524 
    11525 > color sel #55ffffff
    11526 
    11527 > color sel #ffaaffff
    11528 
    11529 > show #!18 models
    11530 
    11531 > show #18.1 models
    11532 
    11533 > hide #18.1 models
    11534 
    11535 > show #30.14 models
    11536 
    11537 > show #31.7 models
    11538 
    11539 > hide #31.7 models
    11540 
    11541 > hide #!31 models
    11542 
    11543 > show #!15 models
    11544 
    11545 > show #15.15 models
    11546 
    11547 > hide #!18 models
    11548 
    11549 > show #14.1 models
    11550 
    11551 > hide #!15 models
    11552 
    11553 > hide #15.15 models
    11554 
    11555 > hide #14.1 models
    11556 
    11557 > hide #!14 models
    11558 
    11559 > hide #!30 models
    11560 
    11561 > hide #30.14 models
    11562 
    11563 > show #12.1 models
    11564 
    11565 > select clear
    11566 
    11567 > open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
    11568 
    11569 Chain information for ger2.pdb #48 
    11570 --- 
    11571 Chain | Description 
    11572 A | No description available 
    11573 C | No description available 
    11574  
    11575 
    11576 > mmaker #48 to #45
    11577 
    11578 Parameters 
    11579 --- 
    11580 Chain pairing | bb 
    11581 Alignment algorithm | Needleman-Wunsch 
    11582 Similarity matrix | BLOSUM-62 
    11583 SS fraction | 0.3 
    11584 Gap open (HH/SS/other) | 18/18/6 
    11585 Gap extend | 1 
    11586 SS matrix |  |  | H | S | O 
    11587 ---|---|---|--- 
    11588 H | 6 | -9 | -6 
    11589 S |  | 6 | -6 
    11590 O |  |  | 4 
    11591 Iteration cutoff | 2 
    11592  
    11593 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
    11594 with ger2.pdb, chain C (#48), sequence alignment score = 995.5 
    11595 RMSD between 173 pruned atom pairs is 1.250 angstroms; (across all 201 pairs:
    11596 1.472) 
    11597  
    11598 
    11599 > mmaker #12 to #48
    11600 
    11601 Parameters 
    11602 --- 
    11603 Chain pairing | bb 
    11604 Alignment algorithm | Needleman-Wunsch 
    11605 Similarity matrix | BLOSUM-62 
    11606 SS fraction | 0.3 
    11607 Gap open (HH/SS/other) | 18/18/6 
    11608 Gap extend | 1 
    11609 SS matrix |  |  | H | S | O 
    11610 ---|---|---|--- 
    11611 H | 6 | -9 | -6 
    11612 S |  | 6 | -6 
    11613 O |  |  | 4 
    11614 Iteration cutoff | 2 
    11615  
    11616 Matchmaker ger2.pdb, chain A (#48) with 2k5u.pdb, chain A (#12.1), sequence
    11617 alignment score = 695 
    11618 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    11619 5.084) 
    11620  
    11621 
    11622 > hide #48 models
    11623 
    11624 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/hemi.png
    11625 > transparentBackground true supersample 3
    11626 
    11627 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/hemi-side.png
    11628 > transparentBackground true supersample 3
    11629 
    11630 > turn 0 90
    11631 
    11632 Expected an axis vector or a keyword 
    11633 
    11634 > turn 1 90
    11635 
    11636 Expected an axis vector or a keyword 
    11637 
    11638 > turn x 1 90
    11639 
    11640 > turn x 1 90
    11641 
    11642 > turn x 1 90
    11643 
    11644 > turn x 1 90
    11645 
    11646 > turn y 1 90
    11647 
    11648 > turn y 1 90
    11649 
    11650 > turn y 1 90
    11651 
    11652 > rainbow #44-47#12.1
    11653 
    11654 > undo
    11655 
    11656 > preset "overall look" publication
    11657 
    11658 Preset expands to these ChimeraX commands:
    11659 
    11660    
    11661    
    11662     set bg white
    11663     graphics silhouettes t
    11664 
    11665  
    11666 
    11667 > lighting soft
    11668 
    11669 > lighting simple
    11670 
    11671 > lighting soft
    11672 
    11673 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11674 > figures/figures.cxs
    11675 
    11676 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11677 > figures/hemi-side.png transparentBackground true supersample 3
    11678 
    11679 > hide #47 models
    11680 
    11681 > hide #46 models
    11682 
    11683 > hide #45 models
    11684 
    11685 > hide #44 models
    11686 
    11687 > hide #12.1 models
    11688 
    11689 > hide #!12 models
    11690 
    11691 > show #1 models
    11692 
    11693 > show #4 models
    11694 
    11695 > show #!8 models
    11696 
    11697 > show #!26 models
    11698 
    11699 > hide #!26 models
    11700 
    11701 > show #25 models
    11702 
    11703 > show #24 models
    11704 
    11705 > hide #!8 models
    11706 
    11707 > hide #4 models
    11708 
    11709 > show #!26 models
    11710 
    11711 > hide #1 models
    11712 
    11713 > hide #!26 models
    11714 
    11715 > hide #25 models
    11716 
    11717 > hide #24 models
    11718 
    11719 > show #!26 models
    11720 
    11721 > show #!26 surfaces
    11722 
    11723 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/lipids.png
    11724 > transparentBackground true supersample 3
    11725 
    11726 > hide #!26 models
    11727 
    11728 > show #25 models
    11729 
    11730 > show #24 models
    11731 
    11732 > show #1 models
    11733 
    11734 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/closed-
    11735 > membrane.png transparentBackground true supersample 3
    11736 
    11737 > hide #1 models
    11738 
    11739 > show #4 models
    11740 
    11741 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/open-
    11742 > membrane.png transparentBackground true supersample 3
    11743 
    11744 > hide #4 models
    11745 
    11746 > show #!8 models
    11747 
    11748 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/complex-
    11749 > membrane.png transparentBackground true supersample 3
    11750 
    11751 > hide #25 models
    11752 
    11753 > hide #24 models
    11754 
    11755 > hide #!8 models
    11756 
    11757 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
    11758 > gea2.pdb
    11759 
    11760 AF-gea2.pdb title: 
    11761 Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
    11762 (P39993) [more info...] 
    11763  
    11764 Chain information for AF-gea2.pdb #49 
    11765 --- 
    11766 Chain | Description 
    11767 A | arf guanine-nucleotide exchange factor 2 
    11768  
    11769 
    11770 > alphafold #49
    11771 
    11772 Unknown command: palette alphafold #49 
    11773 
    11774 > color pallete
    11775 
    11776 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11777 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    11778 
    11779 > color pallete alphafold #49
    11780 
    11781 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11782 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    11783 
    11784 > color #49 pallete alphafold
    11785 
    11786 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11787 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    11788 
    11789 > color all #49 pallete alphafold
    11790 
    11791 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
    11792 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword 
    11793 
    11794 > ui tool show Log
    11795 
    11796 > select #49
    11797 
    11798 11659 atoms, 11853 bonds, 1459 residues, 1 model selected 
    11799 
    11800 > color bfactor sel
    11801 
    11802 11659 atoms, 1459 residues, atom bfactor range 21 to 98.4 
    11803 
    11804 > select clear
    11805 
    11806 > select #49
    11807 
    11808 11659 atoms, 11853 bonds, 1459 residues, 1 model selected 
    11809 
    11810 > color bfactor sel pallete alphafold
    11811 
    11812 > color byattribute bfactor sel pallete alphafold
    11813 
    11814 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    11815 or a keyword 
    11816 
    11817 > color bfactor sel pallete alphafold ribbons
    11818 
    11819 > color byattribute bfactor sel pallete alphafold ribbons
    11820 
    11821 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    11822 or a keyword 
    11823 
    11824 > color bfactor sel pallete ribbons alphafold
    11825 
    11826 > color byattribute bfactor sel pallete ribbons alphafold
    11827 
    11828 Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
    11829 or a keyword 
    11830 
    11831 > pallete alphafold
    11832 
    11833 Unknown command: pallete alphafold 
    11834 
    11835 > palete alphafold
    11836 
    11837 Unknown command: palete alphafold 
    11838 
    11839 > alphafold
    11840 
    11841 Unknown command: palette alphafold 
    11842 
    11843 >
    11844 
    11845 Incomplete command: palette 
    11846 
    11847 > alphafold
    11848 
    11849 Unknown command: palette alphafold 
    11850 
    11851 > ribbons alphafold
    11852 
    11853 Unknown command: palette ribbons alphafold 
    11854 
    11855 > alphafold
    11856 
    11857 Unknown command: alphafold 
    11858 
    11859 > select clear
    11860 
    11861 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11862 > figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
    11863 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11864 > figures/complex_dimer-FINAL-coot-7.pdb
    11865 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    11866 > figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
    11867 
    11868 Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #50 
    11869 --- 
    11870 Chain | Description 
    11871 A B | No description available 
    11872  
    11873 Chain information for complex_dimer-FINAL-coot-7.pdb #51 
    11874 --- 
    11875 Chain | Description 
    11876 A C | No description available 
    11877 B | No description available 
    11878 D | No description available 
    11879  
    11880 Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #52 
    11881 --- 
    11882 Chain | Description 
    11883 A B | No description available 
    11884  
    11885 
    11886 > select #50/B
    11887 
    11888 19822 atoms, 19979 bonds, 1222 residues, 1 model selected 
    11889 
    11890 > delete atoms sel
    11891 
    11892 > delete bonds sel
    11893 
    11894 > select #52/B
    11895 
    11896 18413 atoms, 18556 bonds, 1129 residues, 1 model selected 
    11897 
    11898 > delete atoms sel
    11899 
    11900 > delete bonds sel
    11901 
    11902 > select #51/C
    11903 
    11904 9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected 
    11905 
    11906 > delete atoms (#!51 & sel)
    11907 
    11908 > delete bonds (#!51 & sel)
    11909 
    11910 > mmaker #50-52 to #49
    11911 
    11912 Parameters 
    11913 --- 
    11914 Chain pairing | bb 
    11915 Alignment algorithm | Needleman-Wunsch 
    11916 Similarity matrix | BLOSUM-62 
    11917 SS fraction | 0.3 
    11918 Gap open (HH/SS/other) | 18/18/6 
    11919 Gap extend | 1 
    11920 SS matrix |  |  | H | S | O 
    11921 ---|---|---|--- 
    11922 H | 6 | -9 | -6 
    11923 S |  | 6 | -6 
    11924 O |  |  | 4 
    11925 Iteration cutoff | 2 
    11926  
    11927 Matchmaker AF-gea2.pdb, chain A (#49) with closed_dimer-FINAL-
    11928 coot-3_real_space_refined_206.pdb, chain A (#50), sequence alignment score =
    11929 5664 
    11930 RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
    11931 2.486) 
    11932  
    11933 Matchmaker AF-gea2.pdb, chain A (#49) with complex_dimer-FINAL-coot-7.pdb,
    11934 chain A (#51), sequence alignment score = 5315 
    11935 RMSD between 717 pruned atom pairs is 1.105 angstroms; (across all 1159 pairs:
    11936 7.498) 
    11937  
    11938 Matchmaker AF-gea2.pdb, chain A (#49) with open_dimer-FINAL-
    11939 coot-5_real_space_refined_208.pdb, chain A (#52), sequence alignment score =
    11940 4981.5 
    11941 RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
    11942 9.500) 
    11943  
    11944 Drag select of 164 residues 
    11945 
    11946 > delete atoms sel
    11947 
    11948 > delete bonds sel
    11949 
    11950 > hide #!51 models
    11951 
    11952 > hide #50 models
    11953 
    11954 > hide #52 models
    11955 
    11956 > show #50 models
    11957 
    11958 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
    11959 > transparentBackground true supersample "3\\\"
    11960 
    11961 Invalid "supersample" argument: Expected an integer 
    11962 
    11963 > hide #50 models
    11964 
    11965 > show #!51 models
    11966 
    11967 > select #51/B
    11968 
    11969 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    11970 
    11971 > color sel #55ffffff
    11972 
    11973 > color sel #ff5500ff
    11974 
    11975 > select clear
    11976 
    11977 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-complex.png
    11978 > transparentBackground true supersample 3
    11979 
    11980 > hide #!51 models
    11981 
    11982 > show #50 models
    11983 
    11984 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
    11985 > transparentBackground true supersample 3
    11986 
    11987 > hide #50 models
    11988 
    11989 > show #52 models
    11990 
    11991 > hide #52 models
    11992 
    11993 > hide #49 models
    11994 
    11995 > show #11 models
    11996 
    11997 > select #11/C
    11998 
    11999 1633 atoms, 1666 bonds, 201 residues, 1 model selected 
    12000 
    12001 > hide sel cartoons
    12002 
    12003 > select #11/A
    12004 
    12005 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    12006 
    12007 > color sel #788ae1ff
    12008 
    12009 > select clear
    12010 
    12011 > show #28 models
    12012 
    12013 > hide #28 models
    12014 
    12015 > show #47 models
    12016 
    12017 > show #46 models
    12018 
    12019 > show #44 models
    12020 
    12021 > hide #47 models
    12022 
    12023 > hide #46 models
    12024 
    12025 > hide #44 models
    12026 
    12027 > show #1 models
    12028 
    12029 > show #20 models
    12030 
    12031 > show #21 models
    12032 
    12033 > mmaker #11 to #1
    12034 
    12035 Parameters 
    12036 --- 
    12037 Chain pairing | bb 
    12038 Alignment algorithm | Needleman-Wunsch 
    12039 Similarity matrix | BLOSUM-62 
    12040 SS fraction | 0.3 
    12041 Gap open (HH/SS/other) | 18/18/6 
    12042 Gap extend | 1 
    12043 SS matrix |  |  | H | S | O 
    12044 ---|---|---|--- 
    12045 H | 6 | -9 | -6 
    12046 S |  | 6 | -6 
    12047 O |  |  | 4 
    12048 Iteration cutoff | 2 
    12049  
    12050 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    12051 with ger2.pdb, chain C (#11), sequence alignment score = 978.1 
    12052 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    12053 1.427) 
    12054  
    12055 
    12056 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    12057 > nfArf1.png transparentBackground true supersample 3
    12058 
    12059 > hide #1 models
    12060 
    12061 > hide #11 models
    12062 
    12063 > show #!8 models
    12064 
    12065 > select #8/D
    12066 
    12067 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    12068 
    12069 > hide sel cartoons
    12070 
    12071 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    12072 > nfArf1.png transparentBackground true supersample 3
    12073 
    12074 > hide #!8 models
    12075 
    12076 > select #8
    12077 
    12078 21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected 
    12079 
    12080 > hide #21 models
    12081 
    12082 > hide #20 models
    12083 
    12084 > show #11 models
    12085 
    12086 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/nfArf1.png
    12087 > transparentBackground true supersample 3
    12088 
    12089 > hide #11 models
    12090 
    12091 > ~select #8
    12092 
    12093 4 models selected 
    12094 
    12095 > show #11 models
    12096 
    12097 > show #1 models
    12098 
    12099 > show #20 models
    12100 
    12101 > show #21 models
    12102 
    12103 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
    12104 > nfArf1-side.png transparentBackground true supersample 3
    12105 
    12106 > hide #1 models
    12107 
    12108 > hide #21 models
    12109 
    12110 > hide #20 models
    12111 
    12112 > save
    12113 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/nfArf1-side.png
    12114 > transparentBackground true supersample 3
    12115 
    12116 > hide #11 models
    12117 
    12118 > show #!8 models
    12119 
    12120 > show #21 models
    12121 
    12122 > show #20 models
    12123 
    12124 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    12125 > nfArf1-side transparentBackground true supersample 3
    12126 
    12127 Cannot determine format for
    12128 'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    12129 nfArf1-side' 
    12130 
    12131 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    12132 > nfArf1-side.png transparentBackground true supersample 3
    12133 
    12134 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
    12135 > nfArf1-side.png transparentBackground true supersample 3
    12136 
    12137 > hide #20 models
    12138 
    12139 > hide #21 models
    12140 
    12141 > hide #!8 models
    12142 
    12143 > show #49 models
    12144 
    12145 > show #50 models
    12146 
    12147 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
    12148 > transparentBackground true supersample 3
    12149 
    12150 > hide #50 models
    12151 
    12152 > show #!51 models
    12153 
    12154 > hide #!51 models
    12155 
    12156 > show #50 models
    12157 
    12158 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
    12159 > transparentBackground true supersample 3
    12160 
    12161 > hide #50 models
    12162 
    12163 > show #!51 models
    12164 
    12165 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-complex.png
    12166 > transparentBackground true supersample 3
    12167 
    12168 > hide #!51 models
    12169 
    12170 > show #52 models
    12171 
    12172 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/af-open.png
    12173 > transparentBackground true supersample 3
    12174 
    12175 > hide #49 models
    12176 
    12177 > hide #52 models
    12178 
    12179 > show #44 models
    12180 
    12181 > hide #44 models
    12182 
    12183 > show #39 models
    12184 
    12185 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    12186 > figures/1r8s.pdb
    12187 
    12188 1r8s.pdb title: 
    12189 ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
    12190 catalytic glutamate to lysine [more info...] 
    12191  
    12192 Chain information for 1r8s.pdb #53 
    12193 --- 
    12194 Chain | Description 
    12195 A | adp-ribosylation factor 1 
    12196 E | ARNO 
    12197  
    12198 Non-standard residues in 1r8s.pdb #53 
    12199 --- 
    12200 BME — β-mercaptoethanol 
    12201 FMT — formic acid 
    12202 GDP — guanosine-5'-diphosphate 
    12203 SO3 — sulfite ion 
    12204 SO4 — sulfate ion 
    12205  
    12206 
    12207 > mmaker #53 to #39
    12208 
    12209 Parameters 
    12210 --- 
    12211 Chain pairing | bb 
    12212 Alignment algorithm | Needleman-Wunsch 
    12213 Similarity matrix | BLOSUM-62 
    12214 SS fraction | 0.3 
    12215 Gap open (HH/SS/other) | 18/18/6 
    12216 Gap extend | 1 
    12217 SS matrix |  |  | H | S | O 
    12218 ---|---|---|--- 
    12219 H | 6 | -9 | -6 
    12220 S |  | 6 | -6 
    12221 O |  |  | 4 
    12222 Iteration cutoff | 2 
    12223  
    12224 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    12225 with 1r8s.pdb, chain E (#53), sequence alignment score = 432.1 
    12226 RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
    12227 5.093) 
    12228  
    12229 
    12230 > select #53
    12231 
    12232 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    12233 
    12234 > hide sel cartoons
    12235 
    12236 > show sel cartoons
    12237 
    12238 > hide sel atoms
    12239 
    12240 > select clear
    12241 
    12242 > select #53/A
    12243 
    12244 1471 atoms, 1345 bonds, 312 residues, 1 model selected 
    12245 
    12246 > select #53/E
    12247 
    12248 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    12249 
    12250 > hide sel surfaces
    12251 
    12252 > hide sel cartoons
    12253 
    12254 > preset cartoons/nucleotides cylinders/stubs
    12255 
    12256 Changed 0 atom styles 
    12257 Preset expands to these ChimeraX commands:
    12258 
    12259    
    12260    
    12261     show nucleic
    12262     hide protein|solvent|H
    12263     surf hide
    12264     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    12265     cartoon
    12266     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    12267     cartoon style ~(nucleic|strand) x round
    12268     cartoon style (nucleic|strand) x rect
    12269     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    12270     cartoon style nucleic x round width 1.6 thick 1.6
    12271     nucleotides stubs
    12272 
    12273  
    12274 
    12275 > select clear
    12276 
    12277 > select #53/E
    12278 
    12279 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    12280 
    12281 > hide sel atoms
    12282 
    12283 > hide sel cartoons
    12284 
    12285 > ui tool show "Side View"
    12286 
    12287 > ui tool show "Side View"
    12288 
    12289 > ui tool show "Side View"
    12290 
    12291 > ui tool show "Side View"
    12292 
    12293 > toolshed show
    12294 
    12295 > lighting soft
    12296 
    12297 > lighting full
    12298 
    12299 > lighting soft
    12300 
    12301 > lighting simple
    12302 
    12303 > lighting soft
    12304 
    12305 > hide #39 models
    12306 
    12307 > show #38 models
    12308 
    12309 > show #41 models
    12310 
    12311 > show #39 models
    12312 
    12313 > hide #41 models
    12314 
    12315 > hide #53 models
    12316 
    12317 > show #!40 models
    12318 
    12319 > hide #!40 models
    12320 
    12321 > show #41 models
    12322 
    12323 > hide #41 models
    12324 
    12325 > show #41 models
    12326 
    12327 > show #53 models
    12328 
    12329 > mmaker #53 to #41
    12330 
    12331 Parameters 
    12332 --- 
    12333 Chain pairing | bb 
    12334 Alignment algorithm | Needleman-Wunsch 
    12335 Similarity matrix | BLOSUM-62 
    12336 SS fraction | 0.3 
    12337 Gap open (HH/SS/other) | 18/18/6 
    12338 Gap extend | 1 
    12339 SS matrix |  |  | H | S | O 
    12340 ---|---|---|--- 
    12341 H | 6 | -9 | -6 
    12342 S |  | 6 | -6 
    12343 O |  |  | 4 
    12344 Iteration cutoff | 2 
    12345  
    12346 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
    12347 with 1r8s.pdb, chain E (#53), sequence alignment score = 444.6 
    12348 RMSD between 129 pruned atom pairs is 1.311 angstroms; (across all 185 pairs:
    12349 2.676) 
    12350  
    12351 
    12352 > hide #41 models
    12353 
    12354 > hide #53 models
    12355 
    12356 > show #!40 models
    12357 
    12358 > hide #39 models
    12359 
    12360 > hide #38 models
    12361 
    12362 > hide #!40 models
    12363 
    12364 > show #39 models
    12365 
    12366 > show #53 models
    12367 
    12368 > hide #53 models
    12369 
    12370 > show #53 models
    12371 
    12372 > mmaker #53 to #39
    12373 
    12374 Parameters 
    12375 --- 
    12376 Chain pairing | bb 
    12377 Alignment algorithm | Needleman-Wunsch 
    12378 Similarity matrix | BLOSUM-62 
    12379 SS fraction | 0.3 
    12380 Gap open (HH/SS/other) | 18/18/6 
    12381 Gap extend | 1 
    12382 SS matrix |  |  | H | S | O 
    12383 ---|---|---|--- 
    12384 H | 6 | -9 | -6 
    12385 S |  | 6 | -6 
    12386 O |  |  | 4 
    12387 Iteration cutoff | 2 
    12388  
    12389 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    12390 with 1r8s.pdb, chain E (#53), sequence alignment score = 432.1 
    12391 RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
    12392 5.093) 
    12393  
    12394 
    12395 > show #43 models
    12396 
    12397 > hide #43 models
    12398 
    12399 > show #42 models
    12400 
    12401 > hide #42 models
    12402 
    12403 > show #48 models
    12404 
    12405 > hide #48 models
    12406 
    12407 > hide #39 models
    12408 
    12409 > show #!40 models
    12410 
    12411 > hide #!40 models
    12412 
    12413 > show #39 models
    12414 
    12415 > show #42 models
    12416 
    12417 > hide #42 models
    12418 
    12419 > show #42 models
    12420 
    12421 > select #42/C
    12422 
    12423 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    12424 
    12425 > hide sel cartoons
    12426 
    12427 > hide #53 models
    12428 
    12429 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12430 > nucleotidefree.png transparentBackground true supersample 3
    12431 
    12432 > hide #42 models
    12433 
    12434 > show #53 models
    12435 
    12436 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
    12437 > transparentBackground true supersample 3
    12438 
    12439 > hide #39 models
    12440 
    12441 > hide #53 models
    12442 
    12443 > show #!40 models
    12444 
    12445 > hide #!40 models
    12446 
    12447 > show #39 models
    12448 
    12449 > show #53 models
    12450 
    12451 > show #!40 models
    12452 
    12453 > hide #!40 models
    12454 
    12455 > show #!40 models
    12456 
    12457 > hide #39 models
    12458 
    12459 > hide #53 models
    12460 
    12461 > show #53 models
    12462 
    12463 > hide #53 models
    12464 
    12465 > show #53 models
    12466 
    12467 > hide #!40 models
    12468 
    12469 > show #39 models
    12470 
    12471 > show #!40 models
    12472 
    12473 > hide #39 models
    12474 
    12475 > show #39 models
    12476 
    12477 > hide #!40 models
    12478 
    12479 > hide #39 models
    12480 
    12481 > show #42 models
    12482 
    12483 > hide #53 models
    12484 
    12485 > show #39 models
    12486 
    12487 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12488 > nucleotidefree.png transparentBackground true supersample 3
    12489 
    12490 > hide #42 models
    12491 
    12492 > show #53 models
    12493 
    12494 > show #42 models
    12495 
    12496 > hide #42 models
    12497 
    12498 > show #42 models
    12499 
    12500 > hide #42 models
    12501 
    12502 > show #42 models
    12503 
    12504 > select #42/C
    12505 
    12506 1635 atoms, 1668 bonds, 201 residues, 1 model selected 
    12507 
    12508 > show sel cartoons
    12509 
    12510 > hide sel cartoons
    12511 
    12512 > hide #42 models
    12513 
    12514 > show #42 models
    12515 
    12516 > hide #53 models
    12517 
    12518 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12519 > nucleotidefree.png transparentBackground true supersample 3
    12520 
    12521 > hide #42 models
    12522 
    12523 > show #53 models
    12524 
    12525 > show #42 models
    12526 
    12527 > hide #42 models
    12528 
    12529 > show #42 models
    12530 
    12531 > hide #42 models
    12532 
    12533 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
    12534 > transparentBackground true supersample 3
    12535 
    12536 > hide #39 models
    12537 
    12538 > show #!40 models
    12539 
    12540 > hide #53 models
    12541 
    12542 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12543 > complex.png transparentBackground true supersample 3
    12544 
    12545 > show #53 models
    12546 
    12547 > hide #!40 models
    12548 
    12549 > show #38 models
    12550 
    12551 > hide #38 models
    12552 
    12553 > show #39 models
    12554 
    12555 > show #!40 models
    12556 
    12557 > hide #!40 models
    12558 
    12559 > show #!40 models
    12560 
    12561 > hide #39 models
    12562 
    12563 > show #39 models
    12564 
    12565 > hide #!40 models
    12566 
    12567 > show #!40 models
    12568 
    12569 > hide #53 models
    12570 
    12571 > hide #39 models
    12572 
    12573 > show #39 models
    12574 
    12575 > hide #!40 models
    12576 
    12577 > show #53 models
    12578 
    12579 > show #!40 models
    12580 
    12581 > hide #39 models
    12582 
    12583 > show #39 models
    12584 
    12585 > hide #!40 models
    12586 
    12587 > show #!40 models
    12588 
    12589 > hide #!40 models
    12590 
    12591 > show #!40 models
    12592 
    12593 > hide #39 models
    12594 
    12595 > show #39 models
    12596 
    12597 > hide #!40 models
    12598 
    12599 > show #!40 models
    12600 
    12601 > hide #39 models
    12602 
    12603 > show #39 models
    12604 
    12605 > hide #!40 models
    12606 
    12607 > show #!40 models
    12608 
    12609 > hide #!40 models
    12610 
    12611 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
    12612 > transparentBackground true supersample 3
    12613 
    12614 > hide #53 models
    12615 
    12616 > show #42 models
    12617 
    12618 > hide #42 models
    12619 
    12620 > show #!40 models
    12621 
    12622 > hide #39 models
    12623 
    12624 > show #39 models
    12625 
    12626 > show #53 models
    12627 
    12628 > hide #39 models
    12629 
    12630 > show #39 models
    12631 
    12632 > hide #!40 models
    12633 
    12634 > show #41 models
    12635 
    12636 > select #42
    12637 
    12638 2990 atoms, 3024 bonds, 389 residues, 1 model selected 
    12639 
    12640 > ~select #42
    12641 
    12642 Nothing selected 
    12643 
    12644 > hide #41 models
    12645 
    12646 > show #!40 models
    12647 
    12648 > hide #39 models
    12649 
    12650 > show #39 models
    12651 
    12652 > hide #!40 models
    12653 
    12654 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
    12655 > transparentBackground true supersample 3
    12656 
    12657 > show #42 models
    12658 
    12659 > hide #39 models
    12660 
    12661 > show #39 models
    12662 
    12663 > hide #53 models
    12664 
    12665 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12666 > nucleotidefree.png transparentBackground true supersample 3
    12667 
    12668 > hide #42 models
    12669 
    12670 > hide #39 models
    12671 
    12672 > show #!40 models
    12673 
    12674 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
    12675 > complex.png transparentBackground true supersample 3
    12676 
    12677 > show #39 models
    12678 
    12679 > hide #!40 models
    12680 
    12681 > show #53 models
    12682 
    12683 > hide #53 models
    12684 
    12685 > hide #39 models
    12686 
    12687 > show #!40 models
    12688 
    12689 > hide #!40 models
    12690 
    12691 > show #!40 models
    12692 
    12693 > show #!31 models
    12694 
    12695 > hide #!31 models
    12696 
    12697 > show #31.7 models
    12698 
    12699 > mmaker #31 to #40
    12700 
    12701 Parameters 
    12702 --- 
    12703 Chain pairing | bb 
    12704 Alignment algorithm | Needleman-Wunsch 
    12705 Similarity matrix | BLOSUM-62 
    12706 SS fraction | 0.3 
    12707 Gap open (HH/SS/other) | 18/18/6 
    12708 Gap extend | 1 
    12709 SS matrix |  |  | H | S | O 
    12710 ---|---|---|--- 
    12711 H | 6 | -9 | -6 
    12712 S |  | 6 | -6 
    12713 O |  |  | 4 
    12714 Iteration cutoff | 2 
    12715  
    12716 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain B (#40) with 2ksq.pdb, chain
    12717 A (#31.7), sequence alignment score = 642.9 
    12718 RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
    12719 4.069) 
    12720  
    12721 
    12722 > show #38 models
    12723 
    12724 > hide #38 models
    12725 
    12726 > show #41 models
    12727 
    12728 > hide #!40 models
    12729 
    12730 > show #43 models
    12731 
    12732 > mmaker #43 to #41
    12733 
    12734 Parameters 
    12735 --- 
    12736 Chain pairing | bb 
    12737 Alignment algorithm | Needleman-Wunsch 
    12738 Similarity matrix | BLOSUM-62 
    12739 SS fraction | 0.3 
    12740 Gap open (HH/SS/other) | 18/18/6 
    12741 Gap extend | 1 
    12742 SS matrix |  |  | H | S | O 
    12743 ---|---|---|--- 
    12744 H | 6 | -9 | -6 
    12745 S |  | 6 | -6 
    12746 O |  |  | 4 
    12747 Iteration cutoff | 2 
    12748  
    12749 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
    12750 with ger2.pdb, chain C (#43), sequence alignment score = 1010.5 
    12751 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    12752 1.454) 
    12753  
    12754 
    12755 > mmaker #31 to #43
    12756 
    12757 Parameters 
    12758 --- 
    12759 Chain pairing | bb 
    12760 Alignment algorithm | Needleman-Wunsch 
    12761 Similarity matrix | BLOSUM-62 
    12762 SS fraction | 0.3 
    12763 Gap open (HH/SS/other) | 18/18/6 
    12764 Gap extend | 1 
    12765 SS matrix |  |  | H | S | O 
    12766 ---|---|---|--- 
    12767 H | 6 | -9 | -6 
    12768 S |  | 6 | -6 
    12769 O |  |  | 4 
    12770 Iteration cutoff | 2 
    12771  
    12772 Matchmaker ger2.pdb, chain A (#43) with 2ksq.pdb, chain A (#31.7), sequence
    12773 alignment score = 665.1 
    12774 RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    12775 3.623) 
    12776  
    12777 
    12778 > hide #43 models
    12779 
    12780 > show #!40 models
    12781 
    12782 > hide #!40 models
    12783 
    12784 > show #42 models
    12785 
    12786 > hide #42 models
    12787 
    12788 > show #43 models
    12789 
    12790 > mmaker #43 to #41
    12791 
    12792 Parameters 
    12793 --- 
    12794 Chain pairing | bb 
    12795 Alignment algorithm | Needleman-Wunsch 
    12796 Similarity matrix | BLOSUM-62 
    12797 SS fraction | 0.3 
    12798 Gap open (HH/SS/other) | 18/18/6 
    12799 Gap extend | 1 
    12800 SS matrix |  |  | H | S | O 
    12801 ---|---|---|--- 
    12802 H | 6 | -9 | -6 
    12803 S |  | 6 | -6 
    12804 O |  |  | 4 
    12805 Iteration cutoff | 2 
    12806  
    12807 Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
    12808 with ger2.pdb, chain C (#43), sequence alignment score = 1010.5 
    12809 RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
    12810 1.454) 
    12811  
    12812 
    12813 > mmaker #31.7 to #43
    12814 
    12815 Parameters 
    12816 --- 
    12817 Chain pairing | bb 
    12818 Alignment algorithm | Needleman-Wunsch 
    12819 Similarity matrix | BLOSUM-62 
    12820 SS fraction | 0.3 
    12821 Gap open (HH/SS/other) | 18/18/6 
    12822 Gap extend | 1 
    12823 SS matrix |  |  | H | S | O 
    12824 ---|---|---|--- 
    12825 H | 6 | -9 | -6 
    12826 S |  | 6 | -6 
    12827 O |  |  | 4 
    12828 Iteration cutoff | 2 
    12829  
    12830 Matchmaker ger2.pdb, chain A (#43) with 2ksq.pdb, chain A (#31.7), sequence
    12831 alignment score = 665.1 
    12832 RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
    12833 3.623) 
    12834  
    12835 
    12836 > hide #43 models
    12837 
    12838 > show #!40 models
    12839 
    12840 > hide #41 models
    12841 
    12842 > hide #31.7 models
    12843 
    12844 > hide #!40 models
    12845 
    12846 > show #41 models
    12847 
    12848 > show #31.7 models
    12849 
    12850 > mmaker #31.7 to #40
    12851 
    12852 Parameters 
    12853 --- 
    12854 Chain pairing | bb 
    12855 Alignment algorithm | Needleman-Wunsch 
    12856 Similarity matrix | BLOSUM-62 
    12857 SS fraction | 0.3 
    12858 Gap open (HH/SS/other) | 18/18/6 
    12859 Gap extend | 1 
    12860 SS matrix |  |  | H | S | O 
    12861 ---|---|---|--- 
    12862 H | 6 | -9 | -6 
    12863 S |  | 6 | -6 
    12864 O |  |  | 4 
    12865 Iteration cutoff | 2 
    12866  
    12867 Matchmaker complex_dimer-FINAL-coot-7.pdb, chain B (#40) with 2ksq.pdb, chain
    12868 A (#31.7), sequence alignment score = 642.9 
    12869 RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
    12870 4.069) 
    12871  
    12872 
    12873 > hide #41 models
    12874 
    12875 > show #!40 models
    12876 
    12877 > hide #!40 models
    12878 
    12879 > show #!40 models
    12880 
    12881 > select #40/B
    12882 
    12883 1332 atoms, 1356 bonds, 165 residues, 1 model selected 
    12884 
    12885 > hide sel cartoons
    12886 
    12887 > show sel cartoons
    12888 
    12889 > hide sel cartoons
    12890 
    12891 > hide #!40 models
    12892 
    12893 > select #40
    12894 
    12895 21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected 
    12896 
    12897 > ~select #40
    12898 
    12899 Nothing selected 
    12900 
    12901 > hide #31.7 models
    12902 
    12903 > hide #!31 models
    12904 
    12905 > show #1 models
    12906 
    12907 > show #!12 models
    12908 
    12909 > show #12.1 models
    12910 
    12911 > hide #12.1 models
    12912 
    12913 > hide #!12 models
    12914 
    12915 > show #15.15 models
    12916 
    12917 > hide #15.15 models
    12918 
    12919 > hide #!15 models
    12920 
    12921 > show #!15 models
    12922 
    12923 > show #!17 models
    12924 
    12925 > show #!18 models
    12926 
    12927 > show #17.1 models
    12928 
    12929 > hide #17.1 models
    12930 
    12931 > hide #!17 models
    12932 
    12933 > show #16 models
    12934 
    12935 > mmaker #16 to #1
    12936 
    12937 Parameters 
    12938 --- 
    12939 Chain pairing | bb 
    12940 Alignment algorithm | Needleman-Wunsch 
    12941 Similarity matrix | BLOSUM-62 
    12942 SS fraction | 0.3 
    12943 Gap open (HH/SS/other) | 18/18/6 
    12944 Gap extend | 1 
    12945 SS matrix |  |  | H | S | O 
    12946 ---|---|---|--- 
    12947 H | 6 | -9 | -6 
    12948 S |  | 6 | -6 
    12949 O |  |  | 4 
    12950 Iteration cutoff | 2 
    12951  
    12952 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    12953 with ger2.pdb, chain C (#16), sequence alignment score = 978.1 
    12954 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    12955 1.427) 
    12956  
    12957 
    12958 > show #18.1 models
    12959 
    12960 > hide #18.1 models
    12961 
    12962 > show #17.1 models
    12963 
    12964 > mmaker #17 to #18
    12965 
    12966 Parameters 
    12967 --- 
    12968 Chain pairing | bb 
    12969 Alignment algorithm | Needleman-Wunsch 
    12970 Similarity matrix | BLOSUM-62 
    12971 SS fraction | 0.3 
    12972 Gap open (HH/SS/other) | 18/18/6 
    12973 Gap extend | 1 
    12974 SS matrix |  |  | H | S | O 
    12975 ---|---|---|--- 
    12976 H | 6 | -9 | -6 
    12977 S |  | 6 | -6 
    12978 O |  |  | 4 
    12979 Iteration cutoff | 2 
    12980  
    12981 Matchmaker 2k5u.pdb, chain A (#18.1) with 2k5u.pdb, chain A (#17.1), sequence
    12982 alignment score = 926 
    12983 RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
    12984 0.000) 
    12985  
    12986 
    12987 > mmaker #17 to #16
    12988 
    12989 Parameters 
    12990 --- 
    12991 Chain pairing | bb 
    12992 Alignment algorithm | Needleman-Wunsch 
    12993 Similarity matrix | BLOSUM-62 
    12994 SS fraction | 0.3 
    12995 Gap open (HH/SS/other) | 18/18/6 
    12996 Gap extend | 1 
    12997 SS matrix |  |  | H | S | O 
    12998 ---|---|---|--- 
    12999 H | 6 | -9 | -6 
    13000 S |  | 6 | -6 
    13001 O |  |  | 4 
    13002 Iteration cutoff | 2 
    13003  
    13004 Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
    13005 alignment score = 695 
    13006 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    13007 5.084) 
    13008  
    13009 
    13010 > hide #16 models
    13011 
    13012 > show #16 models
    13013 
    13014 > hide #16 models
    13015 
    13016 > hide #!15 models
    13017 
    13018 > show #!15 models
    13019 
    13020 > hide #!15 models
    13021 
    13022 > hide #!18 models
    13023 
    13024 > hide #17.1 models
    13025 
    13026 > show #17.1 models
    13027 
    13028 > mmaker #17 to #16
    13029 
    13030 Parameters 
    13031 --- 
    13032 Chain pairing | bb 
    13033 Alignment algorithm | Needleman-Wunsch 
    13034 Similarity matrix | BLOSUM-62 
    13035 SS fraction | 0.3 
    13036 Gap open (HH/SS/other) | 18/18/6 
    13037 Gap extend | 1 
    13038 SS matrix |  |  | H | S | O 
    13039 ---|---|---|--- 
    13040 H | 6 | -9 | -6 
    13041 S |  | 6 | -6 
    13042 O |  |  | 4 
    13043 Iteration cutoff | 2 
    13044  
    13045 Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
    13046 alignment score = 695 
    13047 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    13048 5.084) 
    13049  
    13050 
    13051 > show #31.7 models
    13052 
    13053 > hide #31.7 models
    13054 
    13055 > show #!30 models
    13056 
    13057 > show #!27 models
    13058 
    13059 > show #!37 models
    13060 
    13061 > hide #!37 models
    13062 
    13063 > show #39 models
    13064 
    13065 > hide #39 models
    13066 
    13067 > show #42 models
    13068 
    13069 > hide #42 models
    13070 
    13071 > show #43 models
    13072 
    13073 > hide #43 models
    13074 
    13075 > show #43 models
    13076 
    13077 > hide #!31 models
    13078 
    13079 > hide #!30 models
    13080 
    13081 > mmaker #17 to #43/A
    13082 
    13083 Parameters 
    13084 --- 
    13085 Chain pairing | bb 
    13086 Alignment algorithm | Needleman-Wunsch 
    13087 Similarity matrix | BLOSUM-62 
    13088 SS fraction | 0.3 
    13089 Gap open (HH/SS/other) | 18/18/6 
    13090 Gap extend | 1 
    13091 SS matrix |  |  | H | S | O 
    13092 ---|---|---|--- 
    13093 H | 6 | -9 | -6 
    13094 S |  | 6 | -6 
    13095 O |  |  | 4 
    13096 Iteration cutoff | 2 
    13097  
    13098 Matchmaker ger2.pdb, chain A (#43) with 2k5u.pdb, chain A (#17.1), sequence
    13099 alignment score = 695 
    13100 RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
    13101 5.084) 
    13102  
    13103 
    13104 > mmaker #43/C to #1/A bring #17
    13105 
    13106 Parameters 
    13107 --- 
    13108 Chain pairing | bb 
    13109 Alignment algorithm | Needleman-Wunsch 
    13110 Similarity matrix | BLOSUM-62 
    13111 SS fraction | 0.3 
    13112 Gap open (HH/SS/other) | 18/18/6 
    13113 Gap extend | 1 
    13114 SS matrix |  |  | H | S | O 
    13115 ---|---|---|--- 
    13116 H | 6 | -9 | -6 
    13117 S |  | 6 | -6 
    13118 O |  |  | 4 
    13119 Iteration cutoff | 2 
    13120  
    13121 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
    13122 with ger2.pdb, chain C (#43), sequence alignment score = 978.1 
    13123 RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
    13124 1.427) 
    13125  
    13126 
    13127 > hide #43 models
    13128 
    13129 > show #53 models
    13130 
    13131 > hide #!27 models
    13132 
    13133 > hide #17.1 models
    13134 
    13135 > hide #!17 models
    13136 
    13137 > show #50 models
    13138 
    13139 > hide #50 models
    13140 
    13141 > show #44 models
    13142 
    13143 > hide #44 models
    13144 
    13145 > show #39 models
    13146 
    13147 > hide #1 models
    13148 
    13149 > select ::name="GDP"
    13150 
    13151 828 atoms, 870 bonds, 21 residues, 21 models selected 
    13152 
    13153 > select #27
    13154 
    13155 47232 atoms, 47696 bonds, 2912 residues, 17 models selected 
    13156 
    13157 > ~select #27
    13158 
    13159 Nothing selected 
    13160 
    13161 > select #53 ::name="GDP"
    13162 
    13163 28 atoms, 30 bonds, 1 residue, 1 model selected 
    13164 
    13165 > show sel atoms
    13166 
    13167 > color sel #ff007fff
    13168 
    13169 > color sel #ffffffff
    13170 
    13171 > color sel #ff007fff
    13172 
    13173 > color sel byhetero
    13174 
    13175 > select clear
    13176 
    13177 > mmaker #1 to #39
    13178 
    13179 Parameters 
    13180 --- 
    13181 Chain pairing | bb 
    13182 Alignment algorithm | Needleman-Wunsch 
    13183 Similarity matrix | BLOSUM-62 
    13184 SS fraction | 0.3 
    13185 Gap open (HH/SS/other) | 18/18/6 
    13186 Gap extend | 1 
    13187 SS matrix |  |  | H | S | O 
    13188 ---|---|---|--- 
    13189 H | 6 | -9 | -6 
    13190 S |  | 6 | -6 
    13191 O |  |  | 4 
    13192 Iteration cutoff | 2 
    13193  
    13194 Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
    13195 with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1),
    13196 sequence alignment score = 6255.8 
    13197 RMSD between 1222 pruned atom pairs is 0.000 angstroms; (across all 1222
    13198 pairs: 0.000) 
    13199  
    13200 
    13201 > show #1 models
    13202 
    13203 > hide #39 models
    13204 
    13205 > ui tool show "Show Sequence Viewer"
    13206 
    13207 > sequence chain #1/A
    13208 
    13209 Alignment identifier is 1/A 
    13210 
    13211 > show #38 models
    13212 
    13213 > hide #38 models
    13214 
    13215 > show #39 models
    13216 
    13217 Drag select of 14 residues 
    13218 
    13219 > select clear
    13220 
    13221 Drag select of 2 residues 
    13222 
    13223 > color sel #550000ff
    13224 
    13225 > color sel #aa0000ff
    13226 
    13227 > color sel #ffffffff
    13228 
    13229 > color sel #aa0000ff
    13230 
    13231 > select clear
    13232 
    13233 > hide #39 models
    13234 
    13235 > show #39 models
    13236 
    13237 > hide #39 models
    13238 
    13239 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13240 > figures/1r8s.pdb
    13241 
    13242 1r8s.pdb title: 
    13243 ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
    13244 catalytic glutamate to lysine [more info...] 
    13245  
    13246 Chain information for 1r8s.pdb #54 
    13247 --- 
    13248 Chain | Description 
    13249 A | adp-ribosylation factor 1 
    13250 E | ARNO 
    13251  
    13252 Non-standard residues in 1r8s.pdb #54 
    13253 --- 
    13254 BME — β-mercaptoethanol 
    13255 FMT — formic acid 
    13256 GDP — guanosine-5'-diphosphate 
    13257 SO3 — sulfite ion 
    13258 SO4 — sulfate ion 
    13259  
    13260 
    13261 > mmaker #54 to #53
    13262 
    13263 Parameters 
    13264 --- 
    13265 Chain pairing | bb 
    13266 Alignment algorithm | Needleman-Wunsch 
    13267 Similarity matrix | BLOSUM-62 
    13268 SS fraction | 0.3 
    13269 Gap open (HH/SS/other) | 18/18/6 
    13270 Gap extend | 1 
    13271 SS matrix |  |  | H | S | O 
    13272 ---|---|---|--- 
    13273 H | 6 | -9 | -6 
    13274 S |  | 6 | -6 
    13275 O |  |  | 4 
    13276 Iteration cutoff | 2 
    13277  
    13278 Matchmaker 1r8s.pdb, chain E (#53) with 1r8s.pdb, chain E (#54), sequence
    13279 alignment score = 1042.5 
    13280 RMSD between 187 pruned atom pairs is 0.000 angstroms; (across all 187 pairs:
    13281 0.000) 
    13282  
    13283 
    13284 > select #54/E
    13285 
    13286 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    13287 
    13288 > hide sel atoms
    13289 
    13290 > hide sel cartoons
    13291 
    13292 > preset #54 cartoons/nucleotides cylinders/stubs
    13293 
    13294 No preset name matches '#54 cartoons/nucleotides cylinders/stubs' 
    13295 
    13296 > preset #54 cartoons/nucleotides cylinders/stubs
    13297 
    13298 No preset name matches '#54 cartoons/nucleotides cylinders/stubs' 
    13299 
    13300 > preset cartoons/nucleotides cylinders/stubs #54
    13301 
    13302 No preset name in category 'Cartoons/Nucleotides' matches 'cylinders/stubs
    13303 #54' 
    13304 
    13305 > preset cartoons/nucleotides cylinders/stubs
    13306 
    13307 No preset name in category 'Cartoons/Nucleotides' matches 'cylinders/stubs ' 
    13308 
    13309 > preset #54 cartoons/nucleotides Cylinders/Stubs
    13310 
    13311 No preset name matches '#54 cartoons/nucleotides Cylinders/Stubs ' 
    13312 
    13313 > preset cartoons/nucleotides cylinders/stubs
    13314 
    13315 Changed 0 atom styles 
    13316 Preset expands to these ChimeraX commands:
    13317 
    13318    
    13319    
    13320     show nucleic
    13321     hide protein|solvent|H
    13322     surf hide
    13323     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    13324     cartoon
    13325     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    13326     cartoon style ~(nucleic|strand) x round
    13327     cartoon style (nucleic|strand) x rect
    13328     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    13329     cartoon style nucleic x round width 1.6 thick 1.6
    13330     nucleotides stubs
    13331 
    13332  
    13333 
    13334 > hide sel cartoons
    13335 
    13336 > select #54/E
    13337 
    13338 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    13339 
    13340 > hide #53 models
    13341 
    13342 > show #53 models
    13343 
    13344 > select #53/E
    13345 
    13346 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    13347 
    13348 > hide sel cartoons
    13349 
    13350 > hide #53 models
    13351 
    13352 > select #54
    13353 
    13354 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    13355 
    13356 > select #53
    13357 
    13358 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    13359 
    13360 > ~select #53
    13361 
    13362 Nothing selected 
    13363 
    13364 > select #54
    13365 
    13366 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    13367 
    13368 > hide sel atoms
    13369 
    13370 > select #54 ::name="GDP"
    13371 
    13372 28 atoms, 30 bonds, 1 residue, 1 model selected 
    13373 
    13374 > color sel #ff007fff
    13375 
    13376 > color sel byhetero
    13377 
    13378 > hide #54 models
    13379 
    13380 > select #54
    13381 
    13382 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    13383 
    13384 > ~select #54
    13385 
    13386 Nothing selected 
    13387 
    13388 > show #53 models
    13389 
    13390 > hide #53 models
    13391 
    13392 > show #54 models
    13393 
    13394 > select #54 ::name="GDP"
    13395 
    13396 28 atoms, 30 bonds, 1 residue, 1 model selected 
    13397 
    13398 > show sel atoms
    13399 
    13400 > select clear
    13401 
    13402 > select #54
    13403 
    13404 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    13405 
    13406 > ui mousemode right "translate selected models"
    13407 
    13408 > morph #53,54
    13409 
    13410 Computed 21 frame morph #55 
    13411 
    13412 > coordset #55 1,21
    13413 
    13414 > close #55
    13415 
    13416 > morph #54,53
    13417 
    13418 Computed 21 frame morph #55 
    13419 
    13420 > coordset #55 1,21
    13421 
    13422 > show #!8 models
    13423 
    13424 > show #!9 models
    13425 
    13426 > hide #!8 models
    13427 
    13428 > hide #!9 models
    13429 
    13430 > show #!40 models
    13431 
    13432 > hide #55 models
    13433 
    13434 > show #52 models
    13435 
    13436 > hide #52 models
    13437 
    13438 > ~select #54
    13439 
    13440 Nothing selected 
    13441 
    13442 > hide #1 models
    13443 
    13444 > show #41 models
    13445 
    13446 > hide #41 models
    13447 
    13448 > show #39 models
    13449 
    13450 > morph #39,40
    13451 
    13452 models have different number of chains, 2 (Morph - closed_dimer-FINAL-
    13453 coot-3_real_space_refined_206.pdb #/A,Morph - closed_dimer-FINAL-
    13454 coot-3_real_space_refined_206.pdb #/B) and 4 (complex_dimer-FINAL-coot-7.pdb
    13455 #40/A,complex_dimer-FINAL-coot-7.pdb #40/B,complex_dimer-FINAL-coot-7.pdb
    13456 #40/C,complex_dimer-FINAL-coot-7.pdb #40/D) 
    13457 
    13458 > morph #39,40 same true
    13459 
    13460 Computed 21 frame morph #56 
    13461 
    13462 > coordset #56 1,21
    13463 
    13464 > close #56
    13465 
    13466 > show #55 models
    13467 
    13468 > hide #55 models
    13469 
    13470 > show #!40 models
    13471 
    13472 > show #39 models
    13473 
    13474 > morph #39/A,40/A same true
    13475 
    13476 Require at least 2 structures for morph 
    13477 
    13478 > morph #39,40/A same true
    13479 
    13480 Computed 21 frame morph #56 
    13481 
    13482 > coordset #56 1,21
    13483 
    13484 > morph #39,40/A same true
    13485 
    13486 Computed 21 frame morph #57 
    13487 
    13488 > coordset #57 1,21
    13489 
    13490 > close #56
    13491 
    13492 > close #57
    13493 
    13494 > show #50 models
    13495 
    13496 > hide #50 models
    13497 
    13498 > show #39 models
    13499 
    13500 > show #53 models
    13501 
    13502 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13503 > figures/arf1-closed.pdb models #53 relModel #39
    13504 
    13505 > hide #53 models
    13506 
    13507 > show #53 models
    13508 
    13509 > hide #53 models
    13510 
    13511 > show #53 models
    13512 
    13513 > hide #53 models
    13514 
    13515 > hide #39 models
    13516 
    13517 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13518 > figures/closed-arf1-morph.pdb
    13519 
    13520 Summary of feedback from opening
    13521 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    13522 arf1-morph.pdb 
    13523 --- 
    13524 warnings | Ignored bad PDB record found on line 43510 
    13525 END 
    13526  
    13527 Start residue of secondary structure not found: HELIX 1 1 GLY A 29 GLU A 41 1
    13528 13 
    13529 Start residue of secondary structure not found: HELIX 2 2 GLN A 71 LYS A 73 1
    13530 3 
    13531 Start residue of secondary structure not found: HELIX 3 3 ILE A 74 PHE A 82 1
    13532 9 
    13533 Start residue of secondary structure not found: HELIX 4 4 ASP A 96 GLU A 98 1
    13534 3 
    13535 Start residue of secondary structure not found: HELIX 5 5 ARG A 99 ALA A 112 1
    13536 14 
    13537 10 messages similar to the above omitted 
    13538  
    13539 closed-arf1-morph.pdb title: 
    13540 ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
    13541 catalytic glutamate to lysine [more info...] 
    13542  
    13543 Chain information for closed-arf1-morph.pdb #56 
    13544 --- 
    13545 Chain | Description 
    13546 A | adp-ribosylation factor 1 
    13547 B | No description available 
    13548 C | No description available 
    13549 E | ARNO 
    13550  
    13551 Non-standard residues in closed-arf1-morph.pdb #56 
    13552 --- 
    13553 BME — β-mercaptoethanol 
    13554 FMT — formic acid 
    13555 GDP — guanosine-5'-diphosphate 
    13556 SO3 — sulfite ion 
    13557 SO4 — sulfate ion 
    13558  
    13559 
    13560 > hide #56 models
    13561 
    13562 > show #54 models
    13563 
    13564 > select #54/A
    13565 
    13566 1471 atoms, 1345 bonds, 312 residues, 1 model selected 
    13567 
    13568 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13569 > figures/closed-arf1-morph.pdb
    13570 
    13571 Summary of feedback from opening
    13572 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    13573 arf1-morph.pdb 
    13574 --- 
    13575 warnings | Duplicate atom serial number found: 1 
    13576 Duplicate atom serial number found: 2 
    13577 Duplicate atom serial number found: 3 
    13578 Duplicate atom serial number found: 4 
    13579 Duplicate atom serial number found: 5 
    13580 1301 messages similar to the above omitted 
    13581 Start residue of secondary structure not found: HELIX 10 10 ASN E 62 MET E 74
    13582 1 13 
    13583 Start residue of secondary structure not found: HELIX 11 11 ASP E 75 ASN E 86
    13584 1 12 
    13585 Start residue of secondary structure not found: HELIX 12 12 THR E 92 GLY E 103
    13586 1 12 
    13587 Start residue of secondary structure not found: HELIX 13 13 ASN E 107 GLY E
    13588 116 1 10 
    13589 Start residue of secondary structure not found: HELIX 14 14 GLU E 119 LEU E
    13590 132 1 14 
    13591 5 messages similar to the above omitted 
    13592 Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0 
    13593 PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
    13594 as basis for sequence. 
    13595  
    13596 Chain information for closed-arf1-morph.pdb #57 
    13597 --- 
    13598 Chain | Description 
    13599 A | No description available 
    13600 B | No description available 
    13601  
    13602 
    13603 > hide #54 models
    13604 
    13605 > show #!51 models
    13606 
    13607 > hide #!51 models
    13608 
    13609 > show #!40 models
    13610 
    13611 > morph #57,40 same true
    13612 
    13613 Computed 21 frame morph #58 
    13614 
    13615 > coordset #58 1,21
    13616 
    13617 > close #58
    13618 
    13619 > show #57 models
    13620 
    13621 > show #!40 models
    13622 
    13623 > select #40/D
    13624 
    13625 1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected 
    13626 
    13627 > delete atoms (#!40 & sel)
    13628 
    13629 > delete bonds (#!40 & sel)
    13630 
    13631 > morph #57,40 same true
    13632 
    13633 Computed 21 frame morph #58 
    13634 
    13635 > coordset #58 1,21
    13636 
    13637 > hide #!58 models
    13638 
    13639 > close #58
    13640 
    13641 > show #55 models
    13642 
    13643 > show #56 models
    13644 
    13645 > hide #56 models
    13646 
    13647 > show #57 models
    13648 
    13649 > hide #55 models
    13650 
    13651 > select #57/A
    13652 
    13653 21107 atoms, 21287 bonds, 1382 residues, 1 model selected 
    13654 
    13655 > close #57
    13656 
    13657 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13658 > figures/closed-arf1-morph.pdb
    13659 
    13660 Summary of feedback from opening
    13661 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    13662 arf1-morph.pdb 
    13663 --- 
    13664 warnings | Duplicate atom serial number found: 1 
    13665 Duplicate atom serial number found: 2 
    13666 Duplicate atom serial number found: 3 
    13667 Duplicate atom serial number found: 4 
    13668 Duplicate atom serial number found: 5 
    13669 4536 messages similar to the above omitted 
    13670 Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0 
    13671 Bad residue range for secondary structure: SHEET 4 4 4 GLY A 87 ASP A 93 0 
    13672 PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
    13673 as basis for sequence. 
    13674  
    13675 Chain information for closed-arf1-morph.pdb #57 
    13676 --- 
    13677 Chain | Description 
    13678 A | No description available 
    13679 B | No description available 
    13680 C | No description available 
    13681 E | No description available 
    13682  
    13683 
    13684 > morph #57,40 same true
    13685 
    13686 Computed 21 frame morph #58 
    13687 
    13688 > coordset #58 1,21
    13689 
    13690 > hide #!58 models
    13691 
    13692 > show #!58 models
    13693 
    13694 > close #58
    13695 
    13696 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13697 > figures/complex-morph.pdb
    13698 
    13699 Summary of feedback from opening
    13700 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
    13701 morph.pdb 
    13702 --- 
    13703 warning | Ignored bad PDB record found on line 19939 
    13704 END 
    13705  
    13706 Chain information for complex-morph.pdb #58 
    13707 --- 
    13708 Chain | Description 
    13709 A B | No description available 
    13710 C | No description available 
    13711  
    13712 
    13713 > show #57 models
    13714 
    13715 > hide #57 models
    13716 
    13717 > show #56 models
    13718 
    13719 > hide #56 models
    13720 
    13721 > show #57 models
    13722 
    13723 > mmaker #57 to #58
    13724 
    13725 Parameters 
    13726 --- 
    13727 Chain pairing | bb 
    13728 Alignment algorithm | Needleman-Wunsch 
    13729 Similarity matrix | BLOSUM-62 
    13730 SS fraction | 0.3 
    13731 Gap open (HH/SS/other) | 18/18/6 
    13732 Gap extend | 1 
    13733 SS matrix |  |  | H | S | O 
    13734 ---|---|---|--- 
    13735 H | 6 | -9 | -6 
    13736 S |  | 6 | -6 
    13737 O |  |  | 4 
    13738 Iteration cutoff | 2 
    13739  
    13740 Matchmaker complex-morph.pdb, chain A (#58) with closed-arf1-morph.pdb, chain
    13741 B (#57), sequence alignment score = 5425.2 
    13742 RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
    13743 8.322) 
    13744  
    13745 
    13746 > morph #57,58 same true
    13747 
    13748 Computed 21 frame morph #59 
    13749 
    13750 > coordset #59 1,21
    13751 
    13752 > close #59
    13753 
    13754 > show #!58 models
    13755 
    13756 > show #57 models
    13757 
    13758 > ui mousemode right "translate selected models"
    13759 
    13760 > ui mousemode right "rotate selected models"
    13761 
    13762 > select #58
    13763 
    13764 19934 atoms, 20254 bonds, 44 pseudobonds, 2483 residues, 2 models selected 
    13765 
    13766 > mmaker #57 to #58
    13767 
    13768 Parameters 
    13769 --- 
    13770 Chain pairing | bb 
    13771 Alignment algorithm | Needleman-Wunsch 
    13772 Similarity matrix | BLOSUM-62 
    13773 SS fraction | 0.3 
    13774 Gap open (HH/SS/other) | 18/18/6 
    13775 Gap extend | 1 
    13776 SS matrix |  |  | H | S | O 
    13777 ---|---|---|--- 
    13778 H | 6 | -9 | -6 
    13779 S |  | 6 | -6 
    13780 O |  |  | 4 
    13781 Iteration cutoff | 2 
    13782  
    13783 Matchmaker complex-morph.pdb, chain A (#58) with closed-arf1-morph.pdb, chain
    13784 B (#57), sequence alignment score = 5425.2 
    13785 RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
    13786 8.322) 
    13787  
    13788 
    13789 > select clear
    13790 
    13791 > ui mousemode right "translate selected models"
    13792 
    13793 > ui mousemode right "translate selected atoms"
    13794 
    13795 > ui mousemode right "rotate selected models"
    13796 
    13797 > select #58
    13798 
    13799 19934 atoms, 20254 bonds, 44 pseudobonds, 2483 residues, 2 models selected 
    13800 
    13801 > mmaker #58 to #57
    13802 
    13803 Parameters 
    13804 --- 
    13805 Chain pairing | bb 
    13806 Alignment algorithm | Needleman-Wunsch 
    13807 Similarity matrix | BLOSUM-62 
    13808 SS fraction | 0.3 
    13809 Gap open (HH/SS/other) | 18/18/6 
    13810 Gap extend | 1 
    13811 SS matrix |  |  | H | S | O 
    13812 ---|---|---|--- 
    13813 H | 6 | -9 | -6 
    13814 S |  | 6 | -6 
    13815 O |  |  | 4 
    13816 Iteration cutoff | 2 
    13817  
    13818 Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
    13819 A (#58), sequence alignment score = 5425.2 
    13820 RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
    13821 8.322) 
    13822  
    13823 
    13824 > select clear
    13825 
    13826 > mmaker #58/A to #57/A bring #58/B #58/C
    13827 
    13828 'bring' arg specifies no non-match/ref structures 
    13829 
    13830 Parameters 
    13831 --- 
    13832 Chain pairing | bb 
    13833 Alignment algorithm | Needleman-Wunsch 
    13834 Similarity matrix | BLOSUM-62 
    13835 SS fraction | 0.3 
    13836 Gap open (HH/SS/other) | 18/18/6 
    13837 Gap extend | 1 
    13838 SS matrix |  |  | H | S | O 
    13839 ---|---|---|--- 
    13840 H | 6 | -9 | -6 
    13841 S |  | 6 | -6 
    13842 O |  |  | 4 
    13843 Iteration cutoff | 2 
    13844  
    13845 Matchmaker closed-arf1-morph.pdb, chain A (#57) with complex-morph.pdb, chain
    13846 A (#58), sequence alignment score = 5367.3 
    13847 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    13848 8.396) 
    13849  
    13850 
    13851 > morph #57,58 same true
    13852 
    13853 Computed 21 frame morph #59 
    13854 
    13855 > coordset #59 1,21
    13856 
    13857 > hide #!59 models
    13858 
    13859 > show #!58 models
    13860 
    13861 > show #57 models
    13862 
    13863 > show #!59 models
    13864 
    13865 > hide #!59 models
    13866 
    13867 > hide #!58 models
    13868 
    13869 > show #!58 models
    13870 
    13871 > hide #57 models
    13872 
    13873 > show #!59 models
    13874 
    13875 > hide #!58 models
    13876 
    13877 > morph #58,57 same true
    13878 
    13879 Computed 21 frame morph #60 
    13880 
    13881 > coordset #60 1,21
    13882 
    13883 > hide #!59 models
    13884 
    13885 > hide #!60 models
    13886 
    13887 > show #!58 models
    13888 
    13889 > show #57 models
    13890 
    13891 > hide #57#!58 atoms
    13892 
    13893 > mmaker #58 to #57
    13894 
    13895 Parameters 
    13896 --- 
    13897 Chain pairing | bb 
    13898 Alignment algorithm | Needleman-Wunsch 
    13899 Similarity matrix | BLOSUM-62 
    13900 SS fraction | 0.3 
    13901 Gap open (HH/SS/other) | 18/18/6 
    13902 Gap extend | 1 
    13903 SS matrix |  |  | H | S | O 
    13904 ---|---|---|--- 
    13905 H | 6 | -9 | -6 
    13906 S |  | 6 | -6 
    13907 O |  |  | 4 
    13908 Iteration cutoff | 2 
    13909  
    13910 Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
    13911 A (#58), sequence alignment score = 5425.2 
    13912 RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
    13913 8.322) 
    13914  
    13915 
    13916 > mmaker #58/A to #57/A bring #58/B #58/C
    13917 
    13918 'bring' arg specifies no non-match/ref structures 
    13919 
    13920 Parameters 
    13921 --- 
    13922 Chain pairing | bb 
    13923 Alignment algorithm | Needleman-Wunsch 
    13924 Similarity matrix | BLOSUM-62 
    13925 SS fraction | 0.3 
    13926 Gap open (HH/SS/other) | 18/18/6 
    13927 Gap extend | 1 
    13928 SS matrix |  |  | H | S | O 
    13929 ---|---|---|--- 
    13930 H | 6 | -9 | -6 
    13931 S |  | 6 | -6 
    13932 O |  |  | 4 
    13933 Iteration cutoff | 2 
    13934  
    13935 Matchmaker closed-arf1-morph.pdb, chain A (#57) with complex-morph.pdb, chain
    13936 A (#58), sequence alignment score = 5367.3 
    13937 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    13938 8.396) 
    13939  
    13940 
    13941 > hide #!58 models
    13942 
    13943 > select #57/E
    13944 
    13945 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    13946 
    13947 > delete atoms sel
    13948 
    13949 > delete bonds sel
    13950 
    13951 > show #!58 models
    13952 
    13953 > morph #57,58 same true
    13954 
    13955 Computed 21 frame morph #61 
    13956 
    13957 > coordset #61 1,21
    13958 
    13959 > close #59-61
    13960 
    13961 > show #57 models
    13962 
    13963 > show #56 models
    13964 
    13965 > hide #56 models
    13966 
    13967 > show #!58 models
    13968 
    13969 > hide #57 models
    13970 
    13971 > hide #!58 models
    13972 
    13973 > close #58
    13974 
    13975 > close #56-57
    13976 
    13977 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    13978 > figures/complex-morph.pdb
    13979 > C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    13980 > arf1-morph.pdb
    13981 
    13982 Summary of feedback from opening
    13983 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
    13984 morph.pdb 
    13985 --- 
    13986 warning | Ignored bad PDB record found on line 19939 
    13987 END 
    13988  
    13989 Summary of feedback from opening
    13990 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    13991 arf1-morph.pdb 
    13992 --- 
    13993 warnings | Duplicate atom serial number found: 1 
    13994 Duplicate atom serial number found: 2 
    13995 Duplicate atom serial number found: 3 
    13996 Duplicate atom serial number found: 4 
    13997 Duplicate atom serial number found: 5 
    13998 4536 messages similar to the above omitted 
    13999 Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0 
    14000 Bad residue range for secondary structure: SHEET 4 4 4 GLY A 87 ASP A 93 0 
    14001 PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
    14002 as basis for sequence. 
    14003  
    14004 Chain information for complex-morph.pdb #56 
    14005 --- 
    14006 Chain | Description 
    14007 A B | No description available 
    14008 C | No description available 
    14009  
    14010 Chain information for closed-arf1-morph.pdb #57 
    14011 --- 
    14012 Chain | Description 
    14013 A | No description available 
    14014 B | No description available 
    14015 C | No description available 
    14016 E | No description available 
    14017  
    14018 
    14019 > mmaker #56 to #57
    14020 
    14021 Parameters 
    14022 --- 
    14023 Chain pairing | bb 
    14024 Alignment algorithm | Needleman-Wunsch 
    14025 Similarity matrix | BLOSUM-62 
    14026 SS fraction | 0.3 
    14027 Gap open (HH/SS/other) | 18/18/6 
    14028 Gap extend | 1 
    14029 SS matrix |  |  | H | S | O 
    14030 ---|---|---|--- 
    14031 H | 6 | -9 | -6 
    14032 S |  | 6 | -6 
    14033 O |  |  | 4 
    14034 Iteration cutoff | 2 
    14035  
    14036 Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
    14037 A (#56), sequence alignment score = 5425.2 
    14038 RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
    14039 8.322) 
    14040  
    14041 
    14042 > hide #!56 models
    14043 
    14044 > select #57/E
    14045 
    14046 1735 atoms, 1559 bonds, 392 residues, 1 model selected 
    14047 
    14048 > delete atoms sel
    14049 
    14050 > delete bonds sel
    14051 
    14052 No model chosen to save relative to 
    14053 
    14054 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14055 > figures/closed-arf1-morph.pdb models #57 relModel #57
    14056 
    14057 > close #57
    14058 
    14059 > show #53 models
    14060 
    14061 > hide #53 models
    14062 
    14063 > show #54 models
    14064 
    14065 > show #50 models
    14066 
    14067 > hide #50 models
    14068 
    14069 > show #44 models
    14070 
    14071 > hide #44 models
    14072 
    14073 > show #44 models
    14074 
    14075 > hide #44 models
    14076 
    14077 > show #39 models
    14078 
    14079 > show #53 models
    14080 
    14081 > hide #54 models
    14082 
    14083 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14084 > figures/closed-arf1-morph.pdb models #39,53 relModel #39
    14085 
    14086 > hide #53 models
    14087 
    14088 > hide #39 models
    14089 
    14090 > show #!56 models
    14091 
    14092 > hide #!56 models
    14093 
    14094 > show #54 models
    14095 
    14096 > hide #54 models
    14097 
    14098 > show #53 models
    14099 
    14100 > show #44 models
    14101 
    14102 > hide #44 models
    14103 
    14104 > show #39 models
    14105 
    14106 > select #53
    14107 
    14108 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    14109 
    14110 > select #39
    14111 
    14112 39644 atoms, 39958 bonds, 2444 residues, 1 model selected 
    14113 
    14114 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14115 > figures/closed-arf1-morph.pdb displayedOnly true selectedOnly true relModel
    14116 > #39
    14117 
    14118 > select #53
    14119 
    14120 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    14121 
    14122 > select #39
    14123 
    14124 39644 atoms, 39958 bonds, 2444 residues, 1 model selected 
    14125 No model chosen to save relative to 
    14126 
    14127 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14128 > figures/closed-arf1-morph.pdb selectedOnly true relModel #39
    14129 
    14130 > select #53
    14131 
    14132 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    14133 
    14134 > select #39
    14135 
    14136 39644 atoms, 39958 bonds, 2444 residues, 1 model selected 
    14137 
    14138 > select #53
    14139 
    14140 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    14141 
    14142 > select #39
    14143 
    14144 39644 atoms, 39958 bonds, 2444 residues, 1 model selected 
    14145 
    14146 > select #53
    14147 
    14148 3206 atoms, 2904 bonds, 704 residues, 1 model selected 
    14149 Drag select of 2883 residues, 28 atoms, 30 bonds 
    14150 
    14151 > save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14152 > figures/closed-arf1-morph.pdb selectedOnly true relModel #39
    14153 
    14154 > hide #53 models
    14155 
    14156 > select #39
    14157 
    14158 39644 atoms, 39958 bonds, 2444 residues, 1 model selected 
    14159 
    14160 > hide #39 models
    14161 
    14162 > ~select #39
    14163 
    14164 Nothing selected 
    14165 
    14166 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14167 > figures/closed-arf1-morph.pdb
    14168 
    14169 Summary of feedback from opening
    14170 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    14171 arf1-morph.pdb 
    14172 --- 
    14173 warnings | Ignored bad PDB record found on line 192 
    14174 END 
    14175  
    14176 Ignored bad PDB record found on line 195 
    14177 END 
    14178  
    14179 Ignored bad PDB record found on line 198 
    14180 END 
    14181  
    14182 Ignored bad PDB record found on line 201 
    14183 END 
    14184  
    14185 Ignored bad PDB record found on line 204 
    14186 END 
    14187  
    14188 59 messages similar to the above omitted 
    14189  
    14190 Chain information for closed-arf1-morph.pdb 
    14191 --- 
    14192 Chain | Description 
    14193 57.1/A 57.1/B | No description available 
    14194 57.2/A | No description available 
    14195  
    14196 
    14197 > hide #57.2 models
    14198 
    14199 > hide #!57.1 models
    14200 
    14201 > show #!57.1 models
    14202 
    14203 > show #57.2 models
    14204 
    14205 > show #!56 models
    14206 
    14207 > mmaker #56/A to #57/A bring #56/B #56/C
    14208 
    14209 Specify a single 'to' model only 
    14210 
    14211 > mmaker #56/A to #57.1/A bring #56/B #56/C
    14212 
    14213 'bring' arg specifies no non-match/ref structures 
    14214 
    14215 Parameters 
    14216 --- 
    14217 Chain pairing | bb 
    14218 Alignment algorithm | Needleman-Wunsch 
    14219 Similarity matrix | BLOSUM-62 
    14220 SS fraction | 0.3 
    14221 Gap open (HH/SS/other) | 18/18/6 
    14222 Gap extend | 1 
    14223 SS matrix |  |  | H | S | O 
    14224 ---|---|---|--- 
    14225 H | 6 | -9 | -6 
    14226 S |  | 6 | -6 
    14227 O |  |  | 4 
    14228 Iteration cutoff | 2 
    14229  
    14230 Matchmaker closed-arf1-morph.pdb, chain A (#57.1) with complex-morph.pdb,
    14231 chain A (#56), sequence alignment score = 5451 
    14232 RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
    14233 8.396) 
    14234  
    14235 
    14236 > morph #57,56 same true
    14237 
    14238 Computed 41 frame morph #58 
    14239 
    14240 > coordset #58 1,41
    14241 
    14242 > hide #!57 models
    14243 
    14244 > hide #!58 models
    14245 
    14246 > show #!58 models
    14247 
    14248 > show #!57 models
    14249 
    14250 > hide #!57 models
    14251 
    14252 > hide #!58 models
    14253 
    14254 > show #53 models
    14255 
    14256 > show #39 models
    14257 
    14258 > open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
    14259 > figures/closed-arf1-morph.pdb
    14260 
    14261 Summary of feedback from opening
    14262 C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
    14263 arf1-morph.pdb 
    14264 --- 
    14265 warnings | Duplicate atom serial number found: 1 
    14266 Duplicate atom serial number found: 2 
    14267 Duplicate atom serial number found: 3 
    14268 Duplicate atom serial number found: 4 
    14269 Duplicate atom serial number found: 5 
    14270 3230 messages similar to the above omitted 
    14271 Start residue of secondary structure not found: HELIX 1 1 GLY A 29 GLU A 41 1
    14272 13 
    14273 Start residue of secondary structure not found: HELIX 2 2 GLN A 71 LYS A 73 1
    14274 3 
    14275 Start residue of secondary structure not found: HELIX 3 3 ILE A 74 PHE A 82 1
    14276 9 
    14277 Start residue of secondary structure not found: HELIX 4 4 ASP A 96 GLU A 98 1
    14278 3 
    14279 Start residue of secondary structure not found: HELIX 5 5 ARG A 99 ALA A 112 1
    14280 14 
    14281 10 messages similar to the above omitted 
    14282  
    14283 Chain information for closed-arf1-morph.pdb #59 
    14284 --- 
    14285 Chain | Description 
    14286 A B | No description available 
    14287 C | No description available 
    14288 E | No description available 
    14289  
    14290 
    14291 > hide #53 models
    14292 
    14293 > hide #39 models
    14294 
    14295 > preset cartoons/nucleotides ribbons/slabs
    14296 
    14297 Changed 0 atom styles 
    14298 Preset expands to these ChimeraX commands:
    14299 
    14300    
    14301    
    14302     show nucleic
    14303     hide protein|solvent|H
    14304     surf hide
    14305     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    14306     cartoon
    14307     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    14308     cartoon style ~(nucleic|strand) x round
    14309     cartoon style (nucleic|strand) x rect
    14310     nucleotides tube/slab shape box
    14311 
    14312  
     54
     55[had to delete a substantial portion of the log to make it fit the ticket length; hopefully available in the diff.  I can dredge it from my mail if necessary -- Eric]
    1431356
    1431457> hide #59 models