Changes between Initial Version and Version 1 of Ticket #1713


Ignore:
Timestamp:
Feb 19, 2019, 9:14:58 AM (7 years ago)
Author:
Tom Goddard
Comment:

Legend:

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Removed
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  • Ticket #1713

    • Property Platform → all
    • Property Project → ChimeraX

  • Ticket #1713 – Description

    initial v1  
    1212How to cite UCSF ChimeraX 
    1313
    14 > open CD20_Ritux.cxc
    1514
    16 > open
    17 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb
    18 name '"atomic model"'
    19 
    20 Summary of feedback from opening
    21 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb 
    22 --- 
    23 warnings | Ignored bad PDB record found on line 22 
    24 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 
    25  
    26 Ignored bad PDB record found on line 23 
    27 DEVIATIONS FROM IDEAL VALUES. 
    28  
    29 Ignored bad PDB record found on line 24 
    30 BOND : 0.010 0.065 9358 
    31  
    32 Ignored bad PDB record found on line 25 
    33 ANGLE : 1.092 13.638 12736 
    34  
    35 Ignored bad PDB record found on line 26 
    36 CHIRALITY : 0.065 0.341 1444 
    37  
    38 16 messages similar to the above omitted 
    39 Cannot find LINK/SSBOND residue CYS (87 ) 
    40 Cannot find LINK/SSBOND residue CYS (133 ) 
    41 Cannot find LINK/SSBOND residue CYS (96 ) 
    42 Cannot find LINK/SSBOND residue CYS (148 ) 
    43 Cannot find LINK/SSBOND residue CYS (87 ) 
    44 3 messages similar to the above omitted 
    45  
    46 Chain information for atomic model #1 
    47 --- 
    48 Chain | Description 
    49 C D | No description available 
    50 H I | No description available 
    51 L M | No description available 
    52  
    53 
    54 > open
    55 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc
    56 name '"map"'
    57 
    58 Opened generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc, grid size
    59 310,310,310, pixel 1, shown at level 0.0611, step 2, values float32 
    60 
    61 > open
    62 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc
    63 name '"map sharp"'
    64 
    65 Opened generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc, grid size
    66 310,310,310, pixel 1, shown at level 0.0816, step 2, values float32 
    67 
    68 > name cd20RituxDimer #1
    69 
    70 > name cd20 #1/C,D
    71 
    72 > name cd20Monomer #1/C
    73 
    74 > name cd20H1 #1/C,D:46-70
    75 
    76 > name cd20ECL1 #1/C,D:71-81
    77 
    78 > name cd20H2 #1/C,D:82-105
    79 
    80 > name cd20ICL1 #1/C,D:106-112
    81 
    82 > name cd20H3 #1/C,D:113-140
    83 
    84 > name cd20ECL2 #1/C,D:141-182
    85 
    86 > name cd20ECL2SS #1/C,D:167,183
    87 
    88 > name cd20H4 #1/C,D:183-207
    89 
    90 > name cd20DimerInt #1/C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
    91 
    92 > name Ritux #1/H,L,I,M
    93 
    94 > name RituxH #1/H,I
    95 
    96 > name RituxL #1/L,M
    97 
    98 > name RituxEpitope #1/C,D:168-175
    99 
    100 > set bgColor white
    101 
    102 > set silhouettes true
    103 
    104 > lighting full
    105 
    106 > open CD20_Ritux_color_model.cxc
    107 
    108 > color cd20RituxDimer gray
    109 
    110 > color cd20 burlywood
    111 
    112 > color modify cd20H1 hue - 20
    113 
    114 > color modify cd20H2 hue - 10
    115 
    116 > color modify cd20H3 hue + 0
    117 
    118 > color modify cd20H4 hue + 10
    119 
    120 > color modify cd20ECL1 hue +10
    121 
    122 > color modify cd20ECL2 hue + 40
    123 
    124 > color modify cd20 saturation + 80
    125 
    126 > color Ritux plum
    127 
    128 > color modify RituxH hue - 40
    129 
    130 executed CD20_Ritux_color_model.cxc 
    131 
    132 > hide cd20RituxDimer
    133 
    134 > ribbon cd20RituxDimer
    135 
    136 > show cd20ECL2SS
    137 
    138 > style cd20ECL2SS stick
    139 
    140 Changed 24 atom styles 
    141 
    142 > volume zone #2 nearAtoms Ritux range 10.0 invert true newMap true modelId
    143 100
    144 
    145 > volume zone #100 nearAtoms cd20 range 3.0 invert true newMap true modelId 4
    146 
    147 > close #100
    148 
    149 > volume #2 step 1 level 0.33 color #9999CC
    150 
    151 > volume #3 step 1 level 0.33 color #9999CC
    152 
    153 > volume #4 step 1 level 0.1 color #CCCCFF55
    154 
    155 > display #2,4
    156 
    157 > color zone #2 near cd20RituxDimer distance 4.0
    158 
    159 > color zone #3 near cd20RituxDimer distance 4.0
    160 
    161 > hide #!4 models
    162 
    163 > hide #!3 models
    164 
    165 > hide #!2 models
    166 
    167 > show #!1 models
    168 
    169 > turn x 90
    170 
    171 executed CD20_Ritux.cxc 
    172 
    173 > save /Users/rohoua/Desktop/image8.png supersample 3
    174 
    175 > help scalebar
    176 
    177 No help found for 'scalebar' 
    178 
    179 > help
    180 
    181 Developer warnings in user commands index:
    182 
    183   * didn't expect href to be to tools/sequenceviewer.html on line 246
    184 
    185  
    186 
    187 > help distance
    188 
    189 > distance /L:213@CA /M:213@CA
    190 
    191 Distance between /L GLU 213 CA and /M GLU 213 CA: 142.962Å 
    192 
    193 > turn y 90
    194 
    195 > turn y 180
    196 
    197 > view orient
    198 
    199 > view initial
    200 
    201 > open CD20_Ritux_overview_figures.cxc
    202 
    203 > close
    204 
    205 > open CD20_Ritux.cxc
    206 
    207 > open
    208 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb
    209 name '"atomic model"'
    210 
    211 Summary of feedback from opening
    212 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb 
    213 --- 
    214 warnings | Ignored bad PDB record found on line 22 
    215 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 
    216  
    217 Ignored bad PDB record found on line 23 
    218 DEVIATIONS FROM IDEAL VALUES. 
    219  
    220 Ignored bad PDB record found on line 24 
    221 BOND : 0.010 0.065 9358 
    222  
    223 Ignored bad PDB record found on line 25 
    224 ANGLE : 1.092 13.638 12736 
    225  
    226 Ignored bad PDB record found on line 26 
    227 CHIRALITY : 0.065 0.341 1444 
    228  
    229 16 messages similar to the above omitted 
    230 Cannot find LINK/SSBOND residue CYS (87 ) 
    231 Cannot find LINK/SSBOND residue CYS (133 ) 
    232 Cannot find LINK/SSBOND residue CYS (96 ) 
    233 Cannot find LINK/SSBOND residue CYS (148 ) 
    234 Cannot find LINK/SSBOND residue CYS (87 ) 
    235 3 messages similar to the above omitted 
    236  
    237 Chain information for atomic model #1 
    238 --- 
    239 Chain | Description 
    240 C D | No description available 
    241 H I | No description available 
    242 L M | No description available 
    243  
    244 
    245 > open
    246 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc
    247 name '"map"'
    248 
    249 Opened generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc, grid size
    250 310,310,310, pixel 1, shown at level 0.0611, step 2, values float32 
    251 
    252 > open
    253 /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc
    254 name '"map sharp"'
    255 
    256 Opened generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc, grid size
    257 310,310,310, pixel 1, shown at level 0.0816, step 2, values float32 
    258 
    259 > name cd20RituxDimer #1
    260 
    261 > name cd20 #1/C,D
    262 
    263 > name cd20Monomer #1/C
    264 
    265 > name cd20H1 #1/C,D:46-70
    266 
    267 > name cd20ECL1 #1/C,D:71-81
    268 
    269 > name cd20H2 #1/C,D:82-105
    270 
    271 > name cd20ICL1 #1/C,D:106-112
    272 
    273 > name cd20H3 #1/C,D:113-140
    274 
    275 > name cd20ECL2 #1/C,D:141-182
    276 
    277 > name cd20ECL2SS #1/C,D:167,183
    278 
    279 > name cd20H4 #1/C,D:183-207
    280 
    281 > name cd20DimerInt #1/C,D:62,200,65,196,69,192,73,188,76,185,58,54,50
    282 
    283 > name Ritux #1/H,L,I,M
    284 
    285 > name RituxH #1/H,I
    286 
    287 > name RituxL #1/L,M
    288 
    289 > name RituxEpitope #1/C,D:168-175
    290 
    291 > set bgColor white
    292 
    293 > set silhouettes true
    294 
    295 > lighting full
    296 
    297 > open CD20_Ritux_color_model.cxc
    298 
    299 > color cd20RituxDimer gray
    300 
    301 > color cd20 burlywood
    302 
    303 > color modify cd20H1 hue - 20
    304 
    305 > color modify cd20H2 hue - 10
    306 
    307 > color modify cd20H3 hue + 0
    308 
    309 > color modify cd20H4 hue + 10
    310 
    311 > color modify cd20ECL1 hue +10
    312 
    313 > color modify cd20ECL2 hue + 40
    314 
    315 > color modify cd20 saturation + 80
    316 
    317 > color Ritux plum
    318 
    319 > color modify RituxH hue - 40
    320 
    321 executed CD20_Ritux_color_model.cxc 
    322 
    323 > hide cd20RituxDimer
    324 
    325 > ribbon cd20RituxDimer
    326 
    327 > show cd20ECL2SS
    328 
    329 > style cd20ECL2SS stick
    330 
    331 Changed 24 atom styles 
    332 
    333 > volume zone #2 nearAtoms Ritux range 10.0 invert true newMap true modelId
    334 100
    335 
    336 > volume zone #100 nearAtoms cd20 range 3.0 invert true newMap true modelId 4
    337 
    338 > close #100
    339 
    340 > volume #2 step 1 level 0.33 color #9999CC
    341 
    342 > volume #3 step 1 level 0.33 color #9999CC
    343 
    344 > volume #4 step 1 level 0.1 color #CCCCFF55
    345 
    346 > display #2,4
    347 
    348 > color zone #2 near cd20RituxDimer distance 4.0
    349 
    350 > color zone #3 near cd20RituxDimer distance 4.0
    351 
    352 > hide #!4 models
    353 
    354 > hide #!3 models
    355 
    356 > hide #!2 models
    357 
    358 > show #!1 models
    359 
    360 > turn x 90
    361 
    362 executed CD20_Ritux.cxc 
    363 
    364 > save Figures/CD20_Ritux_overview_ribbons_wideside.png supersample 3
    365 
    366 > turn y 90
    367 
    368 > save Figures/CD20_Ritux_overview_ribbons_narrowside.png supersample 3
    369 
    370 > turn y -90
    371 
    372 > turn x 90
    373 
    374 > save Figures/CD20_Ritux_overview_ribbons_top.png supersample 3
    375 
    376 > turn x -180
    377 
    378 > save Figures/CD20_Ritux_overview_ribbons_bottom.png supersample 3
    379 
    380 > getcrd /L:213@CA model
    381 
    382 Traceback (most recent call last): 
    383 File
    384 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    385 packages/chimerax/core/triggerset.py", line 130, in invoke 
    386 return self._func(self._name, data) 
    387 File
    388 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    389 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    390 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    391 File
    392 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    393 packages/chimerax/ui/options/options.py", line 606, in set 
    394 self.widget.setText(self.labels[list(self.values).index(value)]) 
    395 ValueError: 'command-line specifier' is not in list 
    396  
    397 Error processing trigger "setting changed": 'command-line specifier' is not in
    398 list: 
    399 ValueError: 'command-line specifier' is not in list 
    400  
    401 File
    402 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    403 packages/chimerax/ui/options/options.py", line 606, in set 
    404 self.widget.setText(self.labels[list(self.values).index(value)]) 
    405  
    406 See log for complete Python traceback. 
    407  
    408 Traceback (most recent call last): 
    409 File
    410 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    411 packages/chimerax/core/triggerset.py", line 130, in invoke 
    412 return self._func(self._name, data) 
    413 File
    414 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    415 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    416 self.options[setting_name].set(new_val) 
    417 File
    418 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    419 packages/chimerax/ui/options/options.py", line 606, in set 
    420 self.widget.setText(self.labels[list(self.values).index(value)]) 
    421 ValueError: 'command-line specifier' is not in list 
    422  
    423 Error processing trigger "setting changed": 'command-line specifier' is not in
    424 list: 
    425 ValueError: 'command-line specifier' is not in list 
    426  
    427 File
    428 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    429 packages/chimerax/ui/options/options.py", line 606, in set 
    430 self.widget.setText(self.labels[list(self.values).index(value)]) 
    431  
    432 See log for complete Python traceback. 
    433  
    434 Atom /L:213@CA 226.486 155.374 102.618 
    435 
    436 > getcrd /M:213@CA model
    437 
    438 Traceback (most recent call last): 
    439 File
    440 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    441 packages/chimerax/core/triggerset.py", line 130, in invoke 
    442 return self._func(self._name, data) 
    443 File
    444 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    445 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    446 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    447 File
    448 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    449 packages/chimerax/ui/options/options.py", line 606, in set 
    450 self.widget.setText(self.labels[list(self.values).index(value)]) 
    451 ValueError: 'command-line specifier' is not in list 
    452  
    453 Error processing trigger "setting changed": 'command-line specifier' is not in
    454 list: 
    455 ValueError: 'command-line specifier' is not in list 
    456  
    457 File
    458 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    459 packages/chimerax/ui/options/options.py", line 606, in set 
    460 self.widget.setText(self.labels[list(self.values).index(value)]) 
    461  
    462 See log for complete Python traceback. 
    463  
    464 Traceback (most recent call last): 
    465 File
    466 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    467 packages/chimerax/core/triggerset.py", line 130, in invoke 
    468 return self._func(self._name, data) 
    469 File
    470 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    471 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    472 self.options[setting_name].set(new_val) 
    473 File
    474 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    475 packages/chimerax/ui/options/options.py", line 606, in set 
    476 self.widget.setText(self.labels[list(self.values).index(value)]) 
    477 ValueError: 'command-line specifier' is not in list 
    478  
    479 Error processing trigger "setting changed": 'command-line specifier' is not in
    480 list: 
    481 ValueError: 'command-line specifier' is not in list 
    482  
    483 File
    484 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    485 packages/chimerax/ui/options/options.py", line 606, in set 
    486 self.widget.setText(self.labels[list(self.values).index(value)]) 
    487  
    488 See log for complete Python traceback. 
    489  
    490 Atom /M:213@CA 83.526 154.639 102.618 
    491 
    492 > getcrd /H:16@CA model
    493 
    494 Traceback (most recent call last): 
    495 File
    496 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    497 packages/chimerax/core/triggerset.py", line 130, in invoke 
    498 return self._func(self._name, data) 
    499 File
    500 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    501 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    502 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    503 File
    504 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    505 packages/chimerax/ui/options/options.py", line 606, in set 
    506 self.widget.setText(self.labels[list(self.values).index(value)]) 
    507 ValueError: 'command-line specifier' is not in list 
    508  
    509 Error processing trigger "setting changed": 'command-line specifier' is not in
    510 list: 
    511 ValueError: 'command-line specifier' is not in list 
    512  
    513 File
    514 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    515 packages/chimerax/ui/options/options.py", line 606, in set 
    516 self.widget.setText(self.labels[list(self.values).index(value)]) 
    517  
    518 See log for complete Python traceback. 
    519  
    520 Traceback (most recent call last): 
    521 File
    522 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    523 packages/chimerax/core/triggerset.py", line 130, in invoke 
    524 return self._func(self._name, data) 
    525 File
    526 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    527 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    528 self.options[setting_name].set(new_val) 
    529 File
    530 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    531 packages/chimerax/ui/options/options.py", line 606, in set 
    532 self.widget.setText(self.labels[list(self.values).index(value)]) 
    533 ValueError: 'command-line specifier' is not in list 
    534  
    535 Error processing trigger "setting changed": 'command-line specifier' is not in
    536 list: 
    537 ValueError: 'command-line specifier' is not in list 
    538  
    539 File
    540 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    541 packages/chimerax/ui/options/options.py", line 606, in set 
    542 self.widget.setText(self.labels[list(self.values).index(value)]) 
    543  
    544 See log for complete Python traceback. 
    545  
    546 Atom /H:16@CA 184.924 180.815 122.837 
    547 
    548 > getcrd /L:202@CA model
    549 
    550 Traceback (most recent call last): 
    551 File
    552 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    553 packages/chimerax/core/triggerset.py", line 130, in invoke 
    554 return self._func(self._name, data) 
    555 File
    556 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    557 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    558 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    559 File
    560 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    561 packages/chimerax/ui/options/options.py", line 606, in set 
    562 self.widget.setText(self.labels[list(self.values).index(value)]) 
    563 ValueError: 'command-line specifier' is not in list 
    564  
    565 Error processing trigger "setting changed": 'command-line specifier' is not in
    566 list: 
    567 ValueError: 'command-line specifier' is not in list 
    568  
    569 File
    570 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    571 packages/chimerax/ui/options/options.py", line 606, in set 
    572 self.widget.setText(self.labels[list(self.values).index(value)]) 
    573  
    574 See log for complete Python traceback. 
    575  
    576 Traceback (most recent call last): 
    577 File
    578 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    579 packages/chimerax/core/triggerset.py", line 130, in invoke 
    580 return self._func(self._name, data) 
    581 File
    582 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    583 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    584 self.options[setting_name].set(new_val) 
    585 File
    586 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    587 packages/chimerax/ui/options/options.py", line 606, in set 
    588 self.widget.setText(self.labels[list(self.values).index(value)]) 
    589 ValueError: 'command-line specifier' is not in list 
    590  
    591 Error processing trigger "setting changed": 'command-line specifier' is not in
    592 list: 
    593 ValueError: 'command-line specifier' is not in list 
    594  
    595 File
    596 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    597 packages/chimerax/ui/options/options.py", line 606, in set 
    598 self.widget.setText(self.labels[list(self.values).index(value)]) 
    599  
    600 See log for complete Python traceback. 
    601  
    602 Atom /L:202@CA 210.607 133.184 116.113 
    603 
    604 > getcrd /H:191@CA model
    605 
    606 Traceback (most recent call last): 
    607 File
    608 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    609 packages/chimerax/core/triggerset.py", line 130, in invoke 
    610 return self._func(self._name, data) 
    611 File
    612 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    613 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    614 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    615 File
    616 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    617 packages/chimerax/ui/options/options.py", line 606, in set 
    618 self.widget.setText(self.labels[list(self.values).index(value)]) 
    619 ValueError: 'command-line specifier' is not in list 
    620  
    621 Error processing trigger "setting changed": 'command-line specifier' is not in
    622 list: 
    623 ValueError: 'command-line specifier' is not in list 
    624  
    625 File
    626 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    627 packages/chimerax/ui/options/options.py", line 606, in set 
    628 self.widget.setText(self.labels[list(self.values).index(value)]) 
    629  
    630 See log for complete Python traceback. 
    631  
    632 Traceback (most recent call last): 
    633 File
    634 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    635 packages/chimerax/core/triggerset.py", line 130, in invoke 
    636 return self._func(self._name, data) 
    637 File
    638 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    639 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    640 self.options[setting_name].set(new_val) 
    641 File
    642 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    643 packages/chimerax/ui/options/options.py", line 606, in set 
    644 self.widget.setText(self.labels[list(self.values).index(value)]) 
    645 ValueError: 'command-line specifier' is not in list 
    646  
    647 Error processing trigger "setting changed": 'command-line specifier' is not in
    648 list: 
    649 ValueError: 'command-line specifier' is not in list 
    650  
    651 File
    652 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    653 packages/chimerax/ui/options/options.py", line 606, in set 
    654 self.widget.setText(self.labels[list(self.values).index(value)]) 
    655  
    656 See log for complete Python traceback. 
    657  
    658 Atom /H:191@CA 210.829 151.513 83.648 
    659 
    660 > getcrd /C:111@CA model
    661 
    662 Traceback (most recent call last): 
    663 File
    664 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    665 packages/chimerax/core/triggerset.py", line 130, in invoke 
    666 return self._func(self._name, data) 
    667 File
    668 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    669 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    670 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    671 File
    672 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    673 packages/chimerax/ui/options/options.py", line 606, in set 
    674 self.widget.setText(self.labels[list(self.values).index(value)]) 
    675 ValueError: 'command-line specifier' is not in list 
    676  
    677 Error processing trigger "setting changed": 'command-line specifier' is not in
    678 list: 
    679 ValueError: 'command-line specifier' is not in list 
    680  
    681 File
    682 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    683 packages/chimerax/ui/options/options.py", line 606, in set 
    684 self.widget.setText(self.labels[list(self.values).index(value)]) 
    685  
    686 See log for complete Python traceback. 
    687  
    688 Traceback (most recent call last): 
    689 File
    690 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    691 packages/chimerax/core/triggerset.py", line 130, in invoke 
    692 return self._func(self._name, data) 
    693 File
    694 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    695 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    696 self.options[setting_name].set(new_val) 
    697 File
    698 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    699 packages/chimerax/ui/options/options.py", line 606, in set 
    700 self.widget.setText(self.labels[list(self.values).index(value)]) 
    701 ValueError: 'command-line specifier' is not in list 
    702  
    703 Error processing trigger "setting changed": 'command-line specifier' is not in
    704 list: 
    705 ValueError: 'command-line specifier' is not in list 
    706  
    707 File
    708 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    709 packages/chimerax/ui/options/options.py", line 606, in set 
    710 self.widget.setText(self.labels[list(self.values).index(value)]) 
    711  
    712 See log for complete Python traceback. 
    713  
    714 Atom /C:111@CA 167.859 144.657 197.098 
    715 executed CD20_Ritux_overview_figures.cxc 
    716 
    717 > getcrd /L:213@CA model
    718 
    719 Traceback (most recent call last): 
    720 File
    721 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    722 packages/chimerax/core/triggerset.py", line 130, in invoke 
    723 return self._func(self._name, data) 
    724 File
    725 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    726 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    727 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    728 File
    729 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    730 packages/chimerax/ui/options/options.py", line 606, in set 
    731 self.widget.setText(self.labels[list(self.values).index(value)]) 
    732 ValueError: 'command-line specifier' is not in list 
    733  
    734 Error processing trigger "setting changed": 'command-line specifier' is not in
    735 list: 
    736 ValueError: 'command-line specifier' is not in list 
    737  
    738 File
    739 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    740 packages/chimerax/ui/options/options.py", line 606, in set 
    741 self.widget.setText(self.labels[list(self.values).index(value)]) 
    742  
    743 See log for complete Python traceback. 
    744  
    745 Traceback (most recent call last): 
    746 File
    747 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    748 packages/chimerax/core/triggerset.py", line 130, in invoke 
    749 return self._func(self._name, data) 
    750 File
    751 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    752 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    753 self.options[setting_name].set(new_val) 
    754 File
    755 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    756 packages/chimerax/ui/options/options.py", line 606, in set 
    757 self.widget.setText(self.labels[list(self.values).index(value)]) 
    758 ValueError: 'command-line specifier' is not in list 
    759  
    760 Error processing trigger "setting changed": 'command-line specifier' is not in
    761 list: 
    762 ValueError: 'command-line specifier' is not in list 
    763  
    764 File
    765 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    766 packages/chimerax/ui/options/options.py", line 606, in set 
    767 self.widget.setText(self.labels[list(self.values).index(value)]) 
    768  
    769 See log for complete Python traceback. 
    770  
    771 Atom /L:213@CA 226.486 155.374 102.618 
    772 
    773 > getcrd /L:213@CA
    774 
    775 Traceback (most recent call last): 
    776 File
    777 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    778 packages/chimerax/core/triggerset.py", line 130, in invoke 
    779 return self._func(self._name, data) 
    780 File
    781 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    782 packages/chimerax/ui/options/options.py", line 50, in <lambda> 
    783 data[0] == pself.attr_name and pself.set(pself.get_attribute())) 
    784 File
    785 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    786 packages/chimerax/ui/options/options.py", line 606, in set 
    787 self.widget.setText(self.labels[list(self.values).index(value)]) 
    788 ValueError: 'command-line specifier' is not in list 
    789  
    790 Error processing trigger "setting changed": 'command-line specifier' is not in
    791 list: 
    792 ValueError: 'command-line specifier' is not in list 
    793  
    794 File
    795 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    796 packages/chimerax/ui/options/options.py", line 606, in set 
    797 self.widget.setText(self.labels[list(self.values).index(value)]) 
    798  
    799 See log for complete Python traceback. 
    800  
    801 Traceback (most recent call last): 
    802 File
    803 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    804 packages/chimerax/core/triggerset.py", line 130, in invoke 
    805 return self._func(self._name, data) 
    806 File
    807 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    808 packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed 
    809 self.options[setting_name].set(new_val) 
    810 File
    811 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    812 packages/chimerax/ui/options/options.py", line 606, in set 
    813 self.widget.setText(self.labels[list(self.values).index(value)]) 
    814 ValueError: 'command-line specifier' is not in list 
    815  
    816 Error processing trigger "setting changed": 'command-line specifier' is not in
    817 list: 
    818 ValueError: 'command-line specifier' is not in list 
    819  
    820 File
    821 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
    822 packages/chimerax/ui/options/options.py", line 606, in set 
    823 self.widget.setText(self.labels[list(self.values).index(value)]) 
    824  
    825 See log for complete Python traceback. 
    826  
    827 Atom /L:213@CA 226.486 155.374 102.618 
    828 
    829 > help getcrd
    830 
    831 > close
    83215
    83316> open pdb:1tbq