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Opened 4 years ago
Last modified 4 years ago
#5525 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)Im trying to do a morph
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs
Log from Mon Oct 11 14:17:43 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> dep/closed_dimer-FINAL.ccp4
Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 1.11, step 2, values float32
> volume #1 level 10.07
> volume #1 step 1
> set bgColor white
> lighting soft
> open
> C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2/closed/dimer/closed_dimer-
> coot-1.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2/closed/dimer/closed_dimer-
coot-1.pdb
---
warning | Ignored bad PDB record found on line 39765
END
Chain information for closed_dimer-coot-1.pdb #2
---
Chain | Description
A B | No description available
> hide #!1 models
> close session
> open
> C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2-Arf1/dimer/complex_dimer.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/11_CryoEM/model_building/ScGea2-Arf1/dimer/complex_dimer.pdb
---
warning | Ignored bad PDB record found on line 43136
END
Chain information for complex_dimer.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> color byhetero
> color bychain
> close session
> open C:/Users/Arnold/Downloads/postprocess.mrc
Opened postprocess.mrc, grid size 300,300,300, pixel 1.65, shown at level
0.00536, step 2, values float32
> volume #1 level 0.0239
> volume #1 step 1
> close session
> open C:/Users/Arnold/Downloads/open_dimer-FINAL-
> coot-0_real_space_refined_204.pdb
Chain information for open_dimer-FINAL-coot-0_real_space_refined_204.pdb #1
---
Chain | Description
A B | No description available
> hide #!1 models
> close #1
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-1_real_space_refined_202.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-0_real_space_refined_204.pdb
Chain information for closed_dimer-FINAL-coot-1_real_space_refined_202.pdb #1
---
Chain | Description
A B | No description available
Chain information for open_dimer-FINAL-coot-0_real_space_refined_204.pdb #2
---
Chain | Description
A B | No description available
> mmaker #1 on #2
> matchmaker #1 on #2
Expected a keyword
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-0_real_space_refined_204.pdb, chain A (#2)
with closed_dimer-FINAL-coot-1_real_space_refined_202.pdb, chain B (#1),
sequence alignment score = 5277.9
RMSD between 775 pruned atom pairs is 0.985 angstroms; (across all 1129 pairs:
10.144)
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B
Alignment identifier is 1
Drag select of 1 residues
> ui tool show "Color Actions"
> color sel #ddecf9ff
> color sel #ccccccff
> color sel #c8c5c8ff
> color sel #787718ff
> color sel #8c9297ff
> color sel #9ac2f5ff
> color sel #9cc3f4ff
> color sel #f4e379ff
Drag select of 1 residues
> color sel #ffffffff
> color sel #d7eaf8ff
> color sel #7886a2ff
> color sel #ccccccff
> color sel #f0f0f0ff
> color sel #8e9193ff
> color sel #f7fbfcff
> color sel #f1ebe6ff
> color sel #f2e5dfff
> color sel #e1c4b2ff
> color sel #e3d2c8ff
> color sel #f2e5dfff
> color sel #f6f2eeff
> color sel #e1c4b2ff
> color sel #cce4f7ff
> color sel #867878ff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #90ee90ff
> color sel #4d4f52ff
> color sel #9ac2f5ff
> color sel #f5e27bff
> color sel #f4e379ff
> color sel #4275aeff
> color sel #3c79afff
> color sel #4377a7ff
> color sel #ece691ff
> color sel #9ac2f5ff
> color sel #f4e379ff
> color sel #4377a7ff
> color sel #9ac2f5ff
> color sel #ffffffff
> color sel #f8f8f8ff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #91c37dff
> color sel #ccccccff
> color sel #187778ff
> color sel #928986ff
> color sel #9ac2f5ff
> color sel #ffffffff
> color sel #b3eaf8ff
> color sel #90ee90ff
> color sel #979899ff
> color sel #4377a7ff
> select clear
> lighting soft
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL.ccp4
Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 1.11, step 2, values float32
> volume #3 step 1
> volume #3 level 16.41
> surface zone #3 nearAtoms #1 newMap True
Expected a keyword
> volume zone #3 nearAtoms #1 range 3 newMap true
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> color zone #4 near #1 distance 20
> color sel #9ac2f5ff
> color zone #4 near #1 distance 20
> select clear
> hide #!4 models
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B
Alignment identifier is 1
Drag select of 1 residues
> color sel #f4e379ff
Drag select of 2 residues
> color sel #e1c4b2ff
> select clear
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL.ccp4
Opened open_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 0.978, step 2, values float32
> volume #5 level 9.627
> volume #5 step 1
> volume #5 level 17.41
> volume zone #5 nearAtoms #2 range 3 newMap true
> color zone #6 near #2 distance 20
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color zone #6 near #2 distance 20
Drag select of 1 residues, 6 open_dimer-FINAL.ccp4 zone
> color sel #9ac2f5ff
> color zone #6 near #2 distance 20
> select clear
> hide #!6 models
> hide #!2 models
> show #!6 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!4 models
> surface zone #4 #6 size 5
Expected a keyword
> surface dust #4 #6 size 5
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!4 models
> show #!6 models
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #1
---
Chain | Description
A B | No description available
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting simple
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting flat
> lighting simple
> graphics silhouettes false
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B
Alignment identifier is 1
> select clear
> select clear
Drag select of 2 residues
> color sel #f4e379ff
> color sel #4377a7ff
> color sel #e1c4b2ff
> select clear
> color sel #9ac2f5ff
> select clear
> lighting shadows true
> graphics silhouettes true
> lighting shadows false
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> lighting soft
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL.ccp4
Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
level 1.63, step 2, values float32
> close #2
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL.ccp4
Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 1.11, step 2, values float32
> volume #2 level 13.94
> volume #2 step 1
> surface dust #4 #6 size 5
No surfaces specified
> volume zone #2 nearAtoms #1 range 3 newMap true
> color zone #3 near #1 distance 20
> hide #!3 models
> hide #1 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #4
---
Chain | Description
A B | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B
Alignment identifier is 1
Drag select of 1 residues
> color sel #f4e379ff
Drag select of 1 residues
> color sel #e1c4b2ff
> color sel #9ac2f5ff
> select clear
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL.ccp4
Opened open_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 0.978, step 2, values float32
> volume #5 level 5.92
> volume #5 step 1
> volume #5 level 18.9
> volume zone #5 nearAtoms #4 range 3 newMap true
> hide #4 models
> show #4 models
> color zone #6 nearAtoms #5 distance 20
Expected a keyword
> color zone #6 near #5 distance 20
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> color zone #6 near #4 distance 20
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> hide #4 models
> hide #!6 models
> show #1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #!3 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #!3 models
> show #4 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #4 models
> show #!6 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #!6 models
> show #1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #!3 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #!3 models
> show #4 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #4 models
> show #!6 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #!6 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL.ccp4
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
Chain information for complex_dimer-FINAL-coot-7.pdb #8
---
Chain | Description
A C | No description available
B | No description available
D | No description available
Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
level 1.63, step 2, values float32
> volume #7 level 4.258
> volume #7 step 1
> hide #!8 models
> show #!8 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A #8/C
Alignment identifier is 1
> select #8/A:545
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #f4e379ff
> select #8/A:799
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/A:550
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel #e1c4b2ff
> color sel #9ac2f5ff
> select clear
> select #8/C
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> select #8/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> select #8/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> select clear
> select #8/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> color (#!8 & sel) #ffffffff
> color (#!8 & sel) #000053ff
> color (#!8 & sel) #f0f0f0ff
> color (#!8 & sel) #ffffffff
> color (#!8 & sel) #222222ff
> color (#!8 & sel) #ffffffff
> color (#!8 & sel) #505a8dff
> color (#!8 & sel) #899affff
> color (#!8 & sel) #808feeff
> color (#!8 & sel) #7b89e1ff
> color (#!8 & sel) #7583d5ff
> color (#!8 & sel) #727fcdff
> color (#!8 & sel) #707cc9ff
> color (#!8 & sel) #6f7bc6ff
> color (#!8 & sel) #606dbfff
> color (#!8 & sel) #8091faff
> color (#!8 & sel) #7c8df5ff
> color (#!8 & sel) #7d8df6ff
> color (#!8 & sel) #7d8ef7ff
> color (#!8 & sel) #7d8ef8ff
> color (#!8 & sel) #7e8ff9ff
> color (#!8 & sel) #7c8df4ff
> color (#!8 & sel) #e2e2e2ff
> color (#!8 & sel) #ffffffff
> color (#!8 & sel) #808fe2ff
> color (#!8 & sel) #8c9dffff
> color (#!8 & sel) #8595f8ff
> color (#!8 & sel) #8291f2ff
> color (#!8 & sel) #8090efff
> color (#!8 & sel) #7d8ce7ff
> color (#!8 & sel) #7987deff
> color (#!8 & sel) #7582d4ff
> color (#!8 & sel) #151723ff
> color (#!8 & sel) #6a75bcff
> color (#!8 & sel) #1c1c1cff
> color (#!8 & sel) #5560a7ff
> color (#!8 & sel) #7280dbff
> color (#!8 & sel) #7281dbff
> select clear
> select #8/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #4377a7ff
> color sel #7281dbff
> select clear
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> volume zone #7 nearAtoms #8 range 3 newMap true
> color zone #9 near #7 distance 20
> color zone #9 near #8 distance 20
> volume #9 level 6.374
> volume #9 level 9.196
> volume #9 level 12.72
> volume #9 level 19.43
> hide #!8 models
> surface dust # 9 size 5
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!8 models
> show #!9 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #!9 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #!8 models
> show #!9 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image8.png supersample 3
> hide #!8 models
> show #!9 models
> save C:\Users\Arnold\Desktop\image9.png supersample 3
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!3 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!3 models
> show #4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #4 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #!3 models
> hide #!3 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #4 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!8 models
> show #1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #4 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!8 models
> open C:/Users/Arnold/Downloads/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #10
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open C:/Users/Arnold/Downloads/lipids_slice.pdb
> hide #11 models
> show #11 models
> hide #10 models
> show #10 models
> select #10
11218 atoms, 11405 bonds, 1408 residues, 1 model selected
> ui mousemode right "translate selected models"
> ~select #10
Nothing selected
> ui mousemode right swapaa
> ui mousemode right swapaa
> hide #10 models
> select #11
313093 atoms, 317626 bonds, 3369 residues, 1 model selected
> hide sel atoms
> show sel atoms
> style sel stick
Changed 313093 atom styles
> select clear
> close #11
> show #!3 models
> show #4 models
> hide #4 models
> show #1 models
> hide #!3 models
> hide #1 models
> show #1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #4 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!8 models
> show #!5 models
> hide #!5 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #4 models
> show #1 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #11
---
Chain | Description
A | No description available
C | No description available
> swapaa mousemode #1/A:561 GLN
> select #11
2990 atoms, 3024 bonds, 389 residues, 1 model selected
> swapaa mousemode #11/C:64 ALA
> ui mousemode right translate
> ui mousemode right "translate selected models"
Drag select of 12 atoms, 446 residues, 10 bonds
> hide sel atoms
> select clear
> ui tool show "Fit in Map"
Fit molecule ger2.pdb (#11) to map closed_dimer-FINAL.ccp4 (#2) using 2988
atoms
average map value = 8.317, steps = 232
shifted from previous position = 9.24
rotated from previous position = 42.6 degrees
atoms outside contour = 2063, contour level = 13.94
Position of ger2.pdb (#11) relative to closed_dimer-FINAL.ccp4 (#2)
coordinates:
Matrix rotation and translation
0.93550398 0.15724014 0.31639822 249.10411821
0.19555749 -0.97626931 -0.09303492 328.72846253
0.29426104 0.14890858 -0.94405332 329.51008491
Axis 0.98368142 0.09000417 0.15578869
Axis point 0.00000000 144.22327553 154.42235547
Rotation angle (degrees) 172.93596315
Shift along axis 325.95996886
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2k5u.pdb
2k5u.pdb title:
Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
info...]
Chain information for 2k5u.pdb
---
Chain | Description
12.1/A | adp-ribosylation factor 1
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
12.12/A 12.13/A 12.14/A 12.15/A 12.16/A | adp-ribosylation factor 1
> close #12.2-16
> matchmaker #12 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#11) with 2k5u.pdb, chain A (#12.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> hide #11 models
> hide #1 models
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
Drag select of 43 atoms, 196 residues, 44 bonds
> hide sel atoms
> select clear
> select #12
2952 atoms, 2981 bonds, 182 residues, 2 models selected
> color sel #4377a7ff
> color sel #7281dbff
> color sel #7383ddff
> color sel #7484deff
> color sel #7484dfff
> color sel #7686e2ff
> color sel #7788e5ff
> color sel #798ae8ff
> color sel #7a8beaff
> color sel #7b8bebff
> color sel #7b8cecff
> color sel #7c8deeff
> color sel #7d8eefff
> color sel #7d8ef0ff
> color sel #7e8ff1ff
> color sel #7f90f3ff
> color sel #7f91f4ff
> color sel #8091f5ff
> color sel #8193f7ff
> color sel #8193f8ff
> color sel #8294f9ff
> color sel #8294faff
> color sel #8396fcff
> color sel #8496fdff
> color sel #8497feff
> color sel #8597ffff
> color sel #8497feff
> color sel #8496fdff
> color sel #8294f9ff
> color sel #7f90f3ff
> color sel #7d8eefff
> color sel #7a8beaff
> color sel #7889e7ff
> color sel #7889e6ff
> color sel #7686e2ff
> color sel #7484dfff
> color sel #7383dcff
> color sel #6f7ed4ff
> color sel #6e7dd3ff
> color sel #6d7cd1ff
> color sel #6c7bcfff
> color sel #6b7aceff
> color sel #6a78cbff
> color sel #6876c7ff
> color sel #6471bfff
> color sel #6270bdff
> color sel #626fbcff
> color sel #606db8ff
> color sel #5d6ab3ff
> color sel #5c68b0ff
> color sel #5a67adff
> color sel #5965aaff
> color sel #5763a7ff
> color sel #5662a6ff
> color sel #5662a5ff
> color sel #525e9eff
> color sel #505b9aff
> color sel #4f5a98ff
> color sel #4e5996ff
> color sel #4e5895ff
> color sel #4d5894ff
> color sel #4c5793ff
> color sel #4b5691ff
> color sel #4b5590ff
> color sel #4b5691ff
> color sel #505b9aff
> color sel #525e9eff
> color sel #5460a2ff
> color sel #5662a5ff
> color sel #5763a7ff
> color sel #5965abff
> color sel #5a67adff
> color sel #5c69b1ff
> color sel #5d6ab3ff
> color sel #5f6cb6ff
> color sel #606eb9ff
> color sel #6270bdff
> color sel #6471bfff
> color sel #6573c2ff
> color sel #6775c5ff
> color sel #6876c7ff
> color sel #6877c8ff
> color sel #6b7aceff
> color sel #6c7bcfff
> color sel #6c7bd0ff
> color sel #6f7ed4ff
> color sel #707fd6ff
> color sel #7180d8ff
> color sel #7281daff
> color sel #7383ddff
> color sel #7484dfff
> color sel #7586e1ff
> color sel #7788e5ff
> color sel #7889e7ff
> color sel #7b8bebff
> color sel #7b8cecff
> color sel #7d8eefff
> color sel #7d8ef0ff
> color sel #7e8ff1ff
> color sel #7f90f3ff
> color sel #7f91f4ff
> color sel #8091f5ff
> color sel #8193f7ff
> color sel #8294f9ff
> color sel #8294faff
> color sel #8396fcff
> color sel #8497feff
> color sel #8597ffff
> select clear
> select ::name="MYR"
42 atoms, 41 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> select ::name="GDP"
40 atoms, 42 bonds, 1 residue, 1 model selected
> color sel byhetero
No model chosen to save relative to
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs includeMaps true
> select ::name="GDP"
40 atoms, 42 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel #ffaaffff
> color sel byhetero
> select clear
> select ::name="MYR"
42 atoms, 41 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> show #1 models
> hide #!12 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #4 models
> hide #1 models
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #13
---
Chain | Description
A | No description available
C | No description available
> hide #4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> select #13
2990 atoms, 3024 bonds, 389 residues, 1 model selected
Fit molecule ger2.pdb (#13) to map open_dimer-FINAL.ccp4 (#5) using 2990 atoms
average map value = 2.65, steps = 112
shifted from previous position = 5.18
rotated from previous position = 14.5 degrees
atoms outside contour = 2575, contour level = 18.898
Position of ger2.pdb (#13) relative to open_dimer-FINAL.ccp4 (#5) coordinates:
Matrix rotation and translation
0.83150660 -0.32310828 -0.45188252 334.47827146
-0.40828316 -0.90705896 -0.10270785 338.75699998
-0.37669833 0.26989828 -0.88614519 332.68541347
Axis 0.95652433 -0.19300676 -0.21865407
Axis point 0.00000000 183.98124055 223.78732810
Rotation angle (degrees) 168.76866172
Shift along axis 181.81119216
> select clear
> select #13
2990 atoms, 3024 bonds, 389 residues, 1 model selected
Fit molecule ger2.pdb (#13) to map open_dimer-FINAL.ccp4 (#5) using 2990 atoms
average map value = 9.852, steps = 260
shifted from previous position = 7.6
rotated from previous position = 37.6 degrees
atoms outside contour = 2146, contour level = 18.898
Position of ger2.pdb (#13) relative to open_dimer-FINAL.ccp4 (#5) coordinates:
Matrix rotation and translation
0.89467687 -0.43384390 0.10645546 293.26294690
-0.44670038 -0.87072757 0.20565084 303.40477431
0.00347334 -0.23154475 -0.97281805 345.05274987
Axis -0.97296277 0.22918294 -0.02861163
Axis point 0.00000000 206.04153636 147.44800737
Rotation angle (degrees) 167.01639027
Shift along axis -225.67125473
> select #6
2 models selected
> select clear
> hide #!6 models
> show #!6 models
> hide #!6 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2k5u.pdb
2k5u.pdb title:
Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
info...]
Chain information for 2k5u.pdb
---
Chain | Description
14.1/A | adp-ribosylation factor 1
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
14.12/A 14.13/A 14.14/A 14.15/A 14.16/A | adp-ribosylation factor 1
> close #14.2-16
> matchmaker #14 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#13) with 2k5u.pdb, chain A (#14.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
15.1/A | adp-ribosylation factor 1
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
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-
ribosylation factor 1
Drag select of 5382 atoms, 3600 residues, 4965 bonds
> matchmaker #15 to #15
Specify a single 'to' model only
> matchmaker #15 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.1), sequence
alignment score = 767.7
RMSD between 95 pruned atom pairs is 1.117 angstroms; (across all 180 pairs:
8.424)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.2), sequence
alignment score = 785.8
RMSD between 95 pruned atom pairs is 1.110 angstroms; (across all 180 pairs:
7.715)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.3), sequence
alignment score = 772.6
RMSD between 94 pruned atom pairs is 1.129 angstroms; (across all 180 pairs:
7.309)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.4), sequence
alignment score = 765.4
RMSD between 97 pruned atom pairs is 1.068 angstroms; (across all 180 pairs:
8.269)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.5), sequence
alignment score = 776.8
RMSD between 95 pruned atom pairs is 1.109 angstroms; (across all 180 pairs:
8.459)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.6), sequence
alignment score = 785.2
RMSD between 95 pruned atom pairs is 1.137 angstroms; (across all 180 pairs:
8.055)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.7), sequence
alignment score = 777.4
RMSD between 100 pruned atom pairs is 1.135 angstroms; (across all 180 pairs:
9.001)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.8), sequence
alignment score = 782.2
RMSD between 96 pruned atom pairs is 1.178 angstroms; (across all 180 pairs:
8.591)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.9), sequence
alignment score = 749.8
RMSD between 100 pruned atom pairs is 1.116 angstroms; (across all 180 pairs:
9.079)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.10), sequence
alignment score = 786.4
RMSD between 101 pruned atom pairs is 1.122 angstroms; (across all 180 pairs:
8.786)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.11), sequence
alignment score = 769
RMSD between 95 pruned atom pairs is 1.117 angstroms; (across all 180 pairs:
8.678)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.12), sequence
alignment score = 775.6
RMSD between 95 pruned atom pairs is 1.081 angstroms; (across all 180 pairs:
7.518)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.13), sequence
alignment score = 778.6
RMSD between 102 pruned atom pairs is 1.069 angstroms; (across all 180 pairs:
8.329)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.14), sequence
alignment score = 782.2
RMSD between 92 pruned atom pairs is 1.079 angstroms; (across all 180 pairs:
8.049)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.15), sequence
alignment score = 775
RMSD between 94 pruned atom pairs is 1.224 angstroms; (across all 180 pairs:
9.000)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.16), sequence
alignment score = 764.2
RMSD between 93 pruned atom pairs is 1.072 angstroms; (across all 180 pairs:
9.002)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.17), sequence
alignment score = 779.8
RMSD between 96 pruned atom pairs is 1.161 angstroms; (across all 180 pairs:
8.165)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.18), sequence
alignment score = 767.8
RMSD between 97 pruned atom pairs is 1.130 angstroms; (across all 180 pairs:
8.283)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.19), sequence
alignment score = 772
RMSD between 95 pruned atom pairs is 1.127 angstroms; (across all 180 pairs:
8.772)
Matchmaker 2k5u.pdb, chain A (#14.1) with 2ksq.pdb, chain A (#15.20), sequence
alignment score = 772
RMSD between 98 pruned atom pairs is 1.154 angstroms; (across all 180 pairs:
9.201)
> close #15.2-20
> select clear
> matchmaker #15 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.1), sequence
alignment score = 653.1
RMSD between 107 pruned atom pairs is 1.190 angstroms; (across all 165 pairs:
3.564)
> hide #13 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> close #15
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
15.1/A | adp-ribosylation factor 1
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
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-
ribosylation factor 1
> show #13 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #13 models
> show #13 models
> show #!15 models
> matchmaker #15 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.1), sequence
alignment score = 653.1
RMSD between 107 pruned atom pairs is 1.190 angstroms; (across all 165 pairs:
3.564)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.2), sequence
alignment score = 673.5
RMSD between 114 pruned atom pairs is 1.167 angstroms; (across all 165 pairs:
3.522)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.3), sequence
alignment score = 660.3
RMSD between 110 pruned atom pairs is 1.141 angstroms; (across all 165 pairs:
3.603)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.4), sequence
alignment score = 653.1
RMSD between 110 pruned atom pairs is 1.124 angstroms; (across all 165 pairs:
3.563)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.5), sequence
alignment score = 654.9
RMSD between 110 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.685)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.6), sequence
alignment score = 656.7
RMSD between 107 pruned atom pairs is 1.142 angstroms; (across all 165 pairs:
3.681)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.7), sequence
alignment score = 665.1
RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.623)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.8), sequence
alignment score = 663.9
RMSD between 112 pruned atom pairs is 1.157 angstroms; (across all 165 pairs:
3.648)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.9), sequence
alignment score = 638.1
RMSD between 115 pruned atom pairs is 1.091 angstroms; (across all 165 pairs:
3.623)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.10), sequence
alignment score = 671.1
RMSD between 119 pruned atom pairs is 1.108 angstroms; (across all 165 pairs:
3.493)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.11), sequence
alignment score = 647.1
RMSD between 107 pruned atom pairs is 1.106 angstroms; (across all 165 pairs:
3.749)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.12), sequence
alignment score = 660.3
RMSD between 116 pruned atom pairs is 1.120 angstroms; (across all 165 pairs:
3.698)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.13), sequence
alignment score = 663.3
RMSD between 114 pruned atom pairs is 1.015 angstroms; (across all 165 pairs:
3.578)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.14), sequence
alignment score = 663.9
RMSD between 108 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.655)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.15), sequence
alignment score = 656.7
RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
3.660)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.16), sequence
alignment score = 648.9
RMSD between 114 pruned atom pairs is 1.154 angstroms; (across all 165 pairs:
3.728)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.17), sequence
alignment score = 648.9
RMSD between 108 pruned atom pairs is 1.173 angstroms; (across all 165 pairs:
3.507)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.18), sequence
alignment score = 649.5
RMSD between 110 pruned atom pairs is 1.120 angstroms; (across all 165 pairs:
3.716)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.19), sequence
alignment score = 656.7
RMSD between 110 pruned atom pairs is 1.136 angstroms; (across all 165 pairs:
3.583)
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.20), sequence
alignment score = 656.7
RMSD between 113 pruned atom pairs is 1.167 angstroms; (across all 165 pairs:
3.587)
> hide #15.1 models
> hide #15.2 models
> hide #15.3 models
> hide #15.4 models
> hide #15.5 models
> hide #!15 models
> show #15.1 models
> hide #!15 models
> hide #15.1 models
> hide #15.6 models
> hide #15.8 models
> hide #15.7 models
> hide #15.20 models
> hide #15.19 models
> hide #15.18 models
> hide #15.17 models
> hide #15.16 models
> hide #15.15 models
> hide #15.14 models
> hide #15.13 models
> hide #15.11 models
> hide #15.12 models
> hide #15.10 models
> hide #15.9 models
> show #15.1 models
> hide #15.1 models
> show #15.2 models
> hide #15.2 models
> show #15.3 models
> hide #15.3 models
> show #15.4 models
> hide #15.4 models
> show #15.5 models
> hide #15.5 models
> show #15.6 models
> hide #15.6 models
> show #15.7 models
> hide #15.7 models
> show #15.8 models
> hide #15.8 models
> show #15.9 models
> hide #15.9 models
> show #15.10 models
> hide #15.10 models
> show #15.11 models
> hide #15.11 models
> show #15.12 models
> hide #15.12 models
> show #15.13 models
> hide #15.13 models
> show #15.14 models
> hide #15.14 models
> show #15.15 models
> show #!14 models
> hide #!14 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> close #15.1-14
> hide #!6 models
> close #15.16-20
> hide #13 models
Drag select of 262 atoms, 180 residues, 241 bonds
> hide sel atoms
> select clear
> select ::name="MYR"
126 atoms, 123 bonds, 3 residues, 3 models selected
> select #12
2952 atoms, 2981 bonds, 182 residues, 2 models selected
> ~select #12
Nothing selected
> select clear
> select ::name="MYR"
126 atoms, 123 bonds, 3 residues, 3 models selected
> show sel & #15.15 atoms
> select clear
> select ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide #!15 models
> select #15
3045 atoms, 3079 bonds, 187 residues, 2 models selected
> show #!15 models
> color sel #7281dbff
> color sel #7383dcff
> color sel #7281daff
> color sel #6d7cd1ff
> color sel #6674c3ff
> color sel #616ebaff
> color sel #5e6bb5ff
> color sel #5d6ab3ff
> color sel #5c68b0ff
> color sel #5a67adff
> color sel #5a66acff
> color sel #5965abff
> select clear
Drag select of 85 atoms, 180 residues, 86 bonds
> color sel byhetero
> select clear
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel #ff007fff
> color sel byhetero
> select clear
> hide #!15 models
> hide #15.15 models
> show #1 models
> show #11 models
> hide #11 models
> show #!12 models
> show #13 models
> hide #!12 models
> hide #13 models
> show #!14 models
> show #4 models
> hide #1 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #15.15 models
> hide #15.15 models
> show #15.15 models
> hide #!15 models
> show #!14 models
> show #!15 models
> hide #15.15 models
> hide #!15 models
> show #15.15 models
> hide #4 models
> hide #!14 models
> hide #!15 models
> hide #15.15 models
> show #1 models
> show #4 models
> hide #4 models
> show #11 models
> hide #11 models
> show #!12 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> hide #!12 models
> show #13 models
> hide #13 models
> show #!14 models
> select #14
2952 atoms, 2981 bonds, 182 residues, 2 models selected
> color sel #7281dbff
> color sel byhetero
> color sel #240000ff
> color sel #ccccccff
> color sel #ffffffff
> color sel #d9d9d9ff
> color sel #ffffffff
> color sel #ffaa55ff
> color sel #ffffffff
> color sel #abb8ffff
> color sel #8597ffff
> color sel byhetero
> select clear
> select ::name="GDP"
80 atoms, 84 bonds, 2 residues, 2 models selected
> color (#14.1 & sel) #ffaaffff
> color sel & #14.1 byhetero
> select clear
> hide #12.1 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #4 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> show #!2 models
> hide #!2 models
> hide #12.1 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #4 models
> hide #1 models
> show #!14 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #4 models
> hide #!14 models
> show #!9 models
> hide #!9 models
> show #!8 models
> select #8/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> select #8/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #!8 models
> select #8
21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected
> show #1 models
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right translate
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> show #4 models
> hide #1 models
> show #!14 models
> hide #12.1 models
> show #!15 models
> hide #!15 models
> show #15.15 models
> hide #15.15 models
> show #15.15 models
> hide #15.15 models
> hide #!14 models
> hide #!15 models
> hide #4 models
> show #4 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #4 models
> hide #!12 models
> show #!14 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #!14 models
> hide #12.1 models
> ~select #8
Nothing selected
> hide #4 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> save C:\Users\Arnold\Desktop\image8.png supersample 3
> hide #12.1 models
> hide #!12 models
> show #1 models
> show #12.1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #12.1 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> show #4 models
> hide #1 models
> hide #!12 models
> show #!14 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #4 models
> show #!2 models
> hide #!2 models
> hide #!14 models
> show #!15 models
> show #15.15 models
> hide #!15 models
> show #1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #4 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #4 models
> show #4 models
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> hide #4 models
> hide #15.15 models
> hide #12.1 models
> hide #!12 models
> show #1 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> show #11 models
> hide #11 models
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #16
---
Chain | Description
A | No description available
C | No description available
> select #16
2990 atoms, 3024 bonds, 389 residues, 1 model selected
> ui mousemode right "translate selected models"
Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
2990 atoms
average map value = 2.881, steps = 72
shifted from previous position = 3.15
rotated from previous position = 3.4 degrees
atoms outside contour = 2589, contour level = 13.94
Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
coordinates:
Matrix rotation and translation
-0.91511885 -0.20261121 0.34857737 191.41831251
0.03540339 0.82084041 0.57005931 133.43896567
-0.40162680 0.53401284 -0.74399341 293.87252456
Axis -0.04575115 0.95217945 0.30209457
Axis point 123.84831938 0.00000000 104.11434027
Rotation angle (degrees) 156.80008533
Shift along axis 207.07752694
Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
2990 atoms
average map value = 2.174, steps = 136
shifted from previous position = 3.92
rotated from previous position = 11.1 degrees
atoms outside contour = 2693, contour level = 13.94
Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
coordinates:
Matrix rotation and translation
-0.95811570 -0.20329010 0.20171129 203.21957913
-0.01141659 0.73089825 0.68239095 114.52557294
-0.28615376 0.65150663 -0.70260597 292.79453452
Axis -0.05881058 0.92900290 0.36536957
Axis point 121.00023796 0.00000000 108.40830819
Rotation angle (degrees) 164.77711778
Shift along axis 201.42134211
> matchmaker #16 to #3
No 'to' model specified
> matchmaker #16 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
with ger2.pdb, chain C (#16), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
Fit molecule ger2.pdb (#16) to map closed_dimer-FINAL.ccp4 zone (#3) using
2990 atoms
average map value = 8.581, steps = 124
shifted from previous position = 5.16
rotated from previous position = 21.4 degrees
atoms outside contour = 2090, contour level = 13.94
Position of ger2.pdb (#16) relative to closed_dimer-FINAL.ccp4 zone (#3)
coordinates:
Matrix rotation and translation
-0.93445292 -0.15891148 -0.31866108 250.14498889
-0.19549211 0.97691904 0.08609311 171.18116813
0.29762489 0.14274569 -0.94395079 330.03844216
Axis 0.09138035 -0.99406645 -0.05900439
Axis point 107.34815589 0.00000000 181.15022546
Rotation angle (degrees) 161.94183740
Shift along axis -166.78083774
> ~select #16
Nothing selected
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2k5u.pdb
2k5u.pdb title:
Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
info...]
Chain information for 2k5u.pdb
---
Chain | Description
17.1/A | adp-ribosylation factor 1
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
17.12/A 17.13/A 17.14/A 17.15/A 17.16/A | adp-ribosylation factor 1
> close #17.2-16
> matchmaker #17 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> hide #12.1 models
> hide #!12 models
> hide #16 models
> show #!14 models
> select ::name="GDP"
120 atoms, 126 bonds, 3 residues, 3 models selected
> color (#14.1#17.1 & sel) #55ffffff
> color (#14.1#17.1 & sel) #ffaaffff
> color sel & #14.1#17.1 byhetero
> select clear
> hide #!14 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> hide #!12 models
> hide #12.1 models
> hide #!17 models
> hide #17.1 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #13 models
> hide #13 models
> show #!14 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2k5u.pdb
2k5u.pdb title:
Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
info...]
Chain information for 2k5u.pdb
---
Chain | Description
18.1/A | adp-ribosylation factor 1
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
18.12/A 18.13/A 18.14/A 18.15/A 18.16/A | adp-ribosylation factor 1
> close #18.2-16
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #19
---
Chain | Description
A | No description available
C | No description available
> matchmaker #19 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
with ger2.pdb, chain C (#19), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
> matchmaker #18 to #19
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#19) with 2k5u.pdb, chain A (#18.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> hide #!18 models
> hide #18.1 models
> hide #19 models
> show #!18 models
> hide #!18 models
> show #18.1 models
> view #!9 clip false
No displayed objects specified.
> select ::name="GDP"
160 atoms, 168 bonds, 4 residues, 4 models selected
> color (#14.1#18.1 & sel) #55ffffff
> color (#14.1#18.1 & sel) #ffaaffff
> color sel & #14.1#18.1 byhetero
> select clear
> hide #18.1 models
> hide #!18 models
> hide #!14 models
> hide #4 models
> show #1 models
> show #!12 models
> show #12.1 models
> hide #!12 models
> show #!17 models
> hide #!17 models
> show #17.1 models
> hide #17.1 models
> show #17.1 models
> hide #!17 models
> hide #12.1 models
> hide #17.1 models
> show #17.1 models
> show #12.1 models
> show #!18 models
> hide #!18 models
> show #18.1 models
> hide #18.1 models
> select ::name="GDP"
160 atoms, 168 bonds, 4 residues, 4 models selected
> color (#12.1#17.1 & sel) #55ffffff
> color (#12.1#17.1 & sel) #ffaaffff
> color sel & #12.1#17.1 byhetero
> select clear
> hide #!17 models
> hide #!12 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #17.1 models
> hide #!18 models
> hide #12.1 models
> show #4 models
> hide #1 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #4 models
> show #1 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #1 models
> show #1 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> show #17.1 models
> show #18.1 models
> hide #18.1 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #!12 models
> hide #12.1 models
> hide #!17 models
> hide #17.1 models
> hide #!18 models
> show #4 models
> hide #1 models
> show #!18 models
> hide #!18 models
> show #18.1 models
> show #!14 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #!18 models
> hide #18.1 models
> hide #!14 models
> show #!8 models
> hide #4 models
> select #8/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> show sel cartoons
> select clear
> save C:\Users\Arnold\Desktop\image8.png supersample 3
> hide #!8 models
> show #!15 models
> show #15.15 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #15.15 models
> hide #!15 models
> show #1 models
> open C:/Users/Arnold/Downloads/AF-P39993-F1-model_v1.pdb
AF-P39993-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-P39993-F1-model_v1.pdb #20
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> close #20
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #20
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> matchmaker #20 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#20), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
Drag select of 16 residues
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A #20/A
Alignment identifier is 1
Seqview [ID: 1] region 2 chains [1-207] RMSD: 344.416
Drag select of 14 residues
Seqview [ID: 1] region 2 chains [978-979] RMSD: 388.274
Seqview [ID: 1] region 2 chains [1-977] RMSD: 310.189
> delete atoms (#20 & sel)
> delete bonds (#20 & sel)
Seqview [ID: 1] region 2 chains [993] RMSD: 391.524
Seqview [ID: 1] region 2 chains [999-1001] RMSD: 376.840
Seqview [ID: 1] region 2 chains [998-1408] RMSD: 315.123
> delete atoms (#20 & sel)
> delete bonds (#20 & sel)
> select clear
> select clear
> hide #20 models
> show #20 models
> select #20
155 atoms, 156 bonds, 20 residues, 1 model selected
> ~select #20
Nothing selected
> select #20
155 atoms, 156 bonds, 20 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select #20
155 atoms, 156 bonds, 20 residues, 1 model selected
> color sel #7281dbff
> color sel #4377a7ff
> color sel #ffaaffff
> select clear
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #21
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> matchmaker #20 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#20), sequence alignment score =
2159.3
RMSD between 4 pruned atom pairs is 0.236 angstroms; (across all 4 pairs:
0.236)
> matchmaker #21 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> matchmaker #21 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A #20/A #21/A
Alignment identifier is 1
Drag select of 1 residues
Seqview [ID: 1] region 3 chains [1-976] RMSD: 310.105
> delete atoms (#21 & sel)
> delete bonds (#21 & sel)
Seqview [ID: 1] region 3 chains [999-1408] RMSD: 314.967
> delete atoms (#21 & sel)
> delete bonds (#21 & sel)
> hide #1 models
> hide #20 models
> hide #21 models
> show #4 models
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #22
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> matchmaker #22 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#22), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
> matchmaker #21 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#21), sequence alignment score =
2161.7
RMSD between 6 pruned atom pairs is 0.798 angstroms; (across all 6 pairs:
0.798)
> show #21 models
> hide #21 models
> show #21 models
> hide #21 models
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #23
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> hide #22 models
> hide #23 models
> show #23 models
> matchmaker #23 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#23), sequence alignment score =
3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> hide #23 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #24
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open "C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1 (1).pdb"
AF-P47102-F1-model_v1 (1).pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1 (1).pdb #25
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> matchmaker #24 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#24), sequence alignment score =
3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> hide #24 models
> hide #25 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #4 models
> show #23 models
> show #22 models
> matchmaker #22 to #4/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#4)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#22), sequence alignment score =
3215.1
RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
10.861)
> matchmaker #23 to #4/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
with AF-P47102-F1-model_v1 (1).pdb, chain A (#23), sequence alignment score =
3284.5
RMSD between 394 pruned atom pairs is 1.192 angstroms; (across all 1128 pairs:
11.128)
> hide #23 models
> hide #22 models
> show #24 models
> show #25 models
> show #!8 models
> hide #4 models
> matchmaker #24 to #8/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
AF-P47102-F1-model_v1 (1).pdb, chain A (#24), sequence alignment score =
3470.5
RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
9.022)
> matchmaker #25 to #8/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
AF-P47102-F1-model_v1 (1).pdb, chain A (#25), sequence alignment score = 3462
RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
9.117)
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
Alignment identifier is 1
Drag select of 2 residues
Seqview [ID: 1] region 7 chains [1-977] RMSD: 213.225
> delete atoms (#24-25 & sel)
> delete bonds (#24-25 & sel)
Seqview [ID: 1] region 7 chains [999-1001] RMSD: 244.336
Seqview [ID: 1] region 7 chains [999-1408] RMSD: 263.648
> delete atoms (#24-25 & sel)
> delete bonds (#24-25 & sel)
Drag select of 1 residues
Seqview [ID: 1] region 7 chains [998-1030] RMSD: 280.618
Seqview [ID: 1] region 7 chains [978-998] RMSD: 221.446
> color (#24-25 & sel) #55ffffff
> color (#24-25 & sel) #ffaaffff
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select clear
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/lipids_slice.pdb
> hide #25 models
> hide #24 models
> show #26#!8 surfaces
> hide #!8 models
> show #!8 models
> hide #26#!8 surfaces
> hide #!8 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 1 model selected
> show sel surfaces
> select clear
Drag select of lipids_slice.pdb_1X SES surface, lipids_slice.pdb_CX SES
surface, lipids_slice.pdb_SX SES surface, lipids_slice.pdb_EX SES surface,
lipids_slice.pdb_GX SES surface, 313093 atoms, 317626 bonds
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 1 model selected
> color (#!26 & sel) #ffffffff
> color (#!26 & sel) #ffaaffff
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> close #26
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/lipids_slice.pdb
> show #26 surfaces
> hide #!26 models
> show #23 models
> show #22 models
> show #21 models
> show #20 models
> show #24 models
> show #25 models
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> show #1 models
> hide #1 models
> show #1 models
> show #20 models
> show #21 models
> hide #21 models
> show #22 models
> hide #22 models
> show #21 models
> hide #21 models
> show #24 models
> hide #24 models
> show #23 models
> hide #23 models
> show #22 models
> show #23 models
> hide #23 models
> hide #22 models
> hide #20 models
> close #20-25
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #20
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #21
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> matchmaker #20 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-P47102-F1-model_v1.pdb, chain A (#20), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
> matchmaker #21 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-P47102-F1-model_v1.pdb, chain A (#21), sequence alignment score =
3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> hide #1 models
> hide #20 models
> hide #21 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #22
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #23
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> show #4 models
> matchmaker #22 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-P47102-F1-model_v1.pdb, chain A (#22), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
> matchmaker #22 to #4/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#4)
with AF-P47102-F1-model_v1.pdb, chain A (#22), sequence alignment score =
3215.1
RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
10.861)
> matchmaker #23 to #4/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
with AF-P47102-F1-model_v1.pdb, chain A (#23), sequence alignment score =
3284.5
RMSD between 394 pruned atom pairs is 1.192 angstroms; (across all 1128 pairs:
11.128)
> hide #22 models
> hide #23 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #24
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #25
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> hide #4 models
> show #!8 models
> matchmaker #24 to #8/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
AF-P47102-F1-model_v1.pdb, chain A (#24), sequence alignment score = 3470.5
RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
9.022)
> matchmaker #25 to #8/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3462
RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
9.117)
> hide #24 models
> hide #25 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
Alignment identifier is 1
> show #23 models
> hide #23 models
> show #24 models
> hide #24 models
> show #23 models
> hide #23 models
> show #25 models
Drag select of 2 residues
> select clear
Drag select of 2 residues
> select clear
> select #25/A:977
9 atoms, 8 bonds, 1 residue, 1 model selected
Seqview [ID: 1] region 7 chains [978-999] RMSD: 225.702
Seqview [ID: 1] region 7 chains [1-977] RMSD: 184.260
> show #24 models
> hide #24 models
> delete atoms (#25 & sel)
> delete bonds (#25 & sel)
Seqview [ID: 1] region 7 chains [1000-1408] RMSD: 238.000
> delete atoms (#25 & sel)
> delete bonds (#25 & sel)
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #25 models
> show #25 models
> show #24 models
> show #23 models
> show #22 models
> show #21 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> show #25 models
> show #24 models
> show #23 models
> show #22 models
> show #21 models
> show #20 models
> select #25
168 atoms, 170 bonds, 22 residues, 1 model selected
Seqview [ID: 1] region 7 chains [1-977] RMSD: 198.926
> delete atoms (#20-24 & sel)
> delete bonds (#20-24 & sel)
Seqview [ID: 1] region 7 chains [1031-1408] RMSD: 249.442
> delete atoms (#20-24 & sel)
> delete bonds (#20-24 & sel)
Seqview [ID: 1] region 7 chains [1000-1031] RMSD: 217.674
> delete atoms (#20-24 & sel)
> delete bonds (#20-24 & sel)
> select #10
11218 atoms, 11405 bonds, 1408 residues, 1 model selected
> ~select #10
Nothing selected
> select #20
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #21
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #22
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #23
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #20
168 atoms, 170 bonds, 22 residues, 1 model selected
Drag select of 132 residues
> color sel #ffffffff
> color sel #ffaaffff
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select clear
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> show #1 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #1 models
> show #!26 models
> show #!26 surfaces
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> hide #20 models
> hide #21 models
> show #22 models
> show #23 models
> hide #1 models
> show #4 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> hide #4 models
> hide #22 models
> hide #23 models
> show #24 models
> show #25 models
> show #!8 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> show #!26 models
> hide #!26 models
> show #!26 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!26 models
> hide #25 models
> hide #24 models
> hide #!8 models
> show #!26 models
> show #1 models
> hide #1 models
> save C:\Users\Arnold\Desktop\image4.png supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:\Users\Arnold\Desktop\image5.png supersample 3
> show #!12 models
> hide #!12 models
> show #12.1 models
> show #!17 models
> hide #!17 models
> show #17.1 models
> hide #!17 models
> hide #12.1 models
> save C:\Users\Arnold\Desktop\image6.png supersample 3
> show #12.1 models
> show #!18 models
> hide #!18 models
> show #18.1 models
> hide #18.1 models
> show #!17 models
> save C:\Users\Arnold\Desktop\image7.png supersample 3
> hide #12.1 models
> hide #!12 models
> hide #!18 models
> hide #17.1 models
> hide #!17 models
> hide #20 models
> hide #21 models
> show #22 models
> show #23 models
> hide #1 models
> show #4 models
> save C:\Users\Arnold\Desktop\image8.png supersample 3
> hide #4 models
> show #!8 models
> hide #23 models
> hide #22 models
> show #24 models
> show #25 models
> save C:\Users\Arnold\Desktop\image9.png supersample 3
> hide #25 models
> hide #24 models
> hide #!8 models
> show #!14 models
> save C:\Users\Arnold\Desktop\image10.png supersample 3
> hide #!14 models
> show #!15 models
> show #15.15 models
> save C:\Users\Arnold\Desktop\image11.png supersample 3
> transparentBackground true
Unknown command: transparentBackground true
> hide #15.15 models
> hide #!15 models
> show #!26 models
> saved lipids.png transparentBackground true
Unknown command: saved lipids.png transparentBackground true
> save lipids.png transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #!12 models
> hide #!12 models
> show #12.1 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1'
> hide #17.1 models
> hide #!17 models
> hide #12.1 models
> hide #!12 models
> show #4 models
> hide #1 models
> show #22 models
> show #23 models
> hide #21 models
> hide #20 models
> hide #23 models
> hide #22 models
> hide #4 models
> show #1 models
> show #12.1 models
> show #17.1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #21 models
> hide #20 models
> show #22 models
> show #23 models
> hide #17.1 models
> hide #!17 models
> hide #12.1 models
> hide #!12 models
> show #4 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> show #!8 models
> hide #23 models
> hide #22 models
> show #24 models
> show #25 models
> hide #!8 models
> show #!8 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
> transparentBackground true supersample 3
> hide #24 models
> hide #25 models
> hide #!8 models
> show #!14 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp'
> show #15.15 models
> hide #!14 models
> select ::name="MYR"
210 atoms, 205 bonds, 5 residues, 5 models selected
> hide sel & #15.15 atoms
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #15.15 models
> hide #!15 models
> show #12.1 models
> select #12
2952 atoms, 2981 bonds, 182 residues, 2 models selected
> select #12.1
2952 atoms, 2981 bonds, 182 residues, 1 model selected
> ~select #12.1
Nothing selected
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #!12 models
> show #1 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #12.1 models
> hide #1 models
> show #!26 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #12.1 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #21 models
> hide #20 models
> hide #17.1 models
> hide #!17 models
> hide #12.1 models
> hide #!12 models
> hide #1 models
> show #4 models
> show #22 models
> show #23 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #22 models
> hide #23 models
> show #24 models
> show #25 models
> hide #4 models
> show #!8 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
> transparentBackground true supersample 3
> hide #!8 models
> hide #24 models
> hide #25 models
> show #12.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #12.1 models
> hide #!12 models
> show #17.1 models
> hide #17.1 models
> hide #!17 models
> show #!15 models
> show #15.15 models
> hide #!15 models
> show #!14 models
> hide #15.15 models
> show #!15 models
> show #15.15 models
> hide #!14 models
> hide #14.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #15.15 models
> hide #!15 models
> show #1 models
> show #20 models
> show #21 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> show #!15 models
> hide #!15 models
> show #15.15 models
> hide #15.15 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #!17 models
> hide #!15 models
> hide #!12 models
> hide #12.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> side.png transparentBackground true supersample 3
> show #12.1 models
> show #!15 models
> hide #!15 models
> show #15.15 models
> hide #15.15 models
> hide #17.1 models
> hide #!15 models
> hide #!12 models
> hide #12.1 models
> show #12.1 models
> show #14.1 models
> hide #14.1 models
> show #15.15 models
> hide #15.15 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-side.png transparentBackground true supersample 3
> hide #!12 models
> hide #12.1 models
> hide #!14 models
> hide #!15 models
> hide #!17 models
> hide #17.1 models
> hide #20 models
> hide #21 models
> show #25 models
> show #24 models
> show #!8 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
> side.png transparentBackground true supersample 3
> hide #!8 models
> hide #25 models
> hide #24 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #24 models
> show #25 models
> hide #25 models
> hide #24 models
> show #21 models
> show #20 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!12 models
> show #12.1 models
> show #15.15 models
> hide #15.15 models
> show #!17 models
> show #17.1 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2k5u.pdb
2k5u.pdb title:
Solution structure of myirstoylated yeast ARF1 protein, GDP- bound [more
info...]
Chain information for 2k5u.pdb
---
Chain | Description
27.1/A | adp-ribosylation factor 1
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
27.12/A 27.13/A 27.14/A 27.15/A 27.16/A | adp-ribosylation factor 1
> hide #21 models
> hide #20 models
> hide #17.1 models
> hide #!17 models
> hide #!15 models
> hide #12.1 models
> hide #!12 models
> hide #1 models
> hide #!27 models
> hide #27.1 models
> hide #27.2 models
> hide #27.3 models
> hide #27.4 models
> hide #27.5 models
> hide #27.6 models
> hide #27.7 models
> hide #27.8 models
> hide #27.9 models
> hide #27.10 models
> hide #27.11 models
> hide #27.12 models
> hide #27.13 models
> hide #27.14 models
> hide #27.15 models
> hide #27.16 models
> show #27.1 models
> show #!2 models
> hide #!2 models
> show #1 models
> show #!14 models
> hide #!14 models
> show #14.1 models
> hide #14.1 models
> show #15.15 models
> hide #!15 models
> hide #15.15 models
> hide #!14 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> mmaker #27 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.1), sequence
alignment score = 926
RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
0.000)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.2), sequence
alignment score = 903.3
RMSD between 152 pruned atom pairs is 0.809 angstroms; (across all 180 pairs:
1.974)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.3), sequence
alignment score = 907.5
RMSD between 157 pruned atom pairs is 0.800 angstroms; (across all 180 pairs:
2.934)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.4), sequence
alignment score = 903.9
RMSD between 152 pruned atom pairs is 0.800 angstroms; (across all 180 pairs:
2.457)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.5), sequence
alignment score = 910.5
RMSD between 138 pruned atom pairs is 0.757 angstroms; (across all 180 pairs:
3.101)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.6), sequence
alignment score = 909.3
RMSD between 149 pruned atom pairs is 0.693 angstroms; (across all 180 pairs:
2.209)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.7), sequence
alignment score = 911.7
RMSD between 148 pruned atom pairs is 0.890 angstroms; (across all 180 pairs:
2.359)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.8), sequence
alignment score = 913.5
RMSD between 151 pruned atom pairs is 0.912 angstroms; (across all 180 pairs:
2.728)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.9), sequence
alignment score = 914.1
RMSD between 152 pruned atom pairs is 0.805 angstroms; (across all 180 pairs:
2.409)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.10), sequence
alignment score = 899.7
RMSD between 164 pruned atom pairs is 0.693 angstroms; (across all 180 pairs:
1.622)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.11), sequence
alignment score = 911.1
RMSD between 151 pruned atom pairs is 0.855 angstroms; (across all 180 pairs:
2.173)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.12), sequence
alignment score = 914.1
RMSD between 148 pruned atom pairs is 0.681 angstroms; (across all 180 pairs:
2.489)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.13), sequence
alignment score = 926.7
RMSD between 153 pruned atom pairs is 0.784 angstroms; (across all 180 pairs:
2.320)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.14), sequence
alignment score = 910.5
RMSD between 154 pruned atom pairs is 0.691 angstroms; (across all 180 pairs:
2.124)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.15), sequence
alignment score = 892.5
RMSD between 153 pruned atom pairs is 0.701 angstroms; (across all 180 pairs:
1.911)
Matchmaker 2k5u.pdb, chain A (#12.1) with 2k5u.pdb, chain A (#27.16), sequence
alignment score = 908.1
RMSD between 153 pruned atom pairs is 0.770 angstroms; (across all 180 pairs:
2.227)
> hide #12.1 models
> hide #!12 models
> hide #!27 models
> hide #27.1 models
> show #27.1 models
> show #20 models
> show #21 models
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.3 models
> hide #27.3 models
> show #27.4 models
> hide #27.4 models
> show #27.5 models
> hide #27.5 models
> show #27.6 models
> hide #27.6 models
> show #27.7 models
> hide #27.7 models
> show #27.8 models
> hide #27.8 models
> show #27.9 models
> hide #27.9 models
> show #27.10 models
> hide #27.10 models
> show #27.11 models
> hide #27.11 models
> show #27.12 models
> hide #27.12 models
> show #27.13 models
> show #17.1 models
> hide #17.1 models
> hide #!17 models
> show #12.1 models
> hide #12.1 models
> show #12.1 models
> hide #12.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/sample transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/sample'
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
> transparentBackground true supersample 3
> hide #27.13 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #21 models
> hide #20 models
> transparency #1,3#!27 80
> transparency #1,3#!27 50
> transparency #1,3#!27 0
> hide #!27 models
> hide #!3 models
> hide #1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!8 models
> show #!8 models
> mmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #1 models
> show #!8 models
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> hide #!8 models
> show #!8 models
> hide #1 models
> show #1 models
> hide #!8 models
> show #!8 models
> hide #1 models
> show #25 models
> show #24 models
> hide #24 models
> hide #25 models
> show #!9 models
> select #9
2 models selected
> ~select #9
Nothing selected
> select #9
2 models selected
> ~select #9
Nothing selected
> ui tool show "Fit in Map"
Fit molecule complex_dimer-FINAL-coot-7.pdb (#8) to map complex_dimer-
FINAL.ccp4 zone (#9) using 21258 atoms
average map value = 18.77, steps = 168
shifted from previous position = 7.66
rotated from previous position = 14.8 degrees
atoms outside contour = 11709, contour level = 19.427
Position of complex_dimer-FINAL-coot-7.pdb (#8) relative to complex_dimer-
FINAL.ccp4 zone (#9) coordinates:
Matrix rotation and translation
0.99999998 -0.00017475 -0.00004915 0.04741679
0.00017475 0.99999998 -0.00000981 -0.05040213
0.00004915 0.00000980 1.00000000 -0.01085846
Axis 0.05393815 -0.27037831 0.96124203
Axis point 279.56043468 269.54481820 0.00000000
Rotation angle (degrees) 0.01041596
Shift along axis 0.00574761
> show #25 models
> show #24 models
> hide #24 models
> hide #25 models
> show #23 models
> show #22 models
> hide #22 models
> hide #23 models
> show #21 models
> hide #21 models
> show #25 models
> show #24 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!5 models
> close #25
> close #24
> hide #!9 models
> hide #!8 models
> show #!8 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #24
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/AF-P47102-F1-model_v1.pdb
AF-P47102-F1-model_v1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-P47102-F1-model_v1.pdb #25
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> mmaker #24 #25 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
AF-P47102-F1-model_v1.pdb, chain A (#24), sequence alignment score = 3470.5
RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
9.022)
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain A (#8) with
AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3470.5
RMSD between 451 pruned atom pairs is 1.084 angstroms; (across all 1156 pairs:
9.022)
> mmaker #25 to #8/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#8) with
AF-P47102-F1-model_v1.pdb, chain A (#25), sequence alignment score = 3462
RMSD between 451 pruned atom pairs is 1.094 angstroms; (across all 1156 pairs:
9.117)
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A #20/A #21/A #22/A #23/A #24/A #25/A
Alignment identifier is 1
Drag select of 2 residues
Seqview [ID: 1] region 7 chains [971-976] RMSD: 319.198
Seqview [ID: 1] region 7 chains [1-977] RMSD: 276.169
> delete atoms (#24-25 & sel)
> delete bonds (#24-25 & sel)
Seqview [ID: 1] region 7 chains [985-993] RMSD: 233.627
Seqview [ID: 1] region 7 chains [994-1408] RMSD: 297.153
> delete atoms (#24-25 & sel)
> delete bonds (#24-25 & sel)
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex.png
> transparentBackground true supersample 3
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> ui tool show "Side View"
> ui tool show "Side View"
> view orient
> hide #25 models
> hide #24 models
> show #4 models
> hide #4 models
> show #1 models
> hide #!8 models
> show #!12 models
> show #12.1 models
> show #15.15 models
> hide #15.15 models
> show #18.1 models
> hide #18.1 models
> show #14.1 models
> hide #14.1 models
> show #15.15 models
> hide #15.15 models
> hide #!14 models
> show #14.1 models
> hide #14.1 models
> hide #12.1 models
> show #12.1 models
> show #18.1 models
> hide #18.1 models
> hide #!18 models
> show #17.1 models
> show #20 models
> show #21 models
> hide #!17 models
> select clear
> select clear
> hide #17.1 models
> hide #!15 models
> hide #!14 models
> hide #12.1 models
> show #18.1 models
> hide #18.1 models
> hide #!18 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample'
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample2.png
> transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> hide #21 models
> hide #20 models
> show #24 models
> show #25 models
> hide #!12 models
> hide #1 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #25 models
> hide #24 models
> show #!26 models
> show #!26 surfaces
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #4 models
> hide #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> ui tool show "Side View"
> hide #1 models
> show #!26 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> show #12.1 models
> hide #12.1 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1'
> hide #!17 models
> hide #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1'
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-.png transparentBackground true supersample 3
> hide #!12 models
> hide #!17 models
> hide #17.1 models
> hide #20 models
> hide #21 models
> show #22 models
> show #23 models
> hide #1 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #22 models
> hide #23 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL.ccp4
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL.ccp4
Opened closed_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.66, shown at
level 1.11, step 2, values float32
> close #28
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #28
---
Chain | Description
A B | No description available
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
Chain information for complex_dimer-FINAL-coot-7.pdb #29
---
Chain | Description
A C | No description available
B | No description available
D | No description available
> select #28/B
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #29/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> select #29/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #29/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> close #29
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL.ccp4
Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
level 1.63, step 2, values float32
> close #29
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL.ccp4
Opened complex_dimer-FINAL.ccp4, grid size 300,300,300, pixel 1.65, shown at
level 1.63, step 2, values float32
> close #29
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
Chain information for complex_dimer-FINAL-coot-7.pdb #29
---
Chain | Description
A C | No description available
B | No description available
D | No description available
> select #29/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #29/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> show #1 models
> mmaker #29 #1/B
> matchmaker #29 #1/B
Missing required "to" argument
> mmaker #29 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with complex_dimer-FINAL-coot-7.pdb, chain C (#29), sequence alignment score =
5417.4
RMSD between 739 pruned atom pairs is 1.151 angstroms; (across all 1153 pairs:
8.341)
> show #20 models
> show #21 models
> color zone #29 #1
Missing required "near" argument
> color zone #29 near #1
> color zone #29 near #1 distance 3
> ui tool show "Show Sequence Viewer"
> sequence chain #29/C
Alignment identifier is 29/C
> hide #1 models
> color sel #f4e379ff
Drag select of 1 residues
> select #29/C:799
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #e1c4b2ff
> ui tool show "Color Actions"
> color sel #9ac2f5ff
> select clear
Drag select of 1 residues
> select clear
> select #28/A:544
20 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #28/A
Alignment identifier is 28/A
Drag select of 1 residues
Drag select of 1 residues
> color sel #f4e379ff
> select #28/A:799
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #28/A:799
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #e1c4b2ff
> color sel #9ac2f5ff
> select clear
> select #29/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> color (#!29 & sel) #7281dbff
> select clear
> show #!8 models
> hide #!8 models
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #!29 models
> hide #28 models
> hide #21 models
> hide #20 models
> show #!26 models
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #21 models
> show #20 models
> ui tool show "Side View"
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> hide #1 models
> hide #21 models
> hide #20 models
> show #22 models
> show #23 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #23 models
> hide #22 models
> show #25 models
> show #24 models
> show #28 models
> show #!29 models
> hide #25 models
> hide #24 models
> show #21 models
> show #20 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #21 models
> hide #20 models
> hide #28 models
> hide #!29 models
> show #!12 models
> show #12.1 models
> hide #!12 models
> show #!12 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp'
> show #!15 models
> show #15.15 models
> hide #!12 models
> hide #12.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #15.15 models
> hide #!15 models
> show #14.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #14.1 models
> hide #!14 models
> show #12.1 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #21 models
> hide #20 models
> show #20 models
> show #21 models
> hide #1 models
> hide #!12 models
> hide #12.1 models
> show #28 models
> show #!29 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #28 models
> hide #!29 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> side.png transparentBackground true supersample 3
> hide #1 models
> hide #21 models
> hide #20 models
> show #20 models
> show #21 models
> show #1 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #12.1 models
> hide #12.1 models
> show #18.1 models
> hide #18.1 models
> show #17.1 models
> hide #!18 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-side transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-arf1-side'
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-side.png transparentBackground true supersample 3
> hide #!17 models
> hide #17.1 models
> show #!27 models
> hide #!27 models
> show #28 models
> show #!29 models
> hide #21 models
> show #21 models
> hide #1 models
> hide #!12 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
> side.png transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
> side.png transparentBackground true supersample 3
> mmaker #4 #8 #28 #29 to #1 bring #22-25
'bring' option can only be used when exactly one structure is being matched
> mmaker #4 to #1 bring #22-23
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> mmaker #8 to #1 bring #24-25
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> hide #28 models
> hide #!29 models
> hide #21 models
> hide #20 models
> show #25 models
> show #24 models
> show #!8 models
> show #1 models
> hide #1 models
> hide #25 models
> hide #24 models
> show #28 models
> show #!29 models
> hide #!8 models
> hide #!29 models
> show #!29 models
> show #!15 models
> show #15.15 models
> hide #!15 models
> hide #15.15 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> show #15.15 models
> mmaker #15 to #29/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain D (#29) with 2ksq.pdb, chain
A (#15.15), sequence alignment score = 612.3
RMSD between 105 pruned atom pairs is 1.288 angstroms; (across all 164 pairs:
4.121)
> select #29/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> delete atoms (#!29 & sel)
> delete bonds (#!29 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #15.15/A
Alignment identifier is 15.15/A
> color sel #aa0000ff
> select clear
> select clear
> hide #15.15 models
> hide #!15 models
> show #1 models
> hide #!29 models
> hide #28 models
> show #12.1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #12.1/A
Alignment identifier is 12.1/A
> color sel #ffffffff
> color sel #aa0000ff
> select clear
> select clear
> hide #!12 models
> hide #12.1 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #1 models
> show #!26 models
> ui tool show "Side View"
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> ui tool show "Side View"
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #12.1 models
> show #28 models
> show #!29 models
> show #!27 models
> hide #!27 models
> show #15.15 models
> hide #15.15 models
> hide #!15 models
> hide #!12 models
> hide #12.1 models
> show #17.1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #17.1/A
Alignment identifier is 17.1/A
> color sel #ffffffff
> color sel #aa0000ff
> select clear
> hide #28 models
> hide #!29 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-closed.png
> transparentBackground true supersample 3
> hide #1 models
> hide #21 models
> hide #20 models
> show #22 models
> show #23 models
> hide #17.1 models
> hide #!17 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> show #!29 models
> show #28 models
> show #20 models
> hide #22 models
> hide #23 models
> show #21 models
> show #15.15 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #28 models
> hide #!29 models
> hide #21 models
> hide #20 models
> select ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> color sel #55aa7fff
> color sel byhetero
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #15.15 models
> hide #!15 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> show #1 models
> show #20 models
> show #21 models
> show #!26 models
> hide #1,20-21#!26 surfaces
> style #1,20-21#!26 stick
Changed 353076 atom styles
> nucleotides #1,20-21#!26 atoms
> style nucleic & #1,20-21#!26 stick
Changed 0 atom styles
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> select #4
36826 atoms, 37112 bonds, 2258 residues, 1 model selected
> select #8
21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> select #4
36826 atoms, 37112 bonds, 2258 residues, 1 model selected
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> hide #!26 models
> show #!26 models
> hide #21 models
> hide #20 models
> select clear
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> select clear
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #11 models
> mmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with ger2.pdb, chain C (#11), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> show #15.15 models
> hide #15.15 models
> show #15.15 models
> hide #15.15 models
> show #15.15 models
> hide #15.15 models
> mmaker #15 to #13
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#13) with 2ksq.pdb, chain A (#15.15), sequence
alignment score = 656.7
RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
3.660)
> show #15.15 models
> hide #!15 models
> hide #15.15 models
> show #15.15 models
> show #13 models
> hide #13 models
> hide #11 models
> mmaker #15 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#11) with 2ksq.pdb, chain A (#15.15), sequence
alignment score = 656.7
RMSD between 109 pruned atom pairs is 1.184 angstroms; (across all 165 pairs:
3.660)
> mmaker #17 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#11) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> show #17.1 models
> hide #17.1 models
> hide #!17 models
> hide #15.15 models
> hide #!15 models
> hide #1 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
30.1/A | adp-ribosylation factor 1
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
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-
ribosylation factor 1
> hide #!30 models
> hide #30.1 models
> hide #30.2 models
> hide #30.3 models
> hide #30.4 models
> hide #30.5 models
> hide #30.7 models
> hide #30.8 models
> hide #30.6 models
> hide #30.9 models
> hide #30.10 models
> hide #30.12 models
> hide #30.13 models
> hide #30.14 models
> hide #30.11 models
> hide #30.15 models
> hide #30.16 models
> hide #30.17 models
> hide #30.18 models
> hide #30.19 models
> hide #30.20 models
> show #30.1 models
Drag select of 281 atoms, 180 residues, 258 bonds
> hide sel atoms
> select clear
> select clear
> hide #!30 models
> hide #30.1 models
> show #30.1 models
> show #30.2 models
> hide #30.2 models
> show #30.3 models
> show #30.4 models
> hide #30.3 models
> hide #30.4 models
> show #30.5 models
> hide #30.1 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> hide #30.5 models
> show #30.5 models
Drag select of 265 atoms, 180 residues, 243 bonds
> hide sel atoms
> select clear
> select clear
> show #30.6 models
> hide #30.6 models
> show #30.8 models
> hide #30.8 models
> show #30.9 models
> hide #30.9 models
> show #30.10 models
> hide #30.10 models
> show #30.11 models
> hide #30.11 models
> show #30.12 models
> hide #30.12 models
> show #30.13 models
> hide #30.13 models
> show #30.14 models
> hide #30.5 models
Drag select of 269 atoms, 180 residues, 248 bonds
> hide sel atoms
> select clear
> select clear
> close #30.1-13
> close #30.15-20
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui tool show "Show Sequence Viewer"
> sequence chain #30.14/A
Alignment identifier is 30.14/A
> color sel #aa0000ff
> select clear
> show #1 models
> hide #!30 models
> show #!29 models
> show #28 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> mmaker #29 to #1 bring #20-25
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with complex_dimer-FINAL-coot-7.pdb, chain C (#29), sequence alignment score =
5449.8
RMSD between 719 pruned atom pairs is 1.188 angstroms; (across all 1153 pairs:
8.380)
> hide #25 models
> hide #24 models
> hide #23 models
> hide #22 models
> hide #21 models
> hide #20 models
> mmaker #28 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#28),
sequence alignment score = 6081.2
RMSD between 1222 pruned atom pairs is 0.340 angstroms; (across all 1222
pairs: 0.340)
> hide #30.14 models
> hide #!29 models
> hide #28 models
> show #!29 models
> show #28 models
> hide #1 models
> show #4 models
> mmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> hide #4 models
> show #11 models
> mmaker #11 to #29
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain C (#29) with ger2.pdb, chain
C (#11), sequence alignment score = 1028.5
RMSD between 196 pruned atom pairs is 0.965 angstroms; (across all 201 pairs:
1.024)
> mmaker #30 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#11) with 2ksq.pdb, chain A (#30.14), sequence
alignment score = 663.9
RMSD between 108 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.655)
> show #!30 models
> show #30.14 models
> hide #30.14 models
> hide #!30 models
> hide #!29 models
> hide #28 models
> hide #11 models
> show #!26 models
> show #1 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
31.1/A | adp-ribosylation factor 1
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
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-
ribosylation factor 1
> hide #!31 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> show sel surfaces
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> ~select #26
Nothing selected
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs
> hide #1 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #1 models
> show #1 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> hide #21 models
> show #21 models
> show #!27 models
> hide #!27 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> hide #21 models
> show #21 models
> show #12.1 models
> hide #12.1 models
> show #14.1 models
> hide #14.1 models
> show #15.15 models
> hide #15.15 models
> show #17.1 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-closed.png
> transparentBackground true supersample 3
> hide #!14 models
> hide #!12 models
> hide #!15 models
> hide #!17 models
> hide #17.1 models
> show #4 models
> show #22 models
> show #23 models
> hide #21 models
> hide #20 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #23 models
> hide #22 models
> show #28 models
> show #!29 models
> hide #1 models
> hide #4 models
> show #4 models
> hide #!29 models
> hide #28 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> show #!29 models
> show #28 models
> show #30.14 models
> show #20 models
> show #21 models
> hide #!30 models
> hide #30.14 models
> show #!30 models
> show #30.14 models
> mmaker #31 to #30
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.1), sequence
alignment score = 925.2
RMSD between 162 pruned atom pairs is 0.566 angstroms; (across all 180 pairs:
1.892)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.2), sequence
alignment score = 929.4
RMSD between 162 pruned atom pairs is 0.637 angstroms; (across all 180 pairs:
3.198)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.3), sequence
alignment score = 922.8
RMSD between 159 pruned atom pairs is 0.505 angstroms; (across all 180 pairs:
4.009)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.4), sequence
alignment score = 928.8
RMSD between 165 pruned atom pairs is 0.588 angstroms; (across all 180 pairs:
2.079)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.5), sequence
alignment score = 913.8
RMSD between 162 pruned atom pairs is 0.570 angstroms; (across all 180 pairs:
2.622)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.6), sequence
alignment score = 909
RMSD between 159 pruned atom pairs is 0.598 angstroms; (across all 180 pairs:
3.348)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.7), sequence
alignment score = 914.4
RMSD between 160 pruned atom pairs is 0.771 angstroms; (across all 180 pairs:
3.467)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.8), sequence
alignment score = 939
RMSD between 162 pruned atom pairs is 0.601 angstroms; (across all 180 pairs:
2.232)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.9), sequence
alignment score = 913.2
RMSD between 160 pruned atom pairs is 0.657 angstroms; (across all 180 pairs:
3.047)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.10),
sequence alignment score = 916.8
RMSD between 165 pruned atom pairs is 0.623 angstroms; (across all 180 pairs:
2.568)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.11),
sequence alignment score = 906
RMSD between 160 pruned atom pairs is 0.571 angstroms; (across all 180 pairs:
2.803)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.12),
sequence alignment score = 939
RMSD between 161 pruned atom pairs is 0.537 angstroms; (across all 180 pairs:
3.640)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.13),
sequence alignment score = 922.2
RMSD between 162 pruned atom pairs is 0.631 angstroms; (across all 180 pairs:
3.208)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.14),
sequence alignment score = 945.6
RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
0.000)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.15),
sequence alignment score = 931.8
RMSD between 163 pruned atom pairs is 0.597 angstroms; (across all 180 pairs:
3.138)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.16),
sequence alignment score = 901.2
RMSD between 160 pruned atom pairs is 0.600 angstroms; (across all 180 pairs:
2.591)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.17),
sequence alignment score = 916.8
RMSD between 159 pruned atom pairs is 0.585 angstroms; (across all 180 pairs:
2.919)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.18),
sequence alignment score = 931.2
RMSD between 160 pruned atom pairs is 0.569 angstroms; (across all 180 pairs:
2.533)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.19),
sequence alignment score = 922.2
RMSD between 160 pruned atom pairs is 0.558 angstroms; (across all 180 pairs:
2.973)
Matchmaker 2ksq.pdb, chain A (#30.14) with 2ksq.pdb, chain A (#31.20),
sequence alignment score = 928.8
RMSD between 161 pruned atom pairs is 0.530 angstroms; (across all 180 pairs:
3.897)
> show #!31 models
> hide #!30 models
> hide #30.14 models
> hide #!31 models
> hide #31.1 models
> hide #31.2 models
> hide #31.3 models
> hide #31.4 models
> hide #31.5 models
> hide #31.6 models
> hide #31.7 models
> hide #31.8 models
> hide #31.9 models
> hide #31.10 models
> hide #31.11 models
> hide #31.12 models
> hide #31.13 models
> hide #31.14 models
> hide #31.15 models
> hide #31.16 models
> hide #31.17 models
> hide #31.18 models
> hide #31.19 models
> hide #31.20 models
> show #31.1 models
> hide #31.1 models
> show #31.2 models
> hide #31.2 models
> show #31.3 models
> hide #31.3 models
> show #31.4 models
> hide #31.4 models
> show #31.5 models
> hide #31.5 models
> show #31.6 models
> hide #31.6 models
> show #31.5 models
> show #31.7 models
> hide #31.5 models
> close #31.1-6
> close #31.8-20
> select #31.7
3045 atoms, 3079 bonds, 187 residues, 1 model selected
> hide sel atoms
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color sel #7281dbff
> select clear
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> color (#31.7 & sel) #55aa00ff
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> show sel & #31.7 atoms
> color sel & #31.7 byhetero
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #31.7/A
Alignment identifier is 31.7/A
> color sel #aa0000ff
> select clear
> select clear
> hide #20 models
> hide #21 models
> hide #28 models
> hide #!29 models
> hide #!31 models
> hide #31.7 models
> show #!26 models
> show #!26 surfaces
> show #1 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 surfaces
> show #1 models
> hide #!26 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #20 models
> show #22 models
> show #23 models
> hide #21 models
> hide #17.1 models
> hide #!17 models
> show #4 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #23 models
> hide #22 models
> show #!29 models
> show #28 models
> show #20 models
> show #21 models
> show #!31 models
> show #31.7 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #!31 models
> hide #31.7 models
> show #31.7 models
> hide #!29 models
> hide #28 models
> hide #21 models
> hide #20 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp'
> hide #!31 models
> hide #31.7 models
> show #15.15 models
> hide #15.15 models
> hide #!15 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp'
> hide #17.1 models
> hide #!17 models
> show #31.7 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #!31 models
> hide #31.7 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> show #31.7 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> hide sel & #31.7 surfaces
> hide sel & #31.7 atoms
> hide #31.7 models
> hide #!31 models
> show #!26 models
> show #1 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> select clear
> show #20 models
> show #21 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> show #31.7 models
> ~select #26
5 models selected
> hide #31.7 models
> hide #!31 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> show sel surfaces
> select clear
> ~select #26
Nothing selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> ~select #26
5 models selected
> hide #1 models
> hide #20 models
> hide #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #15.15 models
> hide #15.15 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> show #18.1 models
> hide #18.1 models
> hide #!18 models
> hide #20 models
> hide #21 models
> hide #!15 models
> hide #1 models
> show #4 models
> show #22 models
> show #23 models
> hide #23 models
> show #21 models
> hide #21 models
> show #23 models
> hide #22 models
> show #21 models
> hide #21 models
> show #20 models
> hide #23 models
> hide #20 models
> show #25 models
> hide #25 models
> show #24 models
> show #23 models
> hide #23 models
> show #22 models
> hide #22 models
> show #21 models
> show #22 models
> show #23 models
> hide #24 models
> hide #23 models
> show #23 models
> hide #22 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #23 models
> hide #21 models
> show #20 models
> show #21 models
> hide #4 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> hide #1 models
> show #1 models
> show #!9 models
> hide #!9 models
> show #18.1 models
> hide #18.1 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #!18 models
> hide #!17 models
> show #!31 models
> hide #!31 models
> show #31.7 models
> show #!29 models
> show #28 models
> hide #1 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #31.7 models
> hide #!31 models
> hide #!29 models
> hide #28 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #21 models
> hide #20 models
> show #31.7 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> show sel & #31.7 atoms
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #31.7 models
> hide #!31 models
> show #!18 models
> hide #!18 models
> show #18.1 models
> show #19 models
> hide #19 models
> hide #18.1 models
> hide #!18 models
> hide #17.1 models
> show #!17 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs includeMaps true
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
> transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/sample.png
> transparentBackground true supersample 3
> hide #!17 models
> hide #17.1 models
> show #!17 models
> show #!26 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> hide sel surfaces
> hide #1 models
> hide #20 models
> hide #21 models
> hide #!17 models
> show sel surfaces
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> show #28 models
> show #!29 models
> hide #1 models
> hide #17.1 models
> hide #!17 models
> show #31.7 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activiation.png
> transparentBackground true supersample 3
> hide #31.7 models
> hide #!31 models
> hide #!29 models
> hide #28 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #21 models
> hide #20 models
> show #31.7 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #31.7 models
> hide #!31 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> show #31.7 models
> hide #17.1 models
> hide #!17 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> hide sel & #31.7 atoms
> show #20 models
> show #21 models
> select clear
> show #!29 models
> show #28 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activiation.png
> transparentBackground true supersample 3
> hide #21 models
> hide #20 models
> hide #28 models
> hide #!29 models
> hide #!31 models
> hide #31.7 models
> show #!26 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> hide sel surfaces
> ~select #26
5 models selected
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> show #31.7 models
> show #!29 models
> show #28 models
> hide #17.1 models
> hide #!17 models
> hide #1 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> hide #!29 models
> hide #28 models
> hide #!31 models
> hide #31.7 models
> show #!2 models
> hide #!2 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #21 models
> hide #20 models
> show #31.7 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> show sel & #31.7 atoms
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #31.7 models
> hide #!31 models
> show #!30 models
> hide #!30 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #!17 models
> hide #17.1 models
> show #!26 models
> hide #!26 surfaces
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> ~select #26
5 models selected
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #1 models
> show #!26 models
> hide #!26 surfaces
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #20 models
> show #21 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed.png
> transparentBackground true supersample 3
> hide #1 models
> show #1 models
> show #12.1 models
> hide #12.1 models
> show #14.1 models
> hide #14.1 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1.png transparentBackground true supersample 3
> hide #!14 models
> hide #!12 models
> hide #!17 models
> hide #17.1 models
> hide #1 models
> show #28 models
> show #!29 models
> show #31.7 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> hide sel & #31.7 atoms
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation.png
> transparentBackground true supersample 3
> show sel & #31.7 atoms
> hide #31.7 models
> hide #!31 models
> hide #!29 models
> hide #28 models
> select #30
3045 atoms, 3079 bonds, 187 residues, 2 models selected
> select #30.14
3045 atoms, 3079 bonds, 187 residues, 1 model selected
> select #31
3045 atoms, 3079 bonds, 187 residues, 2 models selected
> ~select #31.7
1 model selected
> select #30.14
3045 atoms, 3079 bonds, 187 residues, 1 model selected
> select #31
3045 atoms, 3079 bonds, 187 residues, 2 models selected
> ~select #31
Nothing selected
> hide #21 models
> show #21 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/open.png
> transparentBackground true supersample 3
> hide #4 models
> hide #21 models
> hide #20 models
> show #!30 models
> show #30.14 models
> hide #!30 models
> hide #30.14 models
> show #!31 models
> show #31.7 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp.png
> transparentBackground true supersample 3
> hide #!31 models
> hide #31.7 models
> show #!27 models
> hide #!27 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp.png
> transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> show #1 models
> show #20 models
> show #21 models
> hide #21 models
> hide #20 models
> hide #1 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 surfaces
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids-
> side.png transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> show #!17 models
> show #17.1 models
> hide #17.1 models
> hide #!17 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> side.png transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-side.png transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> show #!31 models
> show #31.7 models
> hide #!31 models
> show #!31 models
> show #!29 models
> show #28 models
> hide #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
> side.png transparentBackground true supersample 3
> hide #!29 models
> hide #28 models
> hide #!31 models
> hide #31.7 models
> show #!31 models
> show #31.7 models
> show #!29 models
> show #28 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> hide sel & #31.7 surfaces
> hide sel & #31.7 atoms
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
> side.png transparentBackground true supersample 3
> hide #!29 models
> hide #28 models
> hide #21 models
> hide #20 models
> show sel & #31.7 atoms
> select clear
> show #1 models
> hide #1 models
> hide #!31 models
> hide #31.7 models
> show #1 models
> show #20 models
> show #21 models
> ui tool show "Side View"
> show #!26 models
> hide #1,20-21#!26 surfaces
> select #1
39647 atoms, 39961 bonds, 2444 residues, 1 model selected
> undo
> select #21
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #20
168 atoms, 170 bonds, 22 residues, 1 model selected
> select #21
168 atoms, 170 bonds, 22 residues, 1 model selected
> ~select #21
Nothing selected
> hide #21 models
> hide #20 models
> show #21 models
> show #20 models
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> hide #1 models
> hide #20 models
> hide #21 models
> ~select #26
5 models selected
> select #26
313093 atoms, 317626 bonds, 3369 residues, 6 models selected
> show sel surfaces
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/lipids-
> side.png transparentBackground true supersample 3
> hide #!26 models
> show #1 models
> show #20 models
> show #21 models
> show #17.1 models
> hide #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> side.png transparentBackground true supersample 3
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> arf1-side.png transparentBackground true supersample 3
> hide #17.1 models
> hide #!17 models
> hide #1 models
> show #28 models
> show #!29 models
> show #30.14 models
> hide #30.14 models
> show #17.1 models
> hide #!17 models
> hide #17.1 models
> show #!31 models
> show #31.7 models
> select ::name="GTP"
129 atoms, 135 bonds, 3 residues, 3 models selected
> hide sel & #31.7 atoms
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/activation-
> side.png transparentBackground true supersample 3
> show sel & #31.7 atoms
> select clear
> hide #21 models
> hide #20 models
> hide #28 models
> hide #!29 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gtp-
> side.png transparentBackground true supersample 3
> hide #!30 models
> hide #!31 models
> hide #31.7 models
> show #17.1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/arf1-gdp-
> side.png transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs includeMaps true
> toolshed show
> help help:user/tools/toolbar.html
> hide #17.1 models
> hide #!17 models
> show #1 models
> open C:/Users/Arnold/Downloads/io.mc
Unrecognized file suffix '.mc'
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32
---
Chain | Description
A B | No description available
> hide #1 models
> select #32/A
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> color sel #9ac2f5ff
> select #32/B
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> color sel #f4e379ff
> select clear
> lighting soft
Drag select of 8 residues
> show sel atoms
> color sel byhetero
> select clear
Drag select of 1 atoms, 6 residues
> show sel atoms
> color sel byhetero
> select clear
> hbonds #32
3464 hydrogen bonds found
> ~hbonds
> ui mousemode right distance
> ui mousemode right distance
> distance #32/B:17@HZ2 #32/A:413@OG1
Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/B
LYS 17 HZ2 and /A THR 413 OG1: 2.776Å
> distance #32/B:17@HZ3 #32/A:414@OG1
Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/B
LYS 17 HZ3 and /A THR 414 OG1: 3.117Å
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select #33
2 pseudobonds, 2 models selected
> ~select #33
Nothing selected
> hide #33.1 models
> ui mousemode right distance
> distance #32/A:410@HE21 #32/B:21@OD1
Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/A
GLN 410 HE21 and /B ASN 21 OD1: 3.052Å
> show #33.1 models
> hide #33.1 models
Drag select of 4 residues
> show sel atoms
> color sel byhetero
> select clear
> select clear
Drag select of 2 residues
> show sel atoms
> color sel byhetero
> select clear
> select clear
> select clear
> ui mousemode right distance
> distance #32/A:406@HE21 #32/B:24@OG1
Distance between closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #32/A
GLN 406 HE21 and /B THR 24 OG1: 3.960Å
> show #33.1 models
> hide #33.1 models
> hide #32 models
> show #32 models
> hide #!33 models
> select #32
39644 atoms, 39958 bonds, 4 pseudobonds, 2444 residues, 2 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb #32/A SER 1417 OXT and closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb #32/B SER 1417 OXT
> show #10 models
> select #10
11218 atoms, 11405 bonds, 1408 residues, 1 model selected
> mmaker #10 to #32
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#32)
with AF-P47102-F1-model_v1.pdb, chain A (#10), sequence alignment score =
3608.2
RMSD between 515 pruned atom pairs is 1.207 angstroms; (across all 1219 pairs:
5.511)
> mlp sel
Map values for surface "AF-P47102-F1-model_v1.pdb_A SES surface": minimum
-30.22, mean -5.341, maximum 24.77
> coulombic sel
> select clear
> hide #!32 models
> hide #!10 models
> show #!32 models
> ui tool show "Side View"
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/electrostatics.png
> transparentBackground true supersample 3
> hide #!32 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea1.pdb
AF-gea1.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 1
(P47102) [more info...]
Chain information for AF-gea1.pdb #34
---
Chain | Description
A | arf guanine-nucleotide exchange factor 1
> hide #34 models
> show #34 models
> ui tool show "Side View"
> show #1 models
> view
> hide #1 models
> coulombic #34
> show #!32 models
> hide #!32 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea2.pdb
AF-gea2.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-gea2.pdb #35
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> mmaker #35 to #34
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-gea1.pdb, chain A (#34) with AF-gea2.pdb, chain A (#35),
sequence alignment score = 4404
RMSD between 910 pruned atom pairs is 1.051 angstroms; (across all 1388 pairs:
5.497)
> hide #!34 models
> coulombic #35
> show #!34 models
> select #34
11218 atoms, 11405 bonds, 1408 residues, 1 model selected
> ui mousemode right "translate selected models"
> mlp sel
Map values for surface "AF-gea1.pdb_A SES surface": minimum -30.35, mean
-5.339, maximum 24.96
> select #35
11659 atoms, 11853 bonds, 1459 residues, 1 model selected
> ~select #35
1 model selected
> select #34
11218 atoms, 11405 bonds, 1408 residues, 1 model selected
> ~select #34
1 model selected
> select #35
11659 atoms, 11853 bonds, 1459 residues, 1 model selected
> mlp sel
Map values for surface "AF-gea2.pdb_A SES surface": minimum -32.32, mean
-5.657, maximum 27.63
> show #!2 models
> hide #!2 models
> show #1 models
> mmaker #35 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with AF-gea2.pdb, chain A (#35), sequence alignment score = 5664
RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
2.486)
> mmaker #34 to #1/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#1)
with AF-gea1.pdb, chain A (#34), sequence alignment score = 3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> select clear
> select #35
11659 atoms, 11853 bonds, 1459 residues, 1 model selected
> hide sel surfaces
> hide #1 models
> mlp sel
Map values for surface "AF-gea2.pdb_A SES surface": minimum -32.33, mean
-5.655, maximum 27.08
> select #35/A:265@OE1
1 atom, 1 residue, 1 model selected
> select clear
> hide #!34-35 surfaces
Drag select of 171 residues
> show sel atoms
> select clear
> select clear
Drag select of 205 atoms, 275 residues, 168 bonds
> show sel atoms
> select clear
> select clear
> select #34/A:216
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> show sel atoms
> show sel atoms
> select clear
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #36
---
Chain | Description
A B | No description available
Chain information for complex_dimer-FINAL-coot-7.pdb #37
---
Chain | Description
A C | No description available
B | No description available
D | No description available
Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #38
---
Chain | Description
A B | No description available
> hide #!34 models
> mmaker #36-38 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-gea2.pdb, chain A (#35) with closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb, chain A (#36), sequence alignment score =
5664
RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
2.486)
Matchmaker AF-gea2.pdb, chain A (#35) with complex_dimer-FINAL-coot-7.pdb,
chain C (#37), sequence alignment score = 5320.4
RMSD between 689 pruned atom pairs is 1.128 angstroms; (across all 1159 pairs:
7.511)
Matchmaker AF-gea2.pdb, chain A (#35) with open_dimer-FINAL-
coot-5_real_space_refined_208.pdb, chain B (#38), sequence alignment score =
5053.9
RMSD between 662 pruned atom pairs is 1.268 angstroms; (across all 1129 pairs:
9.186)
> hide #!37 models
> hide #36 models
> hide #!35 models
> hide #38 models
> show #36 models
> show #38 models
> show #!37 models
> hide #36 models
> hide #!37 models
> hide #38 models
> show #36 models
> hide #36 models
> show #!37 models
> hide #!37 models
> show #38 models
> hide #38 models
> show #!37 models
> hide #!37 models
> show #36 models
> show #38 models
> morph #36,38
Computed 21 frame morph #39
> coordset #39 1,21
> movie record
> movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!39 models
> show #36 models
> show #38 models
> matchmaker #36 to #38
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38)
with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> matchmaker #38 to #36
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36)
with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> select #38
36826 atoms, 37112 bonds, 2258 residues, 1 model selected
> ~select #38
Nothing selected
> matchmaker #38 to #36
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36)
with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> select #38
36826 atoms, 37112 bonds, 2258 residues, 1 model selected
> select clear
> mmaker #36 to #38
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#38)
with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#36),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> morph #36,38
Computed 21 frame morph #40
> coordset #40 1,21
> coordset #40 1,21
> morph #36,38 method linear
Computed 21 frame morph #41
> coordset #41 1,21
> movie record
> movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> hide #!41 models
> close #39-41
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs includeMaps true
opened ChimeraX session
> show #1 models
> hide #1 models
> show #1 models
> ui mousemode right distance
> ui mousemode right "tape measure"
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #1 models
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> show #1 models
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> ui mousemode right "tape measure"
> hide #1 models
> hide #!3 models
> show #!35 models
> show #!2 models
> hide #!2 models
> show #1 models
> show #28 models
> hide #1 models
> select #28
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select clear
> mmaker #35 to #28
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#28)
with AF-gea2.pdb, chain A (#35), sequence alignment score = 5664
RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
2.486)
> ui tool show "Show Sequence Viewer"
> sequence chain #35/A
Alignment identifier is 35/A
Drag select of 3 residues
> show sel atoms
> color sel byhetero
> show sel atoms
> color sel byhetero
> select clear
Drag select of 1 residues
> show sel atoms
> select clear
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction'
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure3/AF2-prediction.png
> transparentBackground true supersample 3
> hide #!35 models
> hide #28 models
> show #1 models
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> turn #1
Expected an axis vector or a keyword
> view orient
> view orient
> view orient
> view orient
> view orient
> turn #1 x
Expected an axis vector or a keyword
> turn #1 x 90
Expected an axis vector or a keyword
> turn x 90 #1
Expected 'forever' or an integer >= 1 or a keyword
> turn #1
Expected an axis vector or a keyword
> turn #1
Expected an axis vector or a keyword
> turn models #1
> view orient
> view orient
> turn models #1
> turn models #1
> turn models #1
> view orient
> turn z 90 60 models #1
> turn z 1-90 60 model #1
Expected a number or a keyword
> turn z 1 90
> star; turn z 1 90
Unknown command: movie star; turn z 1 90
> start; turn z 1 90
Unknown command: movie start; turn z 1 90
> ; turn z 1 90
Incomplete command: movie
> movie record
> turn z 1 90
> view orient
> turn x 0 45
> movie stop
> turn x 0 45
> turn x 0 45
> turn x 0 45
> turn z 1 90
> turn z 1 90
> roll
> top
Unknown command: top
> stop
> view orient
> view orient
> turn x 1-90
Expected a number or a keyword
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 90-1
Expected a number or a keyword
> turn x 90 1
> turn x
> turn x
> turn x
> turn x -90 -1
Missing or invalid "frames" argument: Must be greater than or equal to 1
> turn x 270 360
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 180
> turn x 1 270
> turn x -1 270
> turn x
> turn x
> turn x -1 90
> turn x -1 90
> wait
> turn y 1 90
> turn x -1 90
> wait
> turn y 1 90
> turn x -1 90
> wait
> turn y 1 90
> turn x
> turn x -1 90
> wait
> turn y 1 360
> view orient
> turn x -1 90
> wait
> turn y 1 180
> view orient
> star; turn x -1 90; wait; turn y 1 180
Unknown command: movie star; turn x -1 90; wait; turn y 1 180
> movie record
> turn x -1 90
> wait
> turn y 1 180
> movie encode C:\Users\Arnold/Desktop
Unrecognized movie file suffix Desktop, use *.webm, *.avi, *.mov, *.mp4,
*.wmv, *.ogv
> movie encode C:\Users\Arnold/Desktop/movie.mp4
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> view orient
> view orient
> movie record
> turn x -1 90
> wait
> turn y 1 180
> movie encode C:\Users\Arnold/Desktop/movie.mp4
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie record
> wait 3
> turn x -1 90
> wait
> turn y 1 180
> movie encode C:\Users\Arnold/Desktop/movie.mp4
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie record
> wait 3
> turn x -1 90
> wait
> turn y 1 180
> wait
> movie encode C:\Users\Arnold/Desktop/movie.mp4
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> view orient
> movie record
> wait
wait requires a frame count argument unless motion is in progress
> wait 20
> turn x -1 90
> wait
> turn y 1 180
> wait
> movie encode C:\Users\Arnold/Desktop/movie.mp4
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> view orient
> hide #1 models
> show #4 models
> movie record
> wait
wait requires a frame count argument unless motion is in progress
> wait 20
> turn x -1 90
> wait
> turn y 1 180
> wait
> movie encode C:\Users\Arnold/Desktop/Gea2Open.mp4
Movie saved to C:\Users\Arnold/Desktop/Gea2Open.mp4
> hide #4 models
> show #!8 models
> mmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with complex_dimer-FINAL-coot-7.pdb, chain A (#8), sequence alignment score =
5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> view orient
> movie record
> wait
wait requires a frame count argument unless motion is in progress
> wait 20
> turn x -1 90
> wait
> turn y 1 180
> wait
> movie encode C:\Users\Arnold/Desktop/Gea2Complex.mp4
Movie saved to C:\Users\Arnold/Desktop/Gea2Complex.mp4
> show #16 models
> hide #16 models
> hide #!8 models
> show #1 models
> show #16 models
> mmaker #16 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with ger2.pdb, chain C (#16), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> show #!8 models
> hide #16 models
> hide #!8 models
> show #!8 models
> hide #1 models
> show #1 models
> hide #!8 models
> show #16 models
> select #16/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> select #16/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> hide #16 models
> select #16
2990 atoms, 3024 bonds, 389 residues, 1 model selected
> show #16 models
> ~select #16
Nothing selected
> hide #1 models
> show #1 models
> show #!8 models
> hide #1 models
> show #1 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #1 models
> hide #16 models
> hide #!8 models
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #4 models
> show #16 models
> mmaker #16 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#4)
with ger2.pdb, chain C (#16), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
> hide #4 models
> hide #16 models
> show #1 models
> hide #1 models
> show #!8 models
> show #!29 models
> hide #!29 models
> show #!29 models
> show #28 models
> hide #!8 models
> hide #!29 models
> hide #28 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #39
---
Chain | Description
A B | No description available
Chain information for complex_dimer-FINAL-coot-7.pdb #40
---
Chain | Description
A C | No description available
B | No description available
D | No description available
Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #41
---
Chain | Description
A B | No description available
> mmaker #40-41 to #39
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with complex_dimer-FINAL-coot-7.pdb, chain A (#40), sequence alignment score =
5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41),
sequence alignment score = 5250.9
RMSD between 628 pruned atom pairs is 1.091 angstroms; (across all 1129 pairs:
10.353)
> hide #39 models
> hide #!40 models
> hide #41 models
> show #39 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/C
Alignment identifier is 8/C
> sequence chain #8/A
Alignment identifier is 8/A
> show #1 models
> hide #1 models
> select clear
Drag select of 2 residues
> ui tool show "Show Sequence Viewer"
> ui tool show "Show Sequence Viewer"
> ui tool show "Color Actions"
> ui tool show "Show Sequence Viewer"
> sequence chain #39/A
Alignment identifier is 39/A
> sequence chain #39/B
Alignment identifier is 39/B
Drag select of 3 residues
> color sel #f5e4deff
> color sel #f8e266ff
> color sel #8fc3faff
> color sel #f8e266ff
> color sel #e7c3afff
> select clear
> color sel #f5e4deff
> color sel #e7c3afff
> select clear
> color sel #8fc3faff
> color sel #2e79abff
> color sel #8fc3faff
> select clear
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> show #!40 models
> hide #39 models
> ui tool show "Show Sequence Viewer"
> sequence chain #40/A
Alignment identifier is 40/A
> sequence chain #40/C
Alignment identifier is 40/C
> select #40/C:545
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel #f8e266ff
> color sel #8fc3faff
> color sel #f8e266ff
> select #40/C:780
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #e7c3afff
> color sel #2e79abff
> color sel #e7c3afff
> color sel #8fc3faff
> color sel #2e79abff
> color sel #8fc3faff
> color sel #2e79abff
> color sel #8fc3faff
> select clear
> select #40/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> show #!8 models
> hide #!40 models
> select #8/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> select clear
> select #40/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color #8 #ffffffff
> undo
> select #40
21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected
> ~select #40
Nothing selected
> select #40/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> show #!40 models
> color sel #f5e4deff
> color sel #31358cff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #000000ff
> color sel #889affff
> color sel #5a66adff
> color sel #6471c1ff
> color sel #7b8cedff
> color sel #6c7acfff
> color sel #7282dcff
> color sel #8192f9ff
> color sel #889affff
> color sel #7887e6ff
> color sel #8192f9ff
> color sel #8293f9ff
> color sel #ffffffff
> color sel #889affff
> select clear
> hide #!8 models
> lighting soft
> select #40/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> color (#!40 & sel) #ffffffff
> color (#!40 & sel) #889affff
> select clear
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #42
---
Chain | Description
A | No description available
C | No description available
> hide #42 models
> hide #!40 models
> show #39 models
> mmaker #42 to #39
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with ger2.pdb, chain C (#42), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> show #42 models
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel cartoons
> select #42/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #e7c3afff
> color sel #889affff
> select clear
> select #42
2990 atoms, 3024 bonds, 389 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #42/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel cartoons
> select #42/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #ffffffff
> color sel #889affff
> color sel #889cffff
> color sel #8497f7ff
> color sel #8396f5ff
> color sel #8295f4ff
> color sel #8295f3ff
> color sel #7e90ecff
> color sel #7d90ebff
> color sel #7c8ee8ff
> color sel #788ae1ff
> select clear
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain #42/A
Alignment identifier is 42/A
> select #6
2 models selected
> undo
> undo
> hide #39 models
> show #4 models
> hide #!6 models
> hide #4 models
> show #39 models
Drag select of 2 residues
> color sel #ffffffff
> color sel #ff0000ff
> color sel #aa55ffff
> color sel #00aaffff
> color sel #ff5500ff
> color sel #ff0000ff
> color sel #aa0000ff
> show sel atoms
> color sel byhetero
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #39/A
Alignment identifier is 39/A
Drag select of 1 residues
Drag select of 2 residues
> show sel atoms
> color sel byhetero
> color sel #ffff7fff
> color sel #ffff00ff
> color sel #aaff7fff
> color sel #ff5500ff
> color sel #ff557fff
> color sel #55557fff
> color sel #555500ff
> color sel #ff0000ff
> color sel #550000ff
> color sel #55007fff
> color sel byhetero
> select clear
> select #42/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #788ae1ff
> hide sel atoms
> hide sel atoms
> color sel red
> color sel #ff0000ff
> color sel #aa0000ff
> color sel #aa007fff
> color sel #ff007fff
> color sel #550000ff
> color sel #aa0000ff
> select clear
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select clear
> select #42/C:201
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #42/C
Alignment identifier is 42/C
> color sel #e7c3afff
> color sel #aa0000ff
> hide sel cartoons
> show #!40 models
> hide #39 models
> hide #42 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/B
Alignment identifier is 8/B
No statusbar messages will be shown due to inadequate OpenGL
> ui tool show "Show Sequence Viewer"
> sequence chain #40/A
Alignment identifier is 40/A
> color sel #005500ff
> color sel #aa0000ff
> undo
> undo
Drag select of 1 residues
> select clear
> select clear
Drag select of 1 residues
> color sel #005500ff
> color sel #aa0000ff
> hide #!40 models
> show #41 models
> show #!40 models
> hide #!40 models
> ui tool show "Show Sequence Viewer"
> sequence chain #41/A
Alignment identifier is 41/A
> ui tool show "Show Sequence Viewer"
> sequence chain #41/B
Alignment identifier is 41/B
Drag select of 1 residues
> color sel #f8e266ff
> color sel #8fc3faff
> color sel #f8e266ff
Drag select of 1 residues
> color sel #e7c3afff
> color sel #aa0000ff
Drag select of 1 residues
> color sel #8fc3faff
> select clear
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #43
---
Chain | Description
A | No description available
C | No description available
> mmaker #43 #41
> matchmaker #43 #41
Missing required "to" argument
> mmaker #43 to #41
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
with ger2.pdb, chain C (#43), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #43/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #788ae1ff
> select #43/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel cartoons
> show #42 models
> hide #41 models
> show #41 models
> hide #42 models
> hide #43 models
> show #!40 models
> hide #41 models
> hide #!40 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #4 models
> show #11 models
> hide #11 models
> show #13 models
> hide #13 models
> show #16 models
> hide #16 models
> hide #4 models
> show #42 models
> hide #42 models
> show #43 models
> hide #43 models
> show #42 models
> show #39 models
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select clear
> show #!37 models
> hide #!37 models
> hide #39 models
> hide #42 models
> show #!40 models
> hide #!40 models
> show #36 models
> show #42 models
> hide #42 models
> show #43 models
> show #42 models
> hide #43 models
> hide #36 models
> show #39 models
> hide #39 models
> show #!37 models
> hide #42 models
> show #!40 models
> hide #!37 models
> hide #!40 models
> show #39 models
> show #!40 models
> show #41 models
> hide #41 models
> hide #!40 models
> hide #39 models
> show #39 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-closed
> transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-closed'
> show #42 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> closed.png transparentBackground true supersample 3
> hide #39 models
> hide #42 models
> show #43 models
> show #38 models
> hide #43 models
> hide #38 models
> show #41 models
> show #43 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> open.png transparentBackground true supersample 3
> hide #41 models
> hide #43 models
> show #!40 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> complex.png transparentBackground true supersample 3
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/closed.png
> transparentBackground true supersample 3
> hide #1 models
> show #39 models
> hide #39 models
> show #41 models
> show #43 models
> hide #41 models
> hide #43 models
> show #39 models
> show #42 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> open.png transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> closed.png transparentBackground true supersample 3
> hide #39 models
> hide #42 models
> show #!40 models
> hide #!40 models
> show #39 models
> show #42 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #39 models
> hide #!40 models
> show #!40 models
> hide #42 models
> hide #!40 models
> show #39 models
> show #42 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> closed.png transparentBackground true supersample 3
> hide #42 models
> hide #39 models
> show #!40 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> complex.png transparentBackground true supersample 3
> hide #!40 models
> show #41 models
> show #43 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/linker-
> open.png transparentBackground true supersample 3
> hide #43 models
> show #42 models
> hide #41 models
> hide #42 models
> show #39 models
> show #42 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash.png
> transparentBackground true supersample 3
> show #1 models
> hide #39 models
> hide #42 models
> show #!29 models
> show #28 models
> hide #1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> hide #!29 models
> hide #28 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #44
---
Chain | Description
A B | No description available
Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #45
---
Chain | Description
A B | No description available
> select #44/A
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #45/B
18413 atoms, 18556 bonds, 1129 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #44/B
Alignment identifier is 44/B
> select #45/A:554
18 atoms, 17 bonds, 1 residue, 1 model selected
> select #44/B:814
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 2 residues
> color sel #f8e266ff
> select #44/B:799
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #45/A
Alignment identifier is 45/A
> color sel #f8e266ff
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> select #45/A:545
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #f8e266ff
> select clear
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea2.pdb
AF-gea2.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-gea2.pdb #46
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> mmaker #46 to #44
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#44)
with AF-gea2.pdb, chain A (#46), sequence alignment score = 5628
RMSD between 756 pruned atom pairs is 1.152 angstroms; (across all 1222 pairs:
2.471)
> ui tool show "Show Sequence Viewer"
> sequence chain #46/A
Alignment identifier is 46/A
Drag select of 8 residues
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> color sel #ffaaffff
> select clear
> select clear
> mmaker #34 to #45
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
with AF-gea1.pdb, chain A (#34), sequence alignment score = 3215.1
RMSD between 437 pruned atom pairs is 1.248 angstroms; (across all 1128 pairs:
10.861)
> show #!34 models
> hide #!34 models
> mmaker #34 to #44
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain B (#44)
with AF-gea1.pdb, chain A (#34), sequence alignment score = 3579.8
RMSD between 524 pruned atom pairs is 1.214 angstroms; (across all 1219 pairs:
5.699)
> show #!34 models
> hide #!34 models
> color sel #55ffffff
> color sel #ffaaffff
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea2.pdb
AF-gea2.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-gea2.pdb #47
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> mmaker #47 to #45
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
with AF-gea2.pdb, chain A (#47), sequence alignment score = 4981.5
RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
9.500)
> ui tool show "Show Sequence Viewer"
> sequence chain #47/A
Alignment identifier is 47/A
Drag select of 12 residues
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> color sel #55ffffff
> color sel #ffaaffff
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> color #44-47 #55ffffff
> color #44-47 #ffaaffff
> undo
> undo
> hide #47 models
> show #47 models
> close #47
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea2.pdb
AF-gea2.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-gea2.pdb #47
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> mmaker #47 to #45
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
with AF-gea2.pdb, chain A (#47), sequence alignment score = 4981.5
RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
9.500)
> ui tool show "Show Sequence Viewer"
> sequence chain #47/A
Alignment identifier is 47/A
> delete atoms sel
> delete bonds sel
> delete atoms sel
> delete bonds sel
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> color sel #55ffffff
> color sel #ffaaffff
> show #!18 models
> show #18.1 models
> hide #18.1 models
> show #30.14 models
> show #31.7 models
> hide #31.7 models
> hide #!31 models
> show #!15 models
> show #15.15 models
> hide #!18 models
> show #14.1 models
> hide #!15 models
> hide #15.15 models
> hide #14.1 models
> hide #!14 models
> hide #!30 models
> hide #30.14 models
> show #12.1 models
> select clear
> open C:/local_data/Cornell/research/fromme_lab/ger2.pdb
Chain information for ger2.pdb #48
---
Chain | Description
A | No description available
C | No description available
> mmaker #48 to #45
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain A (#45)
with ger2.pdb, chain C (#48), sequence alignment score = 995.5
RMSD between 173 pruned atom pairs is 1.250 angstroms; (across all 201 pairs:
1.472)
> mmaker #12 to #48
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#48) with 2k5u.pdb, chain A (#12.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> hide #48 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/hemi.png
> transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/hemi-side.png
> transparentBackground true supersample 3
> turn 0 90
Expected an axis vector or a keyword
> turn 1 90
Expected an axis vector or a keyword
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn x 1 90
> turn y 1 90
> turn y 1 90
> turn y 1 90
> rainbow #44-47#12.1
> undo
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> lighting soft
> lighting simple
> lighting soft
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/figures.cxs
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/hemi-side.png transparentBackground true supersample 3
> hide #47 models
> hide #46 models
> hide #45 models
> hide #44 models
> hide #12.1 models
> hide #!12 models
> show #1 models
> show #4 models
> show #!8 models
> show #!26 models
> hide #!26 models
> show #25 models
> show #24 models
> hide #!8 models
> hide #4 models
> show #!26 models
> hide #1 models
> hide #!26 models
> hide #25 models
> hide #24 models
> show #!26 models
> show #!26 surfaces
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/lipids.png
> transparentBackground true supersample 3
> hide #!26 models
> show #25 models
> show #24 models
> show #1 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/closed-
> membrane.png transparentBackground true supersample 3
> hide #1 models
> show #4 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/open-
> membrane.png transparentBackground true supersample 3
> hide #4 models
> show #!8 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/complex-
> membrane.png transparentBackground true supersample 3
> hide #25 models
> hide #24 models
> hide #!8 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/AF-
> gea2.pdb
AF-gea2.pdb title:
Alphafold V2.0 prediction for arf guanine-nucleotide exchange factor 2
(P39993) [more info...]
Chain information for AF-gea2.pdb #49
---
Chain | Description
A | arf guanine-nucleotide exchange factor 2
> alphafold #49
Unknown command: palette alphafold #49
> color pallete
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color pallete alphafold #49
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #49 pallete alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color all #49 pallete alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> ui tool show Log
> select #49
11659 atoms, 11853 bonds, 1459 residues, 1 model selected
> color bfactor sel
11659 atoms, 1459 residues, atom bfactor range 21 to 98.4
> select clear
> select #49
11659 atoms, 11853 bonds, 1459 residues, 1 model selected
> color bfactor sel pallete alphafold
> color byattribute bfactor sel pallete alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor sel pallete alphafold ribbons
> color byattribute bfactor sel pallete alphafold ribbons
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color bfactor sel pallete ribbons alphafold
> color byattribute bfactor sel pallete ribbons alphafold
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> pallete alphafold
Unknown command: pallete alphafold
> palete alphafold
Unknown command: palete alphafold
> alphafold
Unknown command: palette alphafold
>
Incomplete command: palette
> alphafold
Unknown command: palette alphafold
> ribbons alphafold
Unknown command: palette ribbons alphafold
> alphafold
Unknown command: alphafold
> select clear
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex_dimer-FINAL-coot-7.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/open_dimer-FINAL-coot-5_real_space_refined_208.pdb
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #50
---
Chain | Description
A B | No description available
Chain information for complex_dimer-FINAL-coot-7.pdb #51
---
Chain | Description
A C | No description available
B | No description available
D | No description available
Chain information for open_dimer-FINAL-coot-5_real_space_refined_208.pdb #52
---
Chain | Description
A B | No description available
> select #50/B
19822 atoms, 19979 bonds, 1222 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #52/B
18413 atoms, 18556 bonds, 1129 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #51/C
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!51 & sel)
> delete bonds (#!51 & sel)
> mmaker #50-52 to #49
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-gea2.pdb, chain A (#49) with closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb, chain A (#50), sequence alignment score =
5664
RMSD between 764 pruned atom pairs is 1.164 angstroms; (across all 1222 pairs:
2.486)
Matchmaker AF-gea2.pdb, chain A (#49) with complex_dimer-FINAL-coot-7.pdb,
chain A (#51), sequence alignment score = 5315
RMSD between 717 pruned atom pairs is 1.105 angstroms; (across all 1159 pairs:
7.498)
Matchmaker AF-gea2.pdb, chain A (#49) with open_dimer-FINAL-
coot-5_real_space_refined_208.pdb, chain A (#52), sequence alignment score =
4981.5
RMSD between 734 pruned atom pairs is 1.218 angstroms; (across all 1129 pairs:
9.500)
Drag select of 164 residues
> delete atoms sel
> delete bonds sel
> hide #!51 models
> hide #50 models
> hide #52 models
> show #50 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
> transparentBackground true supersample "3\\\"
Invalid "supersample" argument: Expected an integer
> hide #50 models
> show #!51 models
> select #51/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #55ffffff
> color sel #ff5500ff
> select clear
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-complex.png
> transparentBackground true supersample 3
> hide #!51 models
> show #50 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
> transparentBackground true supersample 3
> hide #50 models
> show #52 models
> hide #52 models
> hide #49 models
> show #11 models
> select #11/C
1633 atoms, 1666 bonds, 201 residues, 1 model selected
> hide sel cartoons
> select #11/A
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> color sel #788ae1ff
> select clear
> show #28 models
> hide #28 models
> show #47 models
> show #46 models
> show #44 models
> hide #47 models
> hide #46 models
> hide #44 models
> show #1 models
> show #20 models
> show #21 models
> mmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with ger2.pdb, chain C (#11), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> nfArf1.png transparentBackground true supersample 3
> hide #1 models
> hide #11 models
> show #!8 models
> select #8/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> hide sel cartoons
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
> nfArf1.png transparentBackground true supersample 3
> hide #!8 models
> select #8
21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected
> hide #21 models
> hide #20 models
> show #11 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/nfArf1.png
> transparentBackground true supersample 3
> hide #11 models
> ~select #8
4 models selected
> show #11 models
> show #1 models
> show #20 models
> show #21 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/closed-
> nfArf1-side.png transparentBackground true supersample 3
> hide #1 models
> hide #21 models
> hide #20 models
> save
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/nfArf1-side.png
> transparentBackground true supersample 3
> hide #11 models
> show #!8 models
> show #21 models
> show #20 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
> nfArf1-side transparentBackground true supersample 3
Cannot determine format for
'C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
nfArf1-side'
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
> nfArf1-side.png transparentBackground true supersample 3
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure6/complex-
> nfArf1-side.png transparentBackground true supersample 3
> hide #20 models
> hide #21 models
> hide #!8 models
> show #49 models
> show #50 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
> transparentBackground true supersample 3
> hide #50 models
> show #!51 models
> hide #!51 models
> show #50 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-closed.png
> transparentBackground true supersample 3
> hide #50 models
> show #!51 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/AF-complex.png
> transparentBackground true supersample 3
> hide #!51 models
> show #52 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/af_sup/af-open.png
> transparentBackground true supersample 3
> hide #49 models
> hide #52 models
> show #44 models
> hide #44 models
> show #39 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.pdb
1r8s.pdb title:
ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
catalytic glutamate to lysine [more info...]
Chain information for 1r8s.pdb #53
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #53
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #53 to #39
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with 1r8s.pdb, chain E (#53), sequence alignment score = 432.1
RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
5.093)
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select #53/A
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> select #53/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select clear
> select #53/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> ui tool show "Side View"
> ui tool show "Side View"
> ui tool show "Side View"
> ui tool show "Side View"
> toolshed show
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> hide #39 models
> show #38 models
> show #41 models
> show #39 models
> hide #41 models
> hide #53 models
> show #!40 models
> hide #!40 models
> show #41 models
> hide #41 models
> show #41 models
> show #53 models
> mmaker #53 to #41
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
with 1r8s.pdb, chain E (#53), sequence alignment score = 444.6
RMSD between 129 pruned atom pairs is 1.311 angstroms; (across all 185 pairs:
2.676)
> hide #41 models
> hide #53 models
> show #!40 models
> hide #39 models
> hide #38 models
> hide #!40 models
> show #39 models
> show #53 models
> hide #53 models
> show #53 models
> mmaker #53 to #39
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with 1r8s.pdb, chain E (#53), sequence alignment score = 432.1
RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
5.093)
> show #43 models
> hide #43 models
> show #42 models
> hide #42 models
> show #48 models
> hide #48 models
> hide #39 models
> show #!40 models
> hide #!40 models
> show #39 models
> show #42 models
> hide #42 models
> show #42 models
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> hide sel cartoons
> hide #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> nucleotidefree.png transparentBackground true supersample 3
> hide #42 models
> show #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
> transparentBackground true supersample 3
> hide #39 models
> hide #53 models
> show #!40 models
> hide #!40 models
> show #39 models
> show #53 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #39 models
> hide #53 models
> show #53 models
> hide #53 models
> show #53 models
> hide #!40 models
> show #39 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> hide #39 models
> show #42 models
> hide #53 models
> show #39 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> nucleotidefree.png transparentBackground true supersample 3
> hide #42 models
> show #53 models
> show #42 models
> hide #42 models
> show #42 models
> hide #42 models
> show #42 models
> select #42/C
1635 atoms, 1668 bonds, 201 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide #42 models
> show #42 models
> hide #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> nucleotidefree.png transparentBackground true supersample 3
> hide #42 models
> show #53 models
> show #42 models
> hide #42 models
> show #42 models
> hide #42 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
> transparentBackground true supersample 3
> hide #39 models
> show #!40 models
> hide #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> complex.png transparentBackground true supersample 3
> show #53 models
> hide #!40 models
> show #38 models
> hide #38 models
> show #39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #!40 models
> hide #53 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #53 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
> transparentBackground true supersample 3
> hide #53 models
> show #42 models
> hide #42 models
> show #!40 models
> hide #39 models
> show #39 models
> show #53 models
> hide #39 models
> show #39 models
> hide #!40 models
> show #41 models
> select #42
2990 atoms, 3024 bonds, 389 residues, 1 model selected
> ~select #42
Nothing selected
> hide #41 models
> show #!40 models
> hide #39 models
> show #39 models
> hide #!40 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-gdp.png
> transparentBackground true supersample 3
> show #42 models
> hide #39 models
> show #39 models
> hide #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> nucleotidefree.png transparentBackground true supersample 3
> hide #42 models
> hide #39 models
> show #!40 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/figure5/clash-
> complex.png transparentBackground true supersample 3
> show #39 models
> hide #!40 models
> show #53 models
> hide #53 models
> hide #39 models
> show #!40 models
> hide #!40 models
> show #!40 models
> show #!31 models
> hide #!31 models
> show #31.7 models
> mmaker #31 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain B (#40) with 2ksq.pdb, chain
A (#31.7), sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> show #38 models
> hide #38 models
> show #41 models
> hide #!40 models
> show #43 models
> mmaker #43 to #41
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
with ger2.pdb, chain C (#43), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
> mmaker #31 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#43) with 2ksq.pdb, chain A (#31.7), sequence
alignment score = 665.1
RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.623)
> hide #43 models
> show #!40 models
> hide #!40 models
> show #42 models
> hide #42 models
> show #43 models
> mmaker #43 to #41
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker open_dimer-FINAL-coot-5_real_space_refined_208.pdb, chain B (#41)
with ger2.pdb, chain C (#43), sequence alignment score = 1010.5
RMSD between 172 pruned atom pairs is 1.233 angstroms; (across all 201 pairs:
1.454)
> mmaker #31.7 to #43
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#43) with 2ksq.pdb, chain A (#31.7), sequence
alignment score = 665.1
RMSD between 116 pruned atom pairs is 1.150 angstroms; (across all 165 pairs:
3.623)
> hide #43 models
> show #!40 models
> hide #41 models
> hide #31.7 models
> hide #!40 models
> show #41 models
> show #31.7 models
> mmaker #31.7 to #40
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex_dimer-FINAL-coot-7.pdb, chain B (#40) with 2ksq.pdb, chain
A (#31.7), sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> hide #41 models
> show #!40 models
> hide #!40 models
> show #!40 models
> select #40/B
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide #!40 models
> select #40
21258 atoms, 21601 bonds, 46 pseudobonds, 2647 residues, 2 models selected
> ~select #40
Nothing selected
> hide #31.7 models
> hide #!31 models
> show #1 models
> show #!12 models
> show #12.1 models
> hide #12.1 models
> hide #!12 models
> show #15.15 models
> hide #15.15 models
> hide #!15 models
> show #!15 models
> show #!17 models
> show #!18 models
> show #17.1 models
> hide #17.1 models
> hide #!17 models
> show #16 models
> mmaker #16 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with ger2.pdb, chain C (#16), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> show #18.1 models
> hide #18.1 models
> show #17.1 models
> mmaker #17 to #18
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2k5u.pdb, chain A (#18.1) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 926
RMSD between 180 pruned atom pairs is 0.000 angstroms; (across all 180 pairs:
0.000)
> mmaker #17 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> hide #16 models
> show #16 models
> hide #16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!18 models
> hide #17.1 models
> show #17.1 models
> mmaker #17 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#16) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> show #31.7 models
> hide #31.7 models
> show #!30 models
> show #!27 models
> show #!37 models
> hide #!37 models
> show #39 models
> hide #39 models
> show #42 models
> hide #42 models
> show #43 models
> hide #43 models
> show #43 models
> hide #!31 models
> hide #!30 models
> mmaker #17 to #43/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ger2.pdb, chain A (#43) with 2k5u.pdb, chain A (#17.1), sequence
alignment score = 695
RMSD between 105 pruned atom pairs is 1.135 angstroms; (across all 165 pairs:
5.084)
> mmaker #43/C to #1/A bring #17
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1)
with ger2.pdb, chain C (#43), sequence alignment score = 978.1
RMSD between 177 pruned atom pairs is 1.102 angstroms; (across all 201 pairs:
1.427)
> hide #43 models
> show #53 models
> hide #!27 models
> hide #17.1 models
> hide #!17 models
> show #50 models
> hide #50 models
> show #44 models
> hide #44 models
> show #39 models
> hide #1 models
> select ::name="GDP"
828 atoms, 870 bonds, 21 residues, 21 models selected
> select #27
47232 atoms, 47696 bonds, 2912 residues, 17 models selected
> ~select #27
Nothing selected
> select #53 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #ff007fff
> color sel #ffffffff
> color sel #ff007fff
> color sel byhetero
> select clear
> mmaker #1 to #39
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#39)
with closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#1),
sequence alignment score = 6255.8
RMSD between 1222 pruned atom pairs is 0.000 angstroms; (across all 1222
pairs: 0.000)
> show #1 models
> hide #39 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> show #38 models
> hide #38 models
> show #39 models
Drag select of 14 residues
> select clear
Drag select of 2 residues
> color sel #550000ff
> color sel #aa0000ff
> color sel #ffffffff
> color sel #aa0000ff
> select clear
> hide #39 models
> show #39 models
> hide #39 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.pdb
1r8s.pdb title:
ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
catalytic glutamate to lysine [more info...]
Chain information for 1r8s.pdb #54
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #54
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> mmaker #54 to #53
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1r8s.pdb, chain E (#53) with 1r8s.pdb, chain E (#54), sequence
alignment score = 1042.5
RMSD between 187 pruned atom pairs is 0.000 angstroms; (across all 187 pairs:
0.000)
> select #54/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> preset #54 cartoons/nucleotides cylinders/stubs
No preset name matches '#54 cartoons/nucleotides cylinders/stubs'
> preset #54 cartoons/nucleotides cylinders/stubs
No preset name matches '#54 cartoons/nucleotides cylinders/stubs'
> preset cartoons/nucleotides cylinders/stubs #54
No preset name in category 'Cartoons/Nucleotides' matches 'cylinders/stubs
#54'
> preset cartoons/nucleotides cylinders/stubs
No preset name in category 'Cartoons/Nucleotides' matches 'cylinders/stubs '
> preset #54 cartoons/nucleotides Cylinders/Stubs
No preset name matches '#54 cartoons/nucleotides Cylinders/Stubs '
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide sel cartoons
> select #54/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide #53 models
> show #53 models
> select #53/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel cartoons
> hide #53 models
> select #54
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ~select #53
Nothing selected
> select #54
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> hide sel atoms
> select #54 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> color sel #ff007fff
> color sel byhetero
> hide #54 models
> select #54
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ~select #54
Nothing selected
> show #53 models
> hide #53 models
> show #54 models
> select #54 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #54
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ui mousemode right "translate selected models"
> morph #53,54
Computed 21 frame morph #55
> coordset #55 1,21
> close #55
> morph #54,53
Computed 21 frame morph #55
> coordset #55 1,21
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!40 models
> hide #55 models
> show #52 models
> hide #52 models
> ~select #54
Nothing selected
> hide #1 models
> show #41 models
> hide #41 models
> show #39 models
> morph #39,40
models have different number of chains, 2 (Morph - closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb #/A,Morph - closed_dimer-FINAL-
coot-3_real_space_refined_206.pdb #/B) and 4 (complex_dimer-FINAL-coot-7.pdb
#40/A,complex_dimer-FINAL-coot-7.pdb #40/B,complex_dimer-FINAL-coot-7.pdb
#40/C,complex_dimer-FINAL-coot-7.pdb #40/D)
> morph #39,40 same true
Computed 21 frame morph #56
> coordset #56 1,21
> close #56
> show #55 models
> hide #55 models
> show #!40 models
> show #39 models
> morph #39/A,40/A same true
Require at least 2 structures for morph
> morph #39,40/A same true
Computed 21 frame morph #56
> coordset #56 1,21
> morph #39,40/A same true
Computed 21 frame morph #57
> coordset #57 1,21
> close #56
> close #57
> show #50 models
> hide #50 models
> show #39 models
> show #53 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/arf1-closed.pdb models #53 relModel #39
> hide #53 models
> show #53 models
> hide #53 models
> show #53 models
> hide #53 models
> hide #39 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Ignored bad PDB record found on line 43510
END
Start residue of secondary structure not found: HELIX 1 1 GLY A 29 GLU A 41 1
13
Start residue of secondary structure not found: HELIX 2 2 GLN A 71 LYS A 73 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE A 74 PHE A 82 1
9
Start residue of secondary structure not found: HELIX 4 4 ASP A 96 GLU A 98 1
3
Start residue of secondary structure not found: HELIX 5 5 ARG A 99 ALA A 112 1
14
10 messages similar to the above omitted
closed-arf1-morph.pdb title:
ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
catalytic glutamate to lysine [more info...]
Chain information for closed-arf1-morph.pdb #56
---
Chain | Description
A | adp-ribosylation factor 1
B | No description available
C | No description available
E | ARNO
Non-standard residues in closed-arf1-morph.pdb #56
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
> hide #56 models
> show #54 models
> select #54/A
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
1301 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 10 10 ASN E 62 MET E 74
1 13
Start residue of secondary structure not found: HELIX 11 11 ASP E 75 ASN E 86
1 12
Start residue of secondary structure not found: HELIX 12 12 THR E 92 GLY E 103
1 12
Start residue of secondary structure not found: HELIX 13 13 ASN E 107 GLY E
116 1 10
Start residue of secondary structure not found: HELIX 14 14 GLU E 119 LEU E
132 1 14
5 messages similar to the above omitted
Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for closed-arf1-morph.pdb #57
---
Chain | Description
A | No description available
B | No description available
> hide #54 models
> show #!51 models
> hide #!51 models
> show #!40 models
> morph #57,40 same true
Computed 21 frame morph #58
> coordset #58 1,21
> close #58
> show #57 models
> show #!40 models
> select #40/D
1324 atoms, 1347 bonds, 2 pseudobonds, 164 residues, 2 models selected
> delete atoms (#!40 & sel)
> delete bonds (#!40 & sel)
> morph #57,40 same true
Computed 21 frame morph #58
> coordset #58 1,21
> hide #!58 models
> close #58
> show #55 models
> show #56 models
> hide #56 models
> show #57 models
> hide #55 models
> select #57/A
21107 atoms, 21287 bonds, 1382 residues, 1 model selected
> close #57
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
4536 messages similar to the above omitted
Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0
Bad residue range for secondary structure: SHEET 4 4 4 GLY A 87 ASP A 93 0
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for closed-arf1-morph.pdb #57
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
> morph #57,40 same true
Computed 21 frame morph #58
> coordset #58 1,21
> hide #!58 models
> show #!58 models
> close #58
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph.pdb
---
warning | Ignored bad PDB record found on line 19939
END
Chain information for complex-morph.pdb #58
---
Chain | Description
A B | No description available
C | No description available
> show #57 models
> hide #57 models
> show #56 models
> hide #56 models
> show #57 models
> mmaker #57 to #58
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex-morph.pdb, chain A (#58) with closed-arf1-morph.pdb, chain
B (#57), sequence alignment score = 5425.2
RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
8.322)
> morph #57,58 same true
Computed 21 frame morph #59
> coordset #59 1,21
> close #59
> show #!58 models
> show #57 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select #58
19934 atoms, 20254 bonds, 44 pseudobonds, 2483 residues, 2 models selected
> mmaker #57 to #58
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex-morph.pdb, chain A (#58) with closed-arf1-morph.pdb, chain
B (#57), sequence alignment score = 5425.2
RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
8.322)
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> select #58
19934 atoms, 20254 bonds, 44 pseudobonds, 2483 residues, 2 models selected
> mmaker #58 to #57
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
A (#58), sequence alignment score = 5425.2
RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
8.322)
> select clear
> mmaker #58/A to #57/A bring #58/B #58/C
'bring' arg specifies no non-match/ref structures
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain A (#57) with complex-morph.pdb, chain
A (#58), sequence alignment score = 5367.3
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> morph #57,58 same true
Computed 21 frame morph #59
> coordset #59 1,21
> hide #!59 models
> show #!58 models
> show #57 models
> show #!59 models
> hide #!59 models
> hide #!58 models
> show #!58 models
> hide #57 models
> show #!59 models
> hide #!58 models
> morph #58,57 same true
Computed 21 frame morph #60
> coordset #60 1,21
> hide #!59 models
> hide #!60 models
> show #!58 models
> show #57 models
> hide #57#!58 atoms
> mmaker #58 to #57
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
A (#58), sequence alignment score = 5425.2
RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
8.322)
> mmaker #58/A to #57/A bring #58/B #58/C
'bring' arg specifies no non-match/ref structures
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain A (#57) with complex-morph.pdb, chain
A (#58), sequence alignment score = 5367.3
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> hide #!58 models
> select #57/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!58 models
> morph #57,58 same true
Computed 21 frame morph #61
> coordset #61 1,21
> close #59-61
> show #57 models
> show #56 models
> hide #56 models
> show #!58 models
> hide #57 models
> hide #!58 models
> close #58
> close #56-57
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph.pdb
> C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
> arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph.pdb
---
warning | Ignored bad PDB record found on line 19939
END
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
4536 messages similar to the above omitted
Bad residue range for secondary structure: SHEET 4 4 1 GLY A 87 ASP A 93 0
Bad residue range for secondary structure: SHEET 4 4 4 GLY A 87 ASP A 93 0
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for complex-morph.pdb #56
---
Chain | Description
A B | No description available
C | No description available
Chain information for closed-arf1-morph.pdb #57
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
> mmaker #56 to #57
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain B (#57) with complex-morph.pdb, chain
A (#56), sequence alignment score = 5425.2
RMSD between 751 pruned atom pairs is 1.121 angstroms; (across all 1153 pairs:
8.322)
> hide #!56 models
> select #57/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
No model chosen to save relative to
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb models #57 relModel #57
> close #57
> show #53 models
> hide #53 models
> show #54 models
> show #50 models
> hide #50 models
> show #44 models
> hide #44 models
> show #44 models
> hide #44 models
> show #39 models
> show #53 models
> hide #54 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb models #39,53 relModel #39
> hide #53 models
> hide #39 models
> show #!56 models
> hide #!56 models
> show #54 models
> hide #54 models
> show #53 models
> show #44 models
> hide #44 models
> show #39 models
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> select #39
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb displayedOnly true selectedOnly true relModel
> #39
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> select #39
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
No model chosen to save relative to
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb selectedOnly true relModel #39
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> select #39
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> select #39
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> select #53
3206 atoms, 2904 bonds, 704 residues, 1 model selected
Drag select of 2883 residues, 28 atoms, 30 bonds
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb selectedOnly true relModel #39
> hide #53 models
> select #39
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> hide #39 models
> ~select #39
Nothing selected
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Ignored bad PDB record found on line 192
END
Ignored bad PDB record found on line 195
END
Ignored bad PDB record found on line 198
END
Ignored bad PDB record found on line 201
END
Ignored bad PDB record found on line 204
END
59 messages similar to the above omitted
Chain information for closed-arf1-morph.pdb
---
Chain | Description
57.1/A 57.1/B | No description available
57.2/A | No description available
> hide #57.2 models
> hide #!57.1 models
> show #!57.1 models
> show #57.2 models
> show #!56 models
> mmaker #56/A to #57/A bring #56/B #56/C
Specify a single 'to' model only
> mmaker #56/A to #57.1/A bring #56/B #56/C
'bring' arg specifies no non-match/ref structures
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed-arf1-morph.pdb, chain A (#57.1) with complex-morph.pdb,
chain A (#56), sequence alignment score = 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> morph #57,56 same true
Computed 41 frame morph #58
> coordset #58 1,41
> hide #!57 models
> hide #!58 models
> show #!58 models
> show #!57 models
> hide #!57 models
> hide #!58 models
> show #53 models
> show #39 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3230 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 GLY A 29 GLU A 41 1
13
Start residue of secondary structure not found: HELIX 2 2 GLN A 71 LYS A 73 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE A 74 PHE A 82 1
9
Start residue of secondary structure not found: HELIX 4 4 ASP A 96 GLU A 98 1
3
Start residue of secondary structure not found: HELIX 5 5 ARG A 99 ALA A 112 1
14
10 messages similar to the above omitted
Chain information for closed-arf1-morph.pdb #59
---
Chain | Description
A B | No description available
C | No description available
E | No description available
> hide #53 models
> hide #39 models
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> hide #59 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/1r8s.pdb C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed_dimer-FINAL-coot-3_real_space_refined_206.pdb
1r8s.pdb title:
ARF1[Δ1-17]-GDP In complex with A SEC7 domain carrying the mutation of the
catalytic glutamate to lysine [more info...]
Chain information for 1r8s.pdb #60
---
Chain | Description
A | adp-ribosylation factor 1
E | ARNO
Non-standard residues in 1r8s.pdb #60
---
BME — β-mercaptoethanol
FMT — formic acid
GDP — guanosine-5'-diphosphate
SO3 — sulfite ion
SO4 — sulfate ion
Chain information for closed_dimer-FINAL-coot-3_real_space_refined_206.pdb #61
---
Chain | Description
A B | No description available
> mmaker #60 to #61
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#61)
with 1r8s.pdb, chain E (#60), sequence alignment score = 432.1
RMSD between 115 pruned atom pairs is 1.246 angstroms; (across all 185 pairs:
5.093)
> select #59/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> select #59
42850 atoms, 42862 bonds, 3148 residues, 1 model selected
> select #60/A
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> select #60/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #61
39644 atoms, 39958 bonds, 2444 residues, 1 model selected
> ~select #61
Nothing selected
> select #60
1471 atoms, 1345 bonds, 312 residues, 1 model selected
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/arf1-closed.pdb models #60 relModel #61
> hide #61 models
> hide #60 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/closed-arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/closed-
arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 41274
END
Chain information for closed-arf1-morph.pdb #62
---
Chain | Description
A B | No description available
C | No description available
> show #59 models
> morph #62,59 same true
Computed 21 frame morph #63
> coordset #63 1,21
> ~select #60
Nothing selected
> hide #63 models
> show #63 models
> hide #63 models
> show #62 models
> show #59 models
> hide #59 models
> hide #62 models
> show #62 models
> show #!56 models
> mmaker #62 to #56
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex-morph.pdb, chain A (#56) with closed-arf1-morph.pdb, chain
A (#62), sequence alignment score = 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> morph #62,56 same true
Computed 21 frame morph #64
> coordset #64 1,21
> show #!56 models
> hide #!56,64 atoms
> hide #!56 models
> show #62 models
> hide #62#!64 cartoons
> show #62#!64 cartoons
> hide #62#!64 atoms
> hide #62 models
> hide #!64 models
> show #55 models
> show #50 models
> hide #50 models
> show #52 models
> hide #52 models
> select #55
3206 atoms, 2904 bonds, 704 residues, 1 model selected
> ~select #55
Nothing selected
> show #!57 models
> hide #!57 models
> show #50 models
> hide #50 models
> show #39 models
> hide #55 models
> show #55 models
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> coordset slider#55
Missing or invalid "structures" argument: invalid structures specifier
> coordset slider #55
> hide #55 models
> hide #39 models
> show #!64 models
> coordset slider #64
> movie record
> movie record
Already recording a movie
> movie stop
> new
Unknown command: movie new
> movie reset
> start
Unknown command: movie start
> movie record
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> show #55 models
> show #50 models
> hide #50 models
> show #39 models
> hide #55 models
> show #55 models
> hide #55 models
> show #55 models
> hide #!64 models
> hide #39 models
> show #!64 models
> hide #55 models
> select #64
19783 atoms, 20100 bonds, 8 pseudobonds, 2466 residues, 2 models selected
> ~select #64
Nothing selected
> select #64 ::name="GDP"
Nothing selected
> show #!64 atoms
> hide #!64 atoms
> hide #!64 models
> show #62 models
> select #62 ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> move #62 ::name="GDP"
Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 28
atoms
> move x 5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x +5 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 05 #62 ::name="GDP"
Expected an integer >= 1 or a keyword
> move x 0 5 #62 ::name="GDP"
Expected a keyword
> move x -2 10 #62 ::name="GDP"
Expected a keyword
> move x -2 10 #62
Expected a keyword
> move x -2 10 #62
Expected a keyword
> move x #62 ::name="GDP"
Expected a number or a keyword
> move x #62
Expected a number or a keyword
> move x #62
Expected a number or a keyword
> move y #64 ::name="GDP"
Expected a number or a keyword
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y models #64 ::name="GDP"
> move y #64 ::name="GDP"
Expected a number or a keyword
> move y atoms #64 ::name="GDP"
> move y atoms #64::name="GDP"
> move y #64::name="GDP"
Expected a number or a keyword
> move y #64
Expected a number or a keyword
> move y 5 #64
Expected an integer >= 1 or a keyword
> move y 5 models #64
> move y atoms #64
> show #!64 models
> hide #!64 models
> move y atoms #62
> move y 10 atoms #62 ::name="GDP"
> move y -10 atoms #62 ::name="GDP"
> select #62/C:131
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!64 models
> hide #!64 models
> show #63 models
> hide #63 models
> show #63 models
> hide #63 models
> undo
> undo
> undo
> undo
> undo
> undo
> show #!64 models
> hide #!64 models
> hide #62 models
> show #!64 models
> show #63 models
> hide #63 models
> show #!58 models
> hide #!58 models
> show #55 models
> select #55/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> hide sel cartoons
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui tool show "Show Sequence Viewer"
> sequence chain #64/C
Alignment identifier is 64/C
> color sel #788ae1ff
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #64/A
Alignment identifier is 64/A
> sequence chain #64/B
Alignment identifier is 64/B
> color sel #f8e266ff
> color sel #e7c3afff
> select clear
> select #64/A:756
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #aa0000ff
> color sel #8fc3faff
> select clear
> color sel #f8e266ff
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> coordset #64 1,21
> select #64 ::name="GDP"
Nothing selected
> hide #!64 models
> show #63 models
> show #!58 models
> hide #!58 models
> hide #63 models
> hide #55 models
> show #55 models
> show #39 models
> coordset #55 1,21
> wait
wait requires a frame count argument unless motion is in progress
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #55 models
> select #55/E
1735 atoms, 1559 bonds, 392 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!64 models
> show #39 models
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #39 models
> mmaker #39 to #64 bring #55
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Morph - closed-arf1-morph.pdb, chain A (#64) with closed_dimer-
FINAL-coot-3_real_space_refined_206.pdb, chain A (#39), sequence alignment
score = 5834
RMSD between 753 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.351)
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!64 models
> show #54 models
> show #55 models
> hide #54 models
> show #39 models
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> hide #!64 models
> show #55 models
> show #39 models
> start
Unknown command: movie start
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie encode
No frames have been recorded
> hide #!64 models
> show #39 models
> show #55 models
> start
Unknown command: movie start
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> movie stop
> movie encode framerate 10
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> movie record
> coordset #55 1,21
> wait 21
> hide #55 #39 models
> show #64 models
> coordset #64 1,21
> show #60 models
> hide #60 models
> show #!31 models
> show #31.7 models
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #64
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #62
> save C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/GTP-
> Arf1-morph.pdb models #31 relModel #56
> show #!56 models
> hide #!56 models
> hide #!64 models
> show #!64 models
> hide #!64 models
> hide #!31 models
> hide #31.7 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph_GTP-Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph_GTP-Arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 23604
END
Chain information for complex-morph_GTP-Arf1-morph.pdb #65
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph_GTP-Arf1-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph_GTP-Arf1-morph.pdb
---
warning | Ignored bad PDB record found on line 23604
END
Chain information for complex-morph_GTP-Arf1-morph.pdb #66
---
Chain | Description
A | No description available
B | No description available
C | No description available
> movie stop
> hide #66 models
> close #66
> show #61 models
> mmaker #65 to #61
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker closed_dimer-FINAL-coot-3_real_space_refined_206.pdb, chain A (#61)
with complex-morph_GTP-Arf1-morph.pdb, chain A (#65), sequence alignment score
= 5451
RMSD between 747 pruned atom pairs is 1.165 angstroms; (across all 1153 pairs:
8.396)
> hide #61 models
> select #65
22979 atoms, 23333 bonds, 2670 residues, 1 model selected
> ~select #65
Nothing selected
> select #65
22979 atoms, 23333 bonds, 2670 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> cartoon style sel modeHelix tube sides 20
> select clear
> hide #65 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #65/A
Alignment identifier is 65/A
> sequence chain #65/B
Alignment identifier is 65/B
> sequence chain #65/C
Alignment identifier is 65/C
> select #65/C
1332 atoms, 1356 bonds, 165 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select clear
Drag select of 1 residues
> color sel #f8e266ff
> color sel #8fc3faff
> color sel #f8e266ff
Drag select of 7 residues
> color sel #e7c3afff
> color sel #788ae1ff
> color sel #e7c3afff
> color sel #8fc3faff
> select clear
> color sel #2e79abff
> color sel #8fc3faff
> color sel #788ae1ff
> select clear
> show #!56 models
> hide #!56 models
> show #!56 models
> morph #56,65 same true
Computed 21 frame morph #66
> coordset #66 1,21
> movie record
> movie encode C:\Users\Arnold/Desktop/movie.mp4 framerate 25.0
Movie saved to C:\Users\Arnold/Desktop/movie.mp4
> close #66
> show #!56 models
> show #65 models
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/complex-morph.pdb
Summary of feedback from opening
C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-figures/complex-
morph.pdb
---
warning | Ignored bad PDB record found on line 19939
END
Chain information for complex-morph.pdb #66
---
Chain | Description
A B | No description available
C | No description available
> select #66/A
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!66 & sel)
> delete bonds (#!66 & sel)
> select #66/B
9301 atoms, 9449 bonds, 22 pseudobonds, 1159 residues, 2 models selected
> delete atoms (#!66 & sel)
> delete bonds (#!66 & sel)
> hide #!56 models
Drag select of 165 residues
> cartoon style sel modeHelix tube sides 20
> color sel #e7c3afff
> color sel #788ae1ff
> mmaker #66 to #65
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex-morph_GTP-Arf1-morph.pdb, chain A (#65) with complex-
morph.pdb, chain C (#66), sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> select clear
> show #31.7 models
> hide #!66 models
> hide #65 models
> show #65 models
> hide #65 models
> show #!66 models
> moprh #66 to #31.7
Unknown command: moprh #66 to #31.7
> morph #66 to #31.7
Expected a keyword
> morph #66 to #31.7 same true
Expected a keyword
> morph #66,31.7 same true
Require at least 2 structures for morph
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> hide #31.7#!66 atoms
> morph #66,31 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> open C:/local_data/Cornell/research/fromme_lab/0_PAPER/maps-for-
> figures/2ksq.pdb
2ksq.pdb title:
The myristoylated yeast ARF1 In A GTP and bicelle bound conformation [more
info...]
Chain information for 2ksq.pdb
---
Chain | Description
67.1/A | adp-ribosylation factor 1
67.2/A 67.3/A 67.4/A 67.5/A 67.6/A 67.7/A 67.8/A 67.9/A 67.10/A 67.11/A
67.12/A 67.13/A 67.14/A 67.15/A 67.16/A 67.17/A 67.18/A 67.19/A 67.20/A | adp-
ribosylation factor 1
> close #67.1-6
> close #67.8-20
> select #67.7 ::name="GDP"
Nothing selected
> select #67.7 ::name="GTP"
43 atoms, 45 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!31 models
> hide #31.7 models
> mmaker #67 to #66
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker complex-morph.pdb, chain C (#66) with 2ksq.pdb, chain A (#67.7),
sequence alignment score = 642.9
RMSD between 114 pruned atom pairs is 1.192 angstroms; (across all 165 pairs:
4.069)
> hide #67.7#!66 cartoons
> show #67.7#!66 cartoons
> hide #67.7#!66 atoms
> cartoon style #66-67 modeHelix tube sides 20
> morph #66,67
Computed 21 frame morph #68
> coordset #68 1,21
> hide #!68 models
> show #67.7 models
> show #!66 models
> hide #!66 models
> show #!66 models
> hide #!66 models
> morph #66,67 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> show #!68 models
> morph #66,67 same true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\morph.py", line 76, in morph
color_segments = color_segments, color_core = color_core)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph
res_groups = motion.interpolate(mol, res_interp)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\morph\motion.py", line 139, in interpolate
nc = sm.coordset_size
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
AttributeError: Execution of 'Structure' object's 'coordset_size' property
raised AttributeError
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 67, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1660/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: OriginPC
Model: NEURON
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 17,093,591,040
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-9600K CPU @ 3.70GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
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