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Opened 96 minutes ago
#19962 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.12.dev202601050431 (2026-01-05 04:31:26 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12.dev202601050431 (2026-01-05)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\shumb\Documents\Glasgow University (MReS)\Structure Programs
> -\ChimeraX\8 March 26 -\STAU1 and ARF1 1 copy Conformational Changes_1.cxs"
> format session
Log from Mon Mar 9 22:15:53 2026UCSF ChimeraX version: 1.12.dev202601050431
(2026-01-05)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/ChimeraX/8 March 26 -/STAU1 and ARF1 1 copy Conformational Changes .cxs"
Log from Sun Mar 8 22:02:21 2026UCSF ChimeraX version: 1.12.dev202601050431
(2026-01-05)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:\Users\shumb\Documents\Glasgow University (MReS)\Structure Programs
> -\ChimeraX\8 March 26 -\STAU1 and ARF1 1 copy Conformational Changes .cxs"
> format session
Log from Sun Mar 8 17:58:01 2026UCSF ChimeraX version: 1.12.dev202601050431
(2026-01-05)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/Alphafold Predictions/fold_stau1_human_o95793_3_original_model_1.cif"
Chain information for fold_stau1_human_o95793_3_original_model_1.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/Alphafold
> Predictions/fold_stau1_human_1_copy_and_arf1_300_nucleotides_model_1.cif"
Chain information for
fold_stau1_human_1_copy_and_arf1_300_nucleotides_model_1.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> ui tool show "Model Panel"
> hide #2 models
> rainbow #1
> select #2:183-382
4066 atoms, 4386 bonds, 318 residues, 1 model selected
> select #2:183-382
4066 atoms, 4386 bonds, 318 residues, 1 model selected
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> select #1:183-382
1564 atoms, 1591 bonds, 200 residues, 1 model selected
> hide #2 models
> show #1 models
> ui mousemode right "translate selected atoms"
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select #1:183-390
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> save TandemRBD3+4_NoRNA_1copy.pdb selectedOnlyTrue
Expected a models specifier or a keyword
> save TandemRBD3+4_NoRNA_1copy.pdb selectedOnly true
> save tandemRBD3+4_NoRNA_1copy.pdb selectedOnly true
> hide #1 models
> show #2 models
> select #2/A:183-390
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> save tandemRBD3+4_ARF1_1copy.pdb selectedOnly true
> hide #2 models
> show #1 models
> hide #1 models
> open C:/Users/shumb/Desktop/TandemRBD3+4_NoRNA_1copy.pdb
> C:/Users/shumb/Desktop/tandemRBD3+4_ARF1_1copy.pdb
Summary of feedback from opening
C:/Users/shumb/Desktop/TandemRBD3+4_NoRNA_1copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 73 LYS A 83 1 11
Start residue of secondary structure not found: HELIX 2 2 ARG A 145 ILE A 159
1 15
Start residue of secondary structure not found: HELIX 3 3 LEU A 160 ASN A 162
1 3
Start residue of secondary structure not found: HELIX 4 4 GLU A 177 ASN A 180
1 4
Start residue of secondary structure not found: HELIX 10 10 PRO A 422 ALA A
425 1 4
13 messages similar to the above omitted
Summary of feedback from opening
C:/Users/shumb/Desktop/tandemRBD3+4_ARF1_1copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 73 LYS A 83 1 11
Start residue of secondary structure not found: HELIX 2 2 ARG A 145 ILE A 159
1 15
Start residue of secondary structure not found: HELIX 3 3 LEU A 160 ASN A 162
1 3
Start residue of secondary structure not found: HELIX 4 4 GLU A 177 ASN A 180
1 4
Start residue of secondary structure not found: HELIX 10 10 PRO A 422 ALA A
425 1 4
13 messages similar to the above omitted
Chain information for TandemRBD3+4_NoRNA_1copy.pdb #3
---
Chain | Description
A | No description available
Chain information for tandemRBD3+4_ARF1_1copy.pdb #4
---
Chain | Description
A | No description available
> color #4 #0055ffff
> color #4 #55aa00ff
> color #4 #005500ff
> color #3 #aa0000ff
> color #3 #55ffffff
> set bgColor white
> color #3 red
> color #3 blue
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> select up
1876 atoms, 1912 bonds, 240 residues, 1 model selected
> select up
4437 atoms, 4528 bonds, 577 residues, 1 model selected
> select up
10776 atoms, 11599 bonds, 877 residues, 1 model selected
> select up
18465 atoms, 19439 bonds, 1870 residues, 4 models selected
> select up
18465 atoms, 19439 bonds, 1870 residues, 4 models selected
> select up
18465 atoms, 19439 bonds, 1870 residues, 4 models selected
> select up
18465 atoms, 19439 bonds, 1870 residues, 4 models selected
> select up
18465 atoms, 19439 bonds, 1870 residues, 4 models selected
> select down
10776 atoms, 11599 bonds, 877 residues, 1 model selected
> select down
4437 atoms, 4528 bonds, 577 residues, 1 model selected
> select down
1876 atoms, 1912 bonds, 240 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select down
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select #3:183-390 #4:183-390
3252 atoms, 3312 bonds, 416 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 1038
RMSD between 74 pruned atom pairs is 0.465 angstroms; (across all 208 pairs:
28.917)
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.89248,0.11128,0.43714,11.784,-0.28462,0.89075,0.35434,-22.486,-0.34995,-0.44066,0.82665,36.14,#4,1,0,0,23.478,0,1,0,-18.945,0,0,1,3.9249
> ui tool show Matchmaker
> matchmaker #3 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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 1038
RMSD between 74 pruned atom pairs is 0.465 angstroms; (across all 208 pairs:
28.917)
> hide #3 models
> hide #4 models
> show #1 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.89248,0.11128,0.43714,11.025,-0.28462,0.89075,0.35434,-64.325,-0.34995,-0.44066,0.82665,40.181,#4,1,0,0,22.72,0,1,0,-60.784,0,0,1,7.9656
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.89248,0.11128,0.43714,14.554,-0.28462,0.89075,0.35434,-94.865,-0.34995,-0.44066,0.82665,42.725,#4,1,0,0,26.248,0,1,0,-91.324,0,0,1,10.51
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-19.185,0,1,0,-34.315,0,0,1,43.492
> view matrix models #1,1,0,0,-17.817,0,1,0,-25.091,0,0,1,51.907
> ui mousemode right select
> select clear
> select #1/A:263
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:264
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #1 models
> show #3 models
> show #4 models
> select #3:183-264 #4:183-264
1274 atoms, 1296 bonds, 164 residues, 2 models selected
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.89248,0.11128,0.43714,46.052,-0.28462,0.89075,0.35434,-110.49,-0.34995,-0.44066,0.82665,128.23,#4,1,0,0,57.747,0,1,0,-106.95,0,0,1,96.019
> view matrix models
> #3,0.89248,0.11128,0.43714,45.979,-0.28462,0.89075,0.35434,-109.48,-0.34995,-0.44066,0.82665,128.2,#4,1,0,0,57.674,0,1,0,-105.94,0,0,1,95.98
> ui mousemode right select
> select clear
> select #3:183-264 #4:183-264
1274 atoms, 1296 bonds, 164 residues, 2 models selected
> select #3:183-264 #4:183-264
1274 atoms, 1296 bonds, 164 residues, 2 models selected
> select #3:183-264 #4:183-264
1274 atoms, 1296 bonds, 164 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 415.8
RMSD between 69 pruned atom pairs is 0.391 angstroms; (across all 82 pairs:
2.880)
> select clear
[Repeated 1 time(s)]
> hide #3 models
> hide #4 models
> show #1 models
> show #2 models
> hide #1 models
> hide #2 models
> show #2 models
> select #2/A
4437 atoms, 4528 bonds, 577 residues, 1 model selected
> save STAU1_ARF1_NoARF1_1copy.pdb selectedOnly true
> hide #2 models
> open C:/Users/shumb/Desktop/STAU1_ARF1_NoARF1_1copy.pdb
Chain information for STAU1_ARF1_NoARF1_1copy.pdb #5
---
Chain | Description
A | No description available
> show #1 models
> hide #1 models
> show #1 models
> color #1 #5555ffff
> color #1 #5500ffff
> color #1 #aa55ffff
> color #1 #0055ffff
> color #1 #aaaaffff
> color #1 #aa00ffff
> color #1 #5555ffff
> color #1 #5500ffff
> color #1 #5555ffff
> color #1 #5500ffff
> color #3 #5500ffff
> color #2 #005500ff
> show #2 models
> hide #2 models
> undo
[Repeated 2 time(s)]
> color #5 #005500ff
> morph #4 #5
Computed 51 frame morph #6
> coordset #6 1,51
> hide #6 models
> morph #1 #5
Computed 51 frame morph #7
> coordset #7 1,51
> color #7 #005500ff
> windowsize 1920 1080
QWindowsWindow::setGeometry: Unable to set geometry 3126x1608+0+29 (frame:
3144x1655-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x991+0+29 (frame: 1938x1038-9-9) margins: 9, 38, 9, 9
minimum size: 425x370 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=549, y=510)))
> graphics rate 60
Expected true or false or a keyword
> reset
Unknown command: reset
> ui tool show "Model Panel"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected atoms"
> ui mousemode right windowing
[Repeated 1 time(s)]
> ui mousemode right select
> ui tool show "Selection Inspector"
> select clear
> save "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/ChimeraX/8 March 26 -/STAU1 and ARF1 1 copy Conformational Changes .cxs"
——— End of log from Sun Mar 8 17:58:01 2026 ———
> view name session-start
opened ChimeraX session
Drag select of 577 residues
> ui mousemode right select
Drag select of 334 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
Drag select of 557 residues
> select clear
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-88.199,0,1,0,4.8152,0,0,1,-82.464
> view matrix models #7,1,0,0,-89.988,0,1,0,2.9757,0,0,1,-83.926
> ui mousemode right select
> select clear
> view #6
No displayed objects specified.
> view #6
No displayed objects specified.
> movie record
> slow 360° rotation (y axis)
Unknown command: slow 360° rotation (y axis)
> slow 360° rotation, y axis
Unknown command: slow 360° rotation, y axis
> slow 360 rotation, y axis
Unknown command: slow 360 rotation, y axis
> slow 360 rotation, y axis
Unknown command: slow 360 rotation, y axis
> turn y 0.5 720
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-119.29,0,1,0,-23.761,0,0,1,-86.942
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.85771,-0.33334,-0.39143,-155.7,0.1491,0.88989,-0.43111,-99.424,0.49204,0.31141,0.81297,-169.47
> ui mousemode right select
> select clear
> wait 720
> view #1 zoom 1.5 frames 120
Expected an integer >= 1 or a keyword
> view #1 zoom 1.5 frames 120
Expected an integer >= 1 or a keyword
> view #7 zoom 1.5 frames 120
Expected an integer >= 1 or a keyword
> view #6 zoom 1.5 frames 120
Expected an integer >= 1 or a keyword
> view #6 zoom 1.5 frames120
Expected an integer >= 1 or a keyword
> view#6 zoom 1.5 frames 120
Unknown command: view#6 zoom 1.5 frames 120
> view #6 zoom 1.5 frames 120
Expected an integer >= 1 or a keyword
> stop movie record
Expected fewer arguments
> stop movie
Expected fewer arguments
> stop movie
Expected fewer arguments
> movie stop
> save movie
Cannot determine format for 'movie'
> hide #7 models
> show #5 models
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-143.45,0,1,0,48.671,0,0,1,17.69
> view matrix models #5,1,0,0,-142.88,0,1,0,48.621,0,0,1,17.45
> ui mousemode right select
> select clear
> show #7 models
> hide #7 models
> show #4 models
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,32.614,0,1,0,28.129,0,0,1,-25.511
> ui mousemode right select
Drag select of 23 residues
Drag select of 520 residues
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-208.74,0,1,0,58.574,0,0,1,48.205
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-34.464,0,1,0,33.955,0,0,1,10.22
> hide #4 models
> show #1 models
> hide #5 models
> hide #1 models
> show #2 models
> select #2/A
4437 atoms, 4528 bonds, 577 residues, 1 model selected
> save STAU1_ARF1_OnlySTAU1_1copy.pdb selectedOnly true
> open C:/Users/shumb/Desktop/STAU1_ARF1_OnlySTAU1_1copy.pdb
Chain information for STAU1_ARF1_OnlySTAU1_1copy.pdb #8
---
Chain | Description
A | No description available
Computing secondary structure
> hide #2 models
> color #8 #005500ff
> hide #8 models
> show #7 models
> close #7
> show #6 models
> hide #6 models
> morph #1 #8
Computed 51 frame morph #7
> coordset #7 1,51
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,76.758,0,1,0,-95.688,0,0,1,0.09887
> view matrix models #7,1,0,0,76.697,0,1,0,-95.445,0,0,1,-0.11185
> ui mousemode right select
> select clear
> hide #7 models
> show #8 models
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,138.47,0,1,0,-32.237,0,0,1,-5.1804
> view matrix models #8,1,0,0,125.88,0,1,0,-30.998,0,0,1,-1.9276
> ui mousemode right select
> show #1 models
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,234.23,0,1,0,-46.301,0,0,1,20.67
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,138.08,0,1,0,-68.839,0,0,1,56.39
> view matrix models #1,1,0,0,99.645,0,1,0,-59.434,0,0,1,53.502
> view matrix models #1,1,0,0,83.136,0,1,0,-54.831,0,0,1,52.99
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,156.91,0,1,0,-29.639,0,0,1,11.95
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.91294,-0.38019,-0.14832,158.05,0.39581,0.91342,0.094915,-49.946,0.099393,-0.14536,0.98437,5.8222
> ui mousemode right select
> select clear
> ui mousemode right select
> select clear
> view #1,8
> view #1,2
> center on both models
Unknown command: center on both models
> ui mousemode right select
Drag select of 1123 residues
Drag select of 1154 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-15.276,0,1,0,-36.081,0,0,1,53.299,#8,0.91294,-0.38019,-0.14832,59.641,0.39581,0.91342,0.094915,-31.196,0.099393,-0.14536,0.98437,6.1317
> view matrix models
> #1,1,0,0,-2.572,0,1,0,-44.237,0,0,1,53.508,#8,0.91294,-0.38019,-0.14832,72.345,0.39581,0.91342,0.094915,-39.352,0.099393,-0.14536,0.98437,6.3407
> view matrix models
> #1,1,0,0,-7.3473,0,1,0,-42.446,0,0,1,53.485,#8,0.91294,-0.38019,-0.14832,67.57,0.39581,0.91342,0.094915,-37.561,0.099393,-0.14536,0.98437,6.3175
> ui mousemode right select
> select clear
> movie record
> slow 360° spin of BOTH models together
Unknown command: slow 360° spin of BOTH models together
> 360° spin of BOTH models together
Unknown command: 360° spin of BOTH models together
> 360° spin model #1 #8
Unknown command: 360° spin model #1 #8
> select model #8 #1
Expected an objects specifier or a keyword
> select #8 #1 360 spin
Expected a keyword
> select #8 #1
8874 atoms, 9056 bonds, 1154 residues, 2 models selected
> spin 360
Unknown command: spin 360
> turn y 1 360
> select clear
> wait 360
[Repeated 1 time(s)]
> movie duplicate 60
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.85 size 40 \
Expected a keyword
> color white bgColor black opacity 0.6 anchor center
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.85 size 40
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.85 size 20
> undo
[Repeated 2 time(s)]
> remove 2d labels
Unknown command: remove 2d labels
> movie stop
> clear 2dlabels
Unknown command: clear 2dlabels
> 2dlabels text clear
> 2dlabels text "Structure comparison" clear
Expected a keyword
> 2dlabels text "Structure comparison" remove
Expected a keyword
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.85 size 20 clear
Expected a keyword
> select clear
[Repeated 1 time(s)]
> ~label #1,8-9 atoms
> ~label #1,8-9 residues
> 2dlabels delete
> save C:\Users\shumb/Desktop\image1.png supersample 3
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.85 size 20
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.9 size 20
> 2dlabels text "Structure comparison" xpos 0.5 ypos 1 size 20
[Repeated 1 time(s)]
> 2dlabels text "Structure comparison" xpos 1 ypos 1 size 20
[Repeated 1 time(s)]
> 2dlabels text "Structure comparison" xpos 1 ypos 1 size 25
> 2dlabels delete
> 2dlabels text "Structure comparison" xpos 1 ypos 1 size 25
> 2dlabels text "Structure comparison" xpos 0.5 ypos 1 size 20
> 2dlabels text "Structure comparison" xpos 1 ypos 1 size 25
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.9 size 20
> 2dlabels text "Model 1: Human Staufen 095793-1" xpos 0.5 ypos 0.75 size 20 \
Expected a keyword
> 2dlabels text "Model 1: Human Staufen 095793-1" xpos 0.5 ypos 0.75 size 20
> 2dlabels text "Model 1: Human Staufen 095793-1" xpos 0 ypos 0.75 size 20
> 2dlabels delete
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 0.75 size 20
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 0.5 size 20
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 1size 20
Invalid "ypos" argument: Expected a number
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 1 size 20
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 0.9 size 20
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 0.8 size 20
> 2dlabels all visibility true frames 60
> wait 60
[Repeated 1 time(s)]
> 2dlabels delete
> movie duplicate 120
> turn y 1 360 wait 360
Expected a keyword
> movie duplicate 60
> movie record
> turn y 1 360 wait 360
Expected a keyword
> turn y 1 360
> wait 360
> movie duplicate 60
> 2dlabels text "Structure comparison" xpos 0.5 ypos 0.9 size 20
> 2dlabels text "Model 1: Human Staufen 095793-1" xpos 0 ypos 0.8 size 20
> 2dlabels text "Model 1: STAU1 ARF1 Complex" xpos 0.5 ypos 0.8 size 20
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels true frames 60 wait 60
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels all true frames 60 wait 60
Expected a keyword
> 2dlabels all #8 #1 frames 60 wait 60
Expected a keyword
> 2dlabels frames 60 wait 60
Expected a keyword
> 2dlabels frames 60 wait 60
Expected a keyword
> movie duplicate 120
> morph #1 #8
Computed 51 frame morph #14
> coordset #14 1,51
> movie stop
> movie encode output two_structures.mp4 framerate 20 quality high
Movie saved to two_structures.mp4
> movie reset
No movie being recorded.
> 2dlabels delete
> hide #14 models
> show #14 models
> hide #14 models
> show #1 models
> hide #1 models
> show #8 models
> save "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/ChimeraX/8 March 26 -/STAU1 and ARF1 1 copy Conformational Changes .cxs"
> show #1 models
> select clear
[Repeated 1 time(s)]
> select #1/A:34
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
[Repeated 3 time(s)]
> select #1/A:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #8 models
> rainbow sel
Drag select of 457 residues
Drag select of 497 residues
> rainbow sel
> select clear
> select #1/A:167
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:184
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1:1-182
1390 atoms, 1419 bonds, 182 residues, 1 model selected
> select #1:1-182 #8:1-182
2780 atoms, 2838 bonds, 364 residues, 2 models selected
> show #8 models
> select #1:1-182
1390 atoms, 1419 bonds, 182 residues, 1 model selected
> save STAU1_RBD2_NoRNA_1copy.pdb selectedOnly true
> select #8:1-182
1390 atoms, 1419 bonds, 182 residues, 1 model selected
> save STAU1_RBD2_ARF1_1copy.pdb selectedOnly true
> hide #8 models
> ui mousemode right clip
> ui mousemode right select
> select clear
> select #1/A:420
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right pivot
[Repeated 2 time(s)]
> select #1:390-577
1427 atoms, 1457 bonds, 188 residues, 1 model selected
> save STAU1_RBD5_NoRNA_1copy.pdb selectedOnly true
> select #8:390-577
1427 atoms, 1457 bonds, 188 residues, 1 model selected
> save STAU1_RBD5_ARF1_1copy.pdb selectedOnly true
> show #8 models
> ui mousemode right select
Drag select of 1154 residues
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select clear
> save "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/ChimeraX/8 March 26 -/STAU1 and ARF1 1 copy Conformational Changes .cxs"
——— End of log from Sun Mar 8 22:02:21 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show "Model Panel"
> color #1 #5500ffff
> movie record
> 2dlabels text "Conformational Change Comparison" xpos 0.25 ypos 0.9 size 25
> 2dlabels text "Model 1: Human Staufen 095793-1" xpos 0.5 ypos 0.8 size 20
> 2dlabels text "Model 2: STAU1 ARF1 Complex" xpos 0.05 ypos 0.8 size 20
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels all visibility true frames 60
> turn y 1 360
> wait 60
> 2dlabels delete
> 2dlabels text "Model 1 morphed into Model 2" xpos 0.25 ypos 0.9 size 25
> morph #1 #8
Computed 51 frame morph #10
> coordset #10 1,51
> movie duplicate 120
> movie stop
> movie encode output two_structures.mp4 framerate 20 quality high
Movie saved to two_structures.mp4
> hide #!9 models
> hide #10 models
> show #3 models
> show #4 models
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76526,0.63191,0.12279,40.887,0.23816,-0.45514,0.85798,16.701,0.59805,-0.62733,-0.4988,72.08
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76526,0.63191,0.12279,18.675,0.23816,-0.45514,0.85798,29.427,0.59805,-0.62733,-0.4988,56.675,#4,1,0,0,-56.677,0,1,0,46.681,0,0,1,-5.1847
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-49.417,0,1,0,38.637,0,0,1,14.598
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.25 ypos 0.9
> size 25
> show #!9 models
> view matrix models #4,1,0,0,-53.31,0,1,0,37.925,0,0,1,23.631
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.76526,0.63191,0.12279,1.9875,0.23816,-0.45514,0.85798,35.476,0.59805,-0.62733,-0.4988,46.027,#4,1,0,0,-69.997,0,1,0,43.973,0,0,1,12.983
> view matrix models
> #3,0.76526,0.63191,0.12279,7.9838,0.23816,-0.45514,0.85798,33.104,0.59805,-0.62733,-0.4988,50.5,#4,1,0,0,-64,0,1,0,41.601,0,0,1,17.457
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.78734,0.58668,0.18947,9.0454,0.12194,-0.44944,0.88495,32.706,0.60434,-0.67365,-0.4254,51.522,#4,0.99651,0.083052,0.0083219,-62.257,-0.082025,0.99287,-0.086535,49.907,-0.015449,0.085551,0.99621,20.442
> view matrix models
> #3,0.78571,0.61237,-0.087519,10.406,0.36823,-0.34933,0.86161,37.813,0.49705,-0.70921,-0.49997,50.315,#4,0.97749,-0.16667,0.12939,-65.65,0.16684,0.98594,0.009599,33.863,-0.12917,0.012206,0.99155,26.953
> hide #9.1 models
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.2 ypos 0.9
> size 25
> 2dlabels delete
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.2 ypos 0.9
> size 25
> ui mousemode right select
> select clear
> 2dlabels text "Model 1: Tandem RBD3+4 no RNA" xpos 0.5 ypos 0.8 size 20
> 2dlabels text "Model 2: Tandem RBD3+4 no RNA" xpos 0.05 ypos 0.8 size 20
> 2dlabels delete
> mmaker #3 #4
> matchmaker #3 #4
Missing required "to" argument
> mmaker #3 #4
> matchmaker #3 #4
Missing required "to" argument
> mmaker #3 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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 1038
RMSD between 74 pruned atom pairs is 0.465 angstroms; (across all 208 pairs:
28.917)
> undo
[Repeated 1 time(s)]Drag select of 31 residues
> select clear
> hide #4 models
Drag select of 57 residues
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.87454,-0.096709,0.4752,-68.585,-0.13507,0.89256,0.43023,76.477,-0.46575,-0.44044,0.76752,64.671
> show #4 models
> hide #3 models
> view matrix models
> #3,0.87454,-0.096709,0.4752,9.7662,-0.13507,0.89256,0.43023,-3.7744,-0.46575,-0.44044,0.76752,23.494
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97749,-0.16667,0.12939,-54.543,0.16684,0.98594,0.009599,-33.071,-0.12917,0.012206,0.99155,21.986
> show #3 models
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97749,-0.16667,0.12939,-81.01,0.16684,0.98594,0.009599,-38.129,-0.12917,0.012206,0.99155,36.114
> view matrix models
> #4,0.97749,-0.16667,0.12939,-80.376,0.16684,0.98594,0.009599,-41.71,-0.12917,0.012206,0.99155,37.361
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99863,-0.026955,0.044836,-80.029,0.035848,0.97678,-0.21121,-37.893,-0.038102,0.21253,0.97641,36.058
> view matrix models
> #4,0.98188,-0.095205,0.16385,-81.116,0.15996,0.88,-0.44723,-35.555,-0.10161,0.46533,0.87928,36.79
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.87454,-0.096709,0.4752,36.125,-0.13507,0.89256,0.43023,13.838,-0.46575,-0.44044,0.76752,17.399
> view matrix models
> #3,0.87454,-0.096709,0.4752,29.77,-0.13507,0.89256,0.43023,9.7387,-0.46575,-0.44044,0.76752,18.817
> view matrix models
> #3,0.87454,-0.096709,0.4752,43.517,-0.13507,0.89256,0.43023,16.903,-0.46575,-0.44044,0.76752,16.342
> view matrix models
> #3,0.87454,-0.096709,0.4752,12.174,-0.13507,0.89256,0.43023,1.5695,-0.46575,-0.44044,0.76752,32.612
> turn x 360
[Repeated 1 time(s)]
> turn y 360
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> turn y 360
[Repeated 1 time(s)]
> 2dlabels text "Model 2: Tandem RBD3+4 no RNA" xpos 0.05 ypos 0.8 size 20
> 2dlabels text "Model 1: Tandem RBD3+4 no RNA" xpos 0.5 ypos 0.8 size 20
> ui mousemode right select
Drag select of 205 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98188,-0.095205,0.16385,88.039,0.15996,0.88,-0.44723,39.313,-0.10161,0.46533,0.87928,-16.795
> ui mousemode right select
Drag select of 197 residues
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.87454,-0.096709,0.4752,-78.228,-0.13507,0.89256,0.43023,-54.983,-0.46575,-0.44044,0.76752,73.033
> view matrix models
> #3,0.87454,-0.096709,0.4752,-66.451,-0.13507,0.89256,0.43023,-47.873,-0.46575,-0.44044,0.76752,67.951
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98188,-0.095205,0.16385,45.346,0.15996,0.88,-0.44723,15.346,-0.10161,0.46533,0.87928,0.34187
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.2 ypos 0.9
> size 25
> 2dlabels delete
> movie record
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.25 ypos 0.9
> size 25
> 2dlabels text "Model 1: Tandem RBD3+4 no RNA" xpos 0.05 ypos 0.8 size 20
> movie stop
> show #1 models
> hide #1 models
> 2dlabels delete
> ui mousemode right select
> select clear
> movie record
[Repeated 1 time(s)]Already recording a movie
> record2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.25 ypos
> 0.9 size 25
Unknown command: movie record2dlabels text "Conformational Change RBD3+4
Comparison" xpos 0.25 ypos 0.9 size 25
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.25 ypos 0.9
> size 25
> 2dlabels text "Model 1: Tandem RBD3+4 ARF1" xpos 0.05 ypos 0.8 size 20
> 2dlabels text "Model 2: Tandem RBD3+4 no RNA" xpos 0.5 ypos 0.8 size 20
> turn y 1 360
> turn x 1 360
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels all visibility true frames 60
> 2dlabels delete
> 2dlabels text "Model 1 morphed into Model 2" xpos 0.25 ypos 0.9 size 25
> morph #3 #4
Computed 51 frame morph #11
> coordset #11 1,51
> mmaker #3 #4
> matchmaker #3 #4
Missing required "to" argument
> mmaker #3 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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 1038
RMSD between 74 pruned atom pairs is 0.465 angstroms; (across all 208 pairs:
28.917)
> show #4 models
> show #3 models
> hide #11 models
> turn x 1 360
> turn y 360
> turn y 360
[Repeated 2 time(s)]
> movie duplicate 120
> movie stop
> movie encode output Tandem RBD3+4_1.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output Tandem RBD3+4.11.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output Tandem RBD3+4.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output Tandem RBD3+4.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output Tandem RBD3_4.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem RBD3_4.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem_RBD3_4.mp4 framerate 20 quality high
Movie saved to tandem_RBD3_4.mp4
> 2dlabels delete
Drag select of 1 residues
> hide #3 models
> ui mousemode right select
Drag select of 208 residues
> select clear
> hide #4 models
> show #3 models
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84607,-0.047742,0.53093,0.64547,0.048799,0.99874,0.012044,-39.599,-0.53084,0.015718,0.84733,120.41
> view matrix models
> #3,0.84607,-0.047742,0.53093,-2.9745,0.048799,0.99874,0.012044,-23.748,-0.53084,0.015718,0.84733,115.41
> show #4 models
> ui mousemode right select
> select clear
Drag select of 208 residues
> hide #3 models
> hide #4 models
> show #1 models
Drag select of 577 residues
> rainbow sel
> select clear
> select #1/A:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> set bgColor black
> color #1 #5500ffff
> hide #1 models
> show #3 models
> show #4 models
> set bgColor white
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.25 ypos 0.9
> size 25
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.2 ypos 0.9
> size 25
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.1ypos 0.9
> size 25
Invalid "xpos" argument: Expected a number
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.1 ypos 0.9
> size 25
> 2dlabels delete
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.1 ypos 0.9 size 25
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.1 ypos 0.8 size 25
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.1 ypos 0.75 size 25
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.2] ypos 0.75 size 25
Invalid "xpos" argument: Expected a number
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.2 ypos 0.75 size 25
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.2 ypos 0.8 size 25
> 2dlabels delete
> movie record
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.1 ypos 0.9
> size 25
> 2dlabels delete
> 2dlabels text "Tandem RBD3+4, RBD3 Matched" xpos 0.2 ypos 0.8 size 25
> select #3:182-266 #4:182-266
1308 atoms, 1330 bonds, 168 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 424.5
RMSD between 70 pruned atom pairs is 0.390 angstroms; (across all 84 pairs:
4.124)
> turn y 1 360
> select clear
> turn y 1 360
> 2dlabels delete
> 2dlabels text "Tandem RBD3+4, RBD4 Matched" xpos 0.2 ypos 0.8 size 25
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
No 'to' model specified
> matchmaker #3 & sel to #4 & sel
No 'to' model specified
> matchmaker #3 & sel to #4 & sel
No 'to' model specified
> select #3:266-390 #4:1266-390
981 atoms, 999 bonds, 125 residues, 1 model selected
> select #3:266-390 #4:266-390
1962 atoms, 1998 bonds, 250 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 618.2
RMSD between 72 pruned atom pairs is 0.390 angstroms; (across all 125 pairs:
23.916)
> select clear
> turn y 1 360
> movie duplicate 120
> movie stop
> movie encode output Tandem RBD3+4_NottheBest.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem RBD3+4_NottheBest.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem RBD3and4_NottheBest.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem RBD3and4_NottheBest.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output tandem RBD3_4_NottheBest.mp4 framerate 20 quality high
Expected ',' or a keyword
> movie encode output TandemRBD3_4_NottheBest.mp4 framerate 20 quality high
Movie saved to TandemRBD3_4_NottheBest.mp4
> 2dlabels delete
> ui mousemode right "rotate selected models"
> ui mousemode right pivot
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84437,-0.04886,0.53353,46.188,0.048901,0.9987,0.014069,16.689,-0.53353,0.014211,0.84566,28.137,#4,0.98188,-0.095205,0.16385,51.9,0.15996,0.88,-0.44723,36.046,-0.10161,0.46533,0.87928,0.18076
> ui mousemode right select
> select clear
> save C:\Users\shumb/Desktop\image1.png supersample 3
> save C:\Users\shumb/Desktop\image2.png supersample 3
> 2dlabels delete
> save C:\Users\shumb/Desktop\image3.png supersample 3
> select #3:182-266 #4:182-266
1308 atoms, 1330 bonds, 168 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 424.5
RMSD between 70 pruned atom pairs is 0.390 angstroms; (across all 84 pairs:
4.124)
> matchmaker #3 & sel to #4 & sel
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 tandemRBD3+4_ARF1_1copy.pdb, chain A (#4) with
TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3), sequence alignment score = 424.5
RMSD between 70 pruned atom pairs is 0.390 angstroms; (across all 84 pairs:
4.124)
> save C:\Users\shumb/Desktop\image4.png supersample 3
Drag select of 7 residues
> select clear
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82609,0.56196,-0.042266,35.859,0.065393,-0.021094,0.99764,21.978,0.55974,-0.8269,-0.054173,40.869,#4,0.98188,-0.095205,0.16385,49.841,0.15996,0.88,-0.44723,6.8657,-0.10161,0.46533,0.87928,12.059
> view matrix models
> #3,0.82609,0.56196,-0.042266,27.548,0.065393,-0.021094,0.99764,23.755,0.55974,-0.8269,-0.054173,40.366,#4,0.98188,-0.095205,0.16385,41.531,0.15996,0.88,-0.44723,8.6421,-0.10161,0.46533,0.87928,11.557
> ui mousemode right select
> select clear
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82609,0.56196,-0.042266,25.106,0.065393,-0.021094,0.99764,-5.4491,0.55974,-0.8269,-0.054173,37.299,#4,0.98188,-0.095205,0.16385,39.088,0.15996,0.88,-0.44723,-20.562,-0.10161,0.46533,0.87928,8.4891
> view matrix models
> #3,0.82609,0.56196,-0.042266,25.118,0.065393,-0.021094,0.99764,-5.3487,0.55974,-0.8269,-0.054173,37.281,#4,0.98188,-0.095205,0.16385,39.101,0.15996,0.88,-0.44723,-20.461,-0.10161,0.46533,0.87928,8.4708
> ui mousemode right select
> select clear
> ui tool show Distances
> select #3/A:339
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:297
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Distances
> distance style color red
[Repeated 2 time(s)]
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style radius 0.21
[Repeated 2 time(s)]
> distance style radius 0.22
[Repeated 2 time(s)]
> distance style radius 0.23
[Repeated 2 time(s)]
> distance style radius 0.24
[Repeated 2 time(s)]
> distance style radius 0.25
[Repeated 2 time(s)]Exactly two atoms must be selected!
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #6/A
Alignment identifier is 1
> select clear
[Repeated 2 time(s)]
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:337
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:185-195,234-251,287-297,337-351
> #6/A:185-195,234-251,287-297,337-351
864 atoms, 860 bonds, 110 residues, 2 models selected
> select #4/A:287 #6/A:287
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #4/A:287 #6/A:287
14 atoms, 14 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [105] RMSD: 43.889
> select #4/A
1626 atoms, 1656 bonds, 208 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4/A:185
9 atoms, 8 bonds, 1 residue, 1 model selected
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right select
> select clear
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right select
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
[Repeated 2 time(s)]
> ui mousemode right select
> select #3/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> ui mousemode right distance
> ui mousemode right select
> select clear
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:287
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right select
> select #4/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> show #11 models
> hide #9 models
> hide #3 models
> hide #4 models
> show #9 models
> show #3 models
> show #4 models
> hide #11 models
> ui mousemode right select
> select clear
> close #9
> open C:/Users/shumb/Desktop/STAU1_RBD2_ARF1_1copy.pdb
> C:/Users/shumb/Desktop/STAU1_RBD2_NoRNA_1copy.pdb
Summary of feedback from opening
C:/Users/shumb/Desktop/STAU1_RBD2_ARF1_1copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 5 5 GLU A 185 LYS A 195 1 11
Start residue of secondary structure not found: HELIX 6 6 LYS A 234 GLU A 248
1 15
Start residue of secondary structure not found: HELIX 7 7 LEU A 249 LYS A 251
1 3
Start residue of secondary structure not found: HELIX 8 8 PRO A 287 ALA A 297
1 11
Start residue of secondary structure not found: HELIX 9 9 LYS A 337 ILE A 351
1 15
17 messages similar to the above omitted
Summary of feedback from opening
C:/Users/shumb/Desktop/STAU1_RBD2_NoRNA_1copy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 5 5 GLU A 185 LYS A 195 1 11
Start residue of secondary structure not found: HELIX 6 6 LYS A 234 GLU A 248
1 15
Start residue of secondary structure not found: HELIX 7 7 LEU A 249 LYS A 251
1 3
Start residue of secondary structure not found: HELIX 8 8 PRO A 287 ALA A 297
1 11
Start residue of secondary structure not found: HELIX 9 9 LYS A 337 ILE A 351
1 15
17 messages similar to the above omitted
Chain information for STAU1_RBD2_ARF1_1copy.pdb #9
---
Chain | Description
A | No description available
Chain information for STAU1_RBD2_NoRNA_1copy.pdb #12
---
Chain | Description
A | No description available
> save "C:/Users/shumb/Documents/Glasgow University (MReS)/Structure Programs
> -/ChimeraX/8 March 26 -/STAU1 and ARF1 1 copy Conformational Changes_1.cxs"
——— End of log from Mon Mar 9 22:15:53 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show "Model Panel"
> select #5/A
4437 atoms, 4528 bonds, 577 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #1/A #2/A #3/A #5/A #8/A #7/A #14/A #10/A #11/A #12/A
Alignment identifier is 1
> select #1/A:577 #2/A:577 #5/A:577 #8/A:577 #7/A:577 #14/A:577 #10/A:577
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #1/A #2/A #3/A #5/A #8/A #7/A #14/A #10/A #11/A #12/A
35701 atoms, 36427 bonds, 4637 residues, 10 models selected
. [ID: 1] region 10 chains [1-577] RMSD: 147.914
> select #1/A:577 #2/A:577 #5/A:577 #8/A:577 #7/A:577 #14/A:577 #10/A:577
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #1/A:575-577 #2/A:575-577 #5/A:575-577 #8/A:575-577 #7/A:575-577
> #14/A:575-577 #10/A:575-577
154 atoms, 147 bonds, 21 residues, 7 models selected
. [ID: 1] region 10 chains [575-577] RMSD: 164.846
> select #1/A:577 #2/A:577 #5/A:577 #8/A:577 #7/A:577 #14/A:577 #10/A:577
49 atoms, 42 bonds, 7 residues, 7 models selected
> select #1/A:577 #2/A:577 #5/A:577 #8/A:577 #7/A:577 #14/A:577 #10/A:577
49 atoms, 42 bonds, 7 residues, 7 models selected
. [ID: 1] region 10 chains [577] RMSD: 164.996
> hide #3 models
> hide #4 models
> hide #9 models
> hide #12 models
> show #1 models
> rainbow sel & #1
> ui mousemode right select
Drag select of 577 residues
> rainbow sel
Drag select of 43 residues
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,9.5635,0,1,0,-133.8,0,0,1,94.123
> view matrix models #1,1,0,0,9.3349,0,1,0,-133.35,0,0,1,93.97
> ui mousemode right select
> select clear
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,47.102,0,1,0,-110.89,0,0,1,129.59
> view matrix models #1,1,0,0,39.147,0,1,0,-125.16,0,0,1,121.07
> view matrix models #1,1,0,0,33.518,0,1,0,-125.77,0,0,1,116.05
> ui mousemode right select
> select clear
> save C:\Users\shumb/Desktop\image8.png supersample 3
> save C:\Users\shumb/Desktop\image9.png supersample 3
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,28.458,0,1,0,-91.576,0,0,1,95.176
> view matrix models #1,1,0,0,28.454,0,1,0,-91.462,0,0,1,95.112
> ui mousemode right select
> select clear
> save C:\Users\shumb/Desktop\image10.png supersample 3
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.55434,0.28393,0.78236,-88.124,0.77213,0.52634,0.35607,-11.464,-0.31068,0.80147,-0.511,22.358
> view matrix models
> #1,0.9035,-0.24742,0.34995,33.325,0.18798,-0.50503,-0.84238,-55.676,0.38516,0.82688,-0.40979,79.329
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9035,-0.24742,0.34995,29.053,0.18798,-0.50503,-0.84238,-24.621,0.38516,0.82688,-0.40979,67.034
> view matrix models
> #1,0.9035,-0.24742,0.34995,29.629,0.18798,-0.50503,-0.84238,-21.617,0.38516,0.82688,-0.40979,63.787
> ui mousemode right select
> select clear
> save C:\Users\shumb/Desktop\image11.png supersample 3
> color #1 #55aaffff
> color #1 #5500ffff
> show #4 models
> hide #1 models
> hide #4 models
> show #9 models
> color #5 #5500ffff
> color #9 #005500ff
> color #12 #5500ffff
> show #12 models
> ui mousemode right select
Drag select of 364 residues
> ui mousemode right "translate selected models"
> view matrix models
> #9,1,0,0,96.158,0,1,0,-11.818,0,0,1,-18.857,#12,1,0,0,96.158,0,1,0,-11.818,0,0,1,-18.857
> view matrix models
> #9,1,0,0,95.707,0,1,0,-11.746,0,0,1,-18.799,#12,1,0,0,95.707,0,1,0,-11.746,0,0,1,-18.799
> ui mousemode right select
> select clear
> ui mousemode right select
Drag select of 182 residues
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,147.3,0,1,0,-27.512,0,0,1,-29.732
> ui mousemode right select
> select clear
> ui mousemode right select
Drag select of 155 residues
Drag select of 183 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.97684,-0.20088,-0.073694,100.77,0.20158,0.97947,0.0020147,-27.813,0.071776,-0.016823,0.99728,-22.238,#12,0.97684,-0.20088,-0.073694,155.14,0.20158,0.97947,0.0020147,-32.878,0.071776,-0.016823,0.99728,-29.173
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.9937,-0.093097,0.062369,95.807,0.10619,0.9601,-0.25872,-9.7795,-0.035793,0.26372,0.96394,-13.298,#12,0.9937,-0.093097,0.062369,147.86,0.10619,0.9601,-0.25872,-16.61,-0.035793,0.26372,0.96394,-29.841
> view matrix models
> #9,0.9937,-0.093952,0.061063,95.853,0.10643,0.96182,-0.25213,-10.01,-0.035044,0.25704,0.96577,-13.37,#12,0.9937,-0.093952,0.061063,147.93,0.10643,0.96182,-0.25213,-16.927,-0.035044,0.25704,0.96577,-29.789
> mmaker #12 #9
> matchmaker #12 #9
Missing required "to" argument
> mmaker #12 to #9
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 STAU1_RBD2_ARF1_1copy.pdb, chain A (#9) with
STAU1_RBD2_NoRNA_1copy.pdb, chain A (#12), sequence alignment score = 833.1
RMSD between 7 pruned atom pairs is 1.091 angstroms; (across all 182 pairs:
36.465)
> ui mousemode right select
> select clear
> select #12:1-182 #9:1-182
2780 atoms, 2838 bonds, 364 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #5 to #9
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 STAU1_RBD2_ARF1_1copy.pdb, chain A (#9) with
STAU1_ARF1_NoARF1_1copy.pdb, chain A (#5), sequence alignment score = 912.3
RMSD between 182 pruned atom pairs is 0.001 angstroms; (across all 182 pairs:
0.001)
> ui tool show Matchmaker
> matchmaker #12 & sel to #9 & sel
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 STAU1_RBD2_ARF1_1copy.pdb, chain A (#9) with
STAU1_RBD2_NoRNA_1copy.pdb, chain A (#12), sequence alignment score = 833.1
RMSD between 7 pruned atom pairs is 1.091 angstroms; (across all 182 pairs:
36.465)
> matchmaker #12 & sel to #9 & sel
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 STAU1_RBD2_ARF1_1copy.pdb, chain A (#9) with
STAU1_RBD2_NoRNA_1copy.pdb, chain A (#12), sequence alignment score = 833.1
RMSD between 7 pruned atom pairs is 1.091 angstroms; (across all 182 pairs:
36.465)
> select clear
> ui mousemode right select
> ui mousemode right pivot
> hide #12 models
> ui mousemode right select
Drag select of 182 residues
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.9937,-0.093952,0.061063,142.32,0.10643,0.96182,-0.25213,8.1256,-0.035044,0.25704,0.96577,-27.225
> view matrix models
> #9,0.9937,-0.093952,0.061063,148.7,0.10643,0.96182,-0.25213,10.421,-0.035044,0.25704,0.96577,-28.193
> ui mousemode right select
> select clear
> show #12 models
> hide #9 models
> ui mousemode right select
Drag select of 182 residues
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.74358,0.63335,-0.21439,151.63,-0.62144,0.53627,-0.57116,-20.558,-0.24677,0.55793,0.79235,-46.256
> view matrix models
> #12,0.74358,0.63335,-0.21439,160.95,-0.62144,0.53627,-0.57116,-24.465,-0.24677,0.55793,0.79235,-37.359
> view matrix models
> #12,0.74358,0.63335,-0.21439,158.35,-0.62144,0.53627,-0.57116,-21.104,-0.24677,0.55793,0.79235,-43.067
> view matrix models
> #12,0.74358,0.63335,-0.21439,148.91,-0.62144,0.53627,-0.57116,-2.895,-0.24677,0.55793,0.79235,10.965
> view matrix models
> #12,0.74358,0.63335,-0.21439,137.44,-0.62144,0.53627,-0.57116,-1.5838,-0.24677,0.55793,0.79235,16.896
> show #9 models
> view matrix models
> #12,0.74358,0.63335,-0.21439,151.67,-0.62144,0.53627,-0.57116,7.2069,-0.24677,0.55793,0.79235,23.192
> view matrix models
> #12,0.74358,0.63335,-0.21439,149.29,-0.62144,0.53627,-0.57116,5.5914,-0.24677,0.55793,0.79235,21.693
> view matrix models
> #12,0.74358,0.63335,-0.21439,148.32,-0.62144,0.53627,-0.57116,5.3204,-0.24677,0.55793,0.79235,22.29
> view matrix models
> #12,0.74358,0.63335,-0.21439,152.76,-0.62144,0.53627,-0.57116,8.8318,-0.24677,0.55793,0.79235,26.646
> ui mousemode right select
Drag select of 179 residues
Drag select of 181 residues
Drag select of 182 residues
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.9937,-0.093952,0.061063,140.94,0.10643,0.96182,-0.25213,4.919,-0.035044,0.25704,0.96577,-33.838
> ui mousemode right select
> select clear
> hide #12 models
> hide #9 models
> show #3 models
> show #4 models
> ui mousemode right select
Drag select of 416 residues
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right pivot
> ui mousemode right select
Drag select of 4 residues
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> ui mousemode right select
> RBD3+RBD4 - select #3:286-390 #4:286-390
Unknown command: RBD3+RBD4 - select #3:286-390 #4:286-390
> select #3:286-390 #4:286-390
1650 atoms, 1678 bonds, 210 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #4 & sel to #3 & sel
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 TandemRBD3+4_NoRNA_1copy.pdb, chain A (#3) with
tandemRBD3+4_ARF1_1copy.pdb, chain A (#4), sequence alignment score = 532
RMSD between 67 pruned atom pairs is 0.372 angstroms; (across all 105 pairs:
25.162)
> select clear
> ui mousemode right distance
[Repeated 5 time(s)]
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> hide #4 models
> hide #3 models
> show #2 models
> ui mousemode right select
Drag select of 877 residues, 600 shapes
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,68.067,0,1,0,9.2739,0,0,1,-18.389
> view matrix models #2,1,0,0,99.879,0,1,0,12.855,0,0,1,-5.8993
> view matrix models #2,1,0,0,95.828,0,1,0,13.531,0,0,1,-4.9828
> ui mousemode right select
> select clear
> ui mousemode right select
Drag select of 877 residues, 600 shapes
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,121.75,0,1,0,40.639,0,0,1,45.732
> view matrix models #2,1,0,0,141.02,0,1,0,44.513,0,0,1,56.044
> ui mousemode right select
> select clear
Drag select of 795 residues, 433 shapes
> save STAU_ARF1_Bound
Cannot determine format for 'STAU_ARF1_Bound'
> save STAU_ARF1_Bound_Full.pdb selectedOnly true
> open C:/Users/shumb/Desktop/STAU_ARF1_Bound_Full.pdb
Chain information for STAU_ARF1_Bound_Full.pdb #13
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #2 models
> color #13 cyan
> undo
> ui mousemode right select
Drag select of 795 residues, 436 shapes
> ui mousemode right "translate selected models"
> view matrix models #13,1,0,0,40.147,0,1,0,-28.193,0,0,1,85.008
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.339,-0.089119,0.93656,94.556,-0.46985,0.84642,0.25061,37.851,-0.81506,-0.525,0.24506,278.01
> view matrix models
> #13,0.4192,-0.58277,0.69617,113.24,-0.50655,0.48622,0.71204,29.647,-0.75344,-0.65113,-0.091378,292.21
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.4192,-0.58277,0.69617,115.25,-0.50655,0.48622,0.71204,28.278,-0.75344,-0.65113,-0.091378,327.8
> view matrix models
> #13,0.4192,-0.58277,0.69617,152.25,-0.50655,0.48622,0.71204,2.2486,-0.75344,-0.65113,-0.091378,371.56
> ui mousemode right select
> select clear
Drag select of 795 residues, 436 shapes
> select clear
> select #13/B
4615 atoms, 5151 bonds, 218 residues, 1 model selected
> select clear
> rotate #13 360
Unknown command: rotate #13 360
> turn #13 360
Expected an axis vector or a keyword
> turn x#13 360
Expected an axis vector or a keyword
> turn x #13 360
Expected a number or a keyword
> turn x #13 360
Expected a number or a keyword
> turn x #13
Expected a number or a keyword
> turn x 360 #13
Expected 'forever' or an integer >= 1 or a keyword
> select #13/B
4615 atoms, 5151 bonds, 218 residues, 1 model selected
> color sel cyan
> select clear
> show #1 models
> ui mousemode right select
Drag select of 795 residues, 436 shapes
> select clear
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9035,-0.24742,0.34995,-128.94,0.18798,-0.50503,-0.84238,-114.02,0.38516,0.82688,-0.40979,-50.913
> view matrix models
> #1,0.9035,-0.24742,0.34995,-138.95,0.18798,-0.50503,-0.84238,-100.93,0.38516,0.82688,-0.40979,-33.492
> show #4 models
> ui mousemode right select
Drag select of 208 residues
Drag select of 5 residues
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77995,0.24705,-0.57502,6.8953,0.49454,0.31979,0.80819,-23.216,0.38355,-0.91471,0.12724,30.252
> ui mousemode right select
Drag select of 577 residues
Drag select of 178 residues
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9035,-0.24742,0.34995,-83.734,0.18798,-0.50503,-0.84238,-106.45,0.38516,0.82688,-0.40979,-33.382
> ui mousemode right select
Drag select of 795 residues, 436 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.4192,-0.58277,0.69617,117.42,-0.50655,0.48622,0.71204,-1.6098,-0.75344,-0.65113,-0.091378,361.87
> ui mousemode right select
Drag select of 208 residues
Drag select of 24 residues
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77995,0.24705,-0.57502,32.604,0.49454,0.31979,0.80819,-15.454,0.38355,-0.91471,0.12724,43.854
> hide #4 models
> show #2 models
> hide #2 models
> show #8 models
> view matrix models
> #4,0.77995,0.24705,-0.57502,-215.75,0.49454,0.31979,0.80819,13.08,0.38355,-0.91471,0.12724,23.39
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.91294,-0.38019,-0.14832,53.545,0.39581,0.91342,0.094915,-19.029,0.099393,-0.14536,0.98437,31.337
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.94989,0.28567,0.12691,40.724,-0.22448,0.34088,0.91291,-34.99,0.21753,-0.89565,0.38793,53.11
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9035,-0.24742,0.34995,-106.53,0.18798,-0.50503,-0.84238,-110.72,0.38516,0.82688,-0.40979,-45.922
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.23278,0.39369,0.88928,-165.65,0.96991,-0.16104,-0.1826,-44.103,0.071321,0.90503,-0.41933,-73.116
> view matrix models
> #1,-0.88002,0.20348,0.42914,-258.73,0.3437,0.89644,0.27977,-111.23,-0.32777,0.3937,-0.85882,-100.89
> view matrix models
> #1,-0.082129,0.094451,-0.99214,-218.95,-0.91832,0.37963,0.11216,-202.81,0.38723,0.92031,0.055557,-39.277
> view matrix models
> #1,0.52048,0.52392,-0.67425,-175.19,0.10831,-0.82377,-0.55649,-103.97,-0.84698,0.21662,-0.4855,-131.11
> view matrix models
> #1,0.81207,0.47647,-0.33693,-144.36,0.55881,-0.80129,0.21369,-53.988,-0.16816,-0.36182,-0.91696,-70.845
> view matrix models
> #1,0.88574,0.45243,-0.1038,-133.5,0.30634,-0.40175,0.86299,-71.695,0.34874,-0.79618,-0.49444,-10.978
> ui mousemode right select
Drag select of 795 residues, 436 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.4192,-0.58277,0.69617,141.41,-0.50655,0.48622,0.71204,2.1241,-0.75344,-0.65113,-0.091378,373.88
> view matrix models
> #13,0.4192,-0.58277,0.69617,134.73,-0.50655,0.48622,0.71204,12.668,-0.75344,-0.65113,-0.091378,388.46
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.94989,0.28567,0.12691,20.313,-0.22448,0.34088,0.91291,-15.873,0.21753,-0.89565,0.38793,77.372
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.88574,0.45243,-0.1038,-156.77,0.30634,-0.40175,0.86299,-60.032,0.34874,-0.79618,-0.49444,1.0114
> view matrix models
> #1,0.88574,0.45243,-0.1038,-154.4,0.30634,-0.40175,0.86299,-61.109,0.34874,-0.79618,-0.49444,-0.03936
> 2dlabels text "Conformational Change RBD3+4 Comparison" xpos 0.1 ypos 0.9
> size 25
> 2dlabels delete
> 2dlabels text "Conformational Change Comparison" xpos 0.1 ypos 0.9 size 25
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels delete
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0.2 ypos 0.8 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0.1 ypos 0.8 size 16
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.8 size 16
> 2dlabels delete
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.8 size 16
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 16
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.2 ypos 0.7 size 16
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3ypos 0.7 size 16
Invalid "xpos" argument: Expected a number
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 16
> 2dlabels delete
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 16
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.25 ypos 0.7 size 16
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels delete
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.4 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.6vypos 0.7 size 14
Invalid "xpos" argument: Expected a number
> 2dlabels text "Model 3: Staufen not bound" xpos 0.6 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.75 ypos 0.7 size 14
> 2dlabels delete
> view matrix models
> #1,0.88574,0.45243,-0.1038,-153.74,0.30634,-0.40175,0.86299,-61.758,0.34874,-0.79618,-0.49444,-0.88794
> view matrix models
> #1,0.88574,0.45243,-0.1038,-154.39,0.30634,-0.40175,0.86299,-54.746,0.34874,-0.79618,-0.49444,9.937
> ui mousemode right select
> select clear
> turn #13 y 1 360
Expected an axis vector or a keyword
> turn y 90 models #1
> undo
> ui mousemode right select
> turn y 90 models #1
> undo
> turn y 90 models #8
> undo
> turn y 1 180 models #1
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-54.131,-0.37877,-0.61554,-0.69112,212.61,-0.4435,-0.53472,0.7193,-115.82
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-141.55,-0.37877,-0.61554,-0.69112,247.62,-0.4435,-0.53472,0.7193,-170.08
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-161.09,-0.37877,-0.61554,-0.69112,254.33,-0.4435,-0.53472,0.7193,-146.09
> ui mousemode right rotate
> ui mousemode right select
Drag select of 1949 residues, 436 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-174.89,-0.37877,-0.61554,-0.69112,258.81,-0.4435,-0.53472,0.7193,-114.14,#8,0.94989,0.28567,0.12691,6.5084,-0.22448,0.34088,0.91291,-11.393,0.21753,-0.89565,0.38793,109.32,#13,0.4192,-0.58277,0.69617,120.92,-0.50655,0.48622,0.71204,17.148,-0.75344,-0.65113,-0.091378,420.4
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-159.99,-0.37877,-0.61554,-0.69112,253.34,-0.4435,-0.53472,0.7193,-112.23,#8,0.94989,0.28567,0.12691,21.411,-0.22448,0.34088,0.91291,-16.86,0.21753,-0.89565,0.38793,111.23,#13,0.4192,-0.58277,0.69617,135.83,-0.50655,0.48622,0.71204,11.681,-0.75344,-0.65113,-0.091378,422.31
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-166.94,-0.37877,-0.61554,-0.69112,256.01,-0.4435,-0.53472,0.7193,-119.85,#8,0.94989,0.28567,0.12691,14.462,-0.22448,0.34088,0.91291,-14.194,0.21753,-0.89565,0.38793,103.61,#13,0.4192,-0.58277,0.69617,128.88,-0.50655,0.48622,0.71204,14.347,-0.75344,-0.65113,-0.091378,414.69
> turn y 1 180 models #1
> undo
> turn y 1 360 models #1 center #1
> turn y 1 360 models #8 center #8
> ui mousemode right select
> select clear
> 2dlabels text "Model 3: Staufen not bound" xpos 0.75 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7ypos 0.7 size 14
Invalid "xpos" argument: Expected a number
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> ui mousemode right select
Drag select of 1949 residues, 436 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-170.42,-0.37877,-0.61554,-0.69112,259.39,-0.4435,-0.53472,0.7193,-100.96,#8,0.94989,0.28567,0.12691,10.987,-0.22448,0.34088,0.91291,-10.811,0.21753,-0.89565,0.38793,122.5,#13,0.4192,-0.58277,0.69617,125.4,-0.50655,0.48622,0.71204,17.73,-0.75344,-0.65113,-0.091378,433.58
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-151.3,-0.37877,-0.61554,-0.69112,252.85,-0.4435,-0.53472,0.7193,-134.67
> ui mousemode right zoom
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.94989,0.28567,0.12691,48.554,-0.22448,0.34088,0.91291,-26.255,0.21753,-0.89565,0.38793,102.17
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.91724,0.12933,-0.37675,57.378,0.39729,-0.36518,0.8419,-2.5079,-0.028701,-0.92191,-0.38634,108.7
> ui mousemode right select
Drag select of 577 residues
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81231,0.57896,-0.070455,-140.67,-0.37877,-0.61554,-0.69112,248.61,-0.4435,-0.53472,0.7193,-142.73
> ui mousemode right select
> select clear
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels delete
> movie record
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> turn y 1 360 models #13 center #13
> turn y 1 360 models #8 center #8
> turn y 1 360 models #1 center #1
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> movie duplicate 120
> movie stop
> movie encode output Video_1_STAU_ARF1.mp4 framerate 20 quality high
Movie saved to Video_1_STAU_ARF1.mp4
> 2dlabels text ARF1 xpos 0 ypos 0.2 size 14
> 2dlabels text ARF1 xpos 0 ypos 0.3 size 14
> 2dlabels text ARF1 xpos 0.2 ypos 0.3 size 14
> 2dlabels text ARF1 xpos 0.1 ypos 0.3 size 14
> 2dlabels text ARF1 xpos 0.05 ypos 0.3 size 14
> 2dlabels text ARF1 xpos 0.05 ypos 0.3 size 10
> 2dlabels delete
> movie record
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels text ARF1 xpos 0.05 ypos 0.3 size 10
> turn y 1 360 models #13 center #13
> turn y 1 360 models #8 center #8
> turn y 1 360 models #1 center #1
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels all visibility true frames 60
> waut 60
Unknown command: waut 60
> movie duplicate 120
> movie stop
> movie encode output Video_STAU1_ARF1_2.mp4 framerate 20 quality high
Movie saved to Video_STAU1_ARF1_2.mp4
> 2dlabels delete
> hide #8 models
> hide #13 models
> hide #1 models
> show #2 models
> select #2:182-390
4156 atoms, 4481 bonds, 328 residues, 1 model selected
> select #2:183-390
4128 atoms, 4451 bonds, 326 residues, 1 model selected
> save TandemRBD3+4_withARF1.pdb selectedOnly true
> hide #2 models
> open C:/Users/shumb/Desktop/TandemRBD3+4_withARF1.pdb
Summary of feedback from opening
C:/Users/shumb/Desktop/TandemRBD3+4_withARF1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 73 LYS A 83 1 11
Start residue of secondary structure not found: HELIX 2 2 ARG A 145 ILE A 159
1 15
Start residue of secondary structure not found: HELIX 3 3 LEU A 160 ASN A 162
1 3
Start residue of secondary structure not found: HELIX 4 4 GLU A 177 ASN A 180
1 4
Start residue of secondary structure not found: HELIX 10 10 PRO A 422 ALA A
425 1 4
13 messages similar to the above omitted
Chain information for TandemRBD3+4_withARF1.pdb #24
---
Chain | Description
A | No description available
B | No description available
> ui mousemode right select
Drag select of 326 residues, 236 shapes
> ui mousemode right "translate selected models"
> view matrix models #24,1,0,0,107.19,0,1,0,25.965,0,0,1,-130.27
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.85941,0.30049,-0.41367,122.7,-0.20448,0.94355,0.26059,28.751,0.46863,-0.13937,0.87233,-147.42
> view matrix models
> #24,0.69215,0.59274,-0.41181,115.24,-0.59179,0.7927,0.14633,74.124,0.41318,0.14242,0.89944,-163.9
> view matrix models
> #24,0.35217,-0.85733,-0.37545,234.89,-0.39648,0.22672,-0.88961,161.24,0.84781,0.46215,-0.26007,-145.97
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.35217,-0.85733,-0.37545,238.44,-0.39648,0.22672,-0.88961,176.42,0.84781,0.46215,-0.26007,-175.3
> view matrix models
> #24,0.35217,-0.85733,-0.37545,291.9,-0.39648,0.22672,-0.88961,185.59,0.84781,0.46215,-0.26007,-233.67
> ui mousemode right select
> select clear
Drag select of 315 residues, 221 shapes
Drag select of 296 residues, 212 shapes
Drag select of 326 residues, 236 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.35217,-0.85733,-0.37545,284.52,-0.39648,0.22672,-0.88961,193.03,0.84781,0.46215,-0.26007,-239.44
> view matrix models
> #24,0.35217,-0.85733,-0.37545,283.47,-0.39648,0.22672,-0.88961,202.22,0.84781,0.46215,-0.26007,-256.89
> view matrix models
> #24,0.35217,-0.85733,-0.37545,304.49,-0.39648,0.22672,-0.88961,195.53,0.84781,0.46215,-0.26007,-270.14
> view matrix models
> #24,0.35217,-0.85733,-0.37545,328.79,-0.39648,0.22672,-0.88961,180,0.84781,0.46215,-0.26007,-269.52
> view matrix models
> #24,0.35217,-0.85733,-0.37545,303.01,-0.39648,0.22672,-0.88961,200.81,0.84781,0.46215,-0.26007,-279.03
> select #24/B
2502 atoms, 2795 bonds, 118 residues, 1 model selected
> color sel blue
> ui mousemode right select
> select clear
> show #13 models
> hide #13 models
> ui mousemode right select
Drag select of 326 residues, 236 shapes
> color sel cyan
> select clear
> select #24/B
2502 atoms, 2795 bonds, 118 residues, 1 model selected
> select clear
> show #13 models
> hide #13 models
Drag select of 326 residues, 236 shapes
> color sel blue
> select clear
> undo
[Repeated 9 time(s)]
> select clear
Drag select of 320 residues, 221 shapes
Drag select of 292 residues, 153 shapes
Drag select of 326 residues, 236 shapes
> color sel blue
> select #24/B
2502 atoms, 2795 bonds, 118 residues, 1 model selected
> color sel cyan
> select clear
> show #13 models
> hide #13 models
> show #4 models
> show #3 models
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77995,0.24705,-0.57502,66.279,0.49454,0.31979,0.80819,-69.355,0.38355,-0.91471,0.12724,-133.44
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82609,0.56196,-0.042266,-156.04,0.065393,-0.021094,0.99764,-20.232,0.55974,-0.8269,-0.054173,255.26
> view matrix models
> #3,0.82609,0.56196,-0.042266,-116.75,0.065393,-0.021094,0.99764,-9.4754,0.55974,-0.8269,-0.054173,194.97
> ui mousemode right select
Drag select of 314 residues, 218 shapes
Drag select of 326 residues, 236 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.35217,-0.85733,-0.37545,248.5,-0.39648,0.22672,-0.88961,198.29,0.84781,0.46215,-0.26007,-216.83
> view matrix models
> #24,0.35217,-0.85733,-0.37545,252.64,-0.39648,0.22672,-0.88961,195.64,0.84781,0.46215,-0.26007,-216.65
> ui mousemode right select
> select clear
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77995,0.24705,-0.57502,-18.778,0.49454,0.31979,0.80819,-80.998,0.38355,-0.91471,0.12724,-23.051
> view matrix models
> #4,0.77995,0.24705,-0.57502,-28.422,0.49454,0.31979,0.80819,-84.296,0.38355,-0.91471,0.12724,-7.1175
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82609,0.56196,-0.042266,-115.43,0.065393,-0.021094,0.99764,-14.337,0.55974,-0.8269,-0.054173,201.98
> ui mousemode right select
Drag select of 326 residues, 236 shapes
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.35217,-0.85733,-0.37545,229.57,-0.39648,0.22672,-0.88961,190.63,0.84781,0.46215,-0.26007,-183.5
> view matrix models
> #24,0.35217,-0.85733,-0.37545,225.63,-0.39648,0.22672,-0.88961,195.13,0.84781,0.46215,-0.26007,-187.1
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.77995,0.24705,-0.57502,-37.439,0.49454,0.31979,0.80819,-71.559,0.38355,-0.91471,0.12724,-19.563
> view matrix models
> #4,0.77995,0.24705,-0.57502,-35.574,0.49454,0.31979,0.80819,-72.95,0.38355,-0.91471,0.12724,-19.137
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.67254,0.6862,0.27718,-47.043,-0.67015,0.40576,0.6215,-61.793,0.314,-0.60373,0.73274,-27.336
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82609,0.56196,-0.042266,-108.3,0.065393,-0.021094,0.99764,-0.61567,0.55974,-0.8269,-0.054173,170.69
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98759,-0.13933,-0.072467,-105.32,0.11009,0.28508,0.95216,-4.3875,-0.112,-0.94832,0.29689,186.22
> view matrix models
> #3,0.75852,-0.56959,0.31657,-92.514,-0.37599,0.01424,0.92652,3.7323,-0.53225,-0.8218,-0.20336,182.54
> view matrix models
> #3,0.37436,0.69621,-0.61249,-112.77,0.83556,0.033169,0.5484,-18.516,0.40212,-0.71707,-0.56931,163.44
> view matrix models
> #3,0.86437,0.47693,0.15936,-104.82,-0.020751,-0.28282,0.95895,1.9676,0.50242,-0.8322,-0.23457,168.53
> ui mousemode right select
> select clear
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> 2dlabels text ARF1 xpos 0.05 ypos 0.3 size 10
> 2dlabels text ARF1 xpos 0 ypos 0.3 size 10
> 2dlabels text ARF1 xpos 00.06 ypos 0.3 size 10
> 2dlabels text ARF1 xpos 0.06 ypos 0.3 size 10
> 2dlabels text ARF1 xpos 0.07 ypos 0.3 size 10
> 2dlabels text ARF1 xpos 0.06 ypos 0.3 size 10
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86437,0.47693,0.15936,-118.77,-0.020751,-0.28282,0.95895,-17.055,0.50242,-0.8322,-0.23457,216.21
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.67254,0.6862,0.27718,-13.302,-0.67015,0.40576,0.6215,-68.778,0.314,-0.60373,0.73274,-51.073
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.47762,0.83711,0.2667,-12.221,-0.87361,0.42033,0.2452,-62.545,0.093152,-0.35011,0.93207,-52.799
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86437,0.47693,0.15936,-126.37,-0.020751,-0.28282,0.95895,-7.5577,0.50242,-0.8322,-0.23457,207.86
> view matrix models
> #3,0.86437,0.47693,0.15936,-119.08,-0.020751,-0.28282,0.95895,-14.478,0.50242,-0.8322,-0.23457,212.09
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.75168,0.17439,0.63606,-107.38,-0.5698,-0.31396,0.75945,-10.289,0.33214,-0.93328,-0.13663,216.73
> ui mousemode right select
> select clear
> turn y 1 360 models #24 center #24
> ui mousemode right select
Drag select of 326 residues, 236 shapes
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.35217,-0.85733,-0.37545,230.49,-0.39648,0.22672,-0.88961,196.97,0.84781,0.46215,-0.26007,-195.43
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right select
Drag select of 208 residues
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.47762,0.83711,0.2667,-14.022,-0.87361,0.42033,0.2452,-59.803,0.093152,-0.35011,0.93207,-54.972
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.40179,0.9001,0.16845,-12.445,-0.90685,0.41667,-0.06339,-55.683,-0.12724,-0.12729,0.98367,-54.742
> ui mousemode right zoom
> ui mousemode right select
> select clear
> 2dlabels delete
> movie record
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1: RNA Bound Staufen" xpos 0 ypos 0.7 size 14
> 2dlabels text "Model 2: RNA Bound Staufen no RNA" xpos 0.3 ypos 0.7 size 14
> 2dlabels text "Model 3: Staufen not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels all visibility true frames 60 wait 60
Expected a keyword
> 2dlabels all visibility true frames 60
> wait 60
> turn y 1 360 models #24 center #24
> 2dlabels text ARF1 xpos 0.06 ypos 0.3 size 10
> turn y 1 360 models #4 center #4
> turn y 1 360 models #3 center #3
> movie duplicate 120
> movie stop
> movie encode output TandemRBD3+4_Video1.mp4 framerate 20 quality high
Movie saved to TandemRBD3+4_Video1.mp4
> 2dlabels delete
> 2dlabels text "Model 1:Tandem RBD3+4 with RNA " xpos 0 ypos 0.7 size 14
> 2dlabels text "Model 2: Bound Tandem RBD3+4 no RNA" xpos 0.3 ypos 0.7 size
> 14
> 2dlabels text "Model 2: Bound Tandem RBD3+4 no RNA" xpos 0.4ypos 0.7 size 14
Invalid "xpos" argument: Expected a number
> 2dlabels text "Model 2: Bound Tandem RBD3+4 no RNA" xpos 0.4 ypos 0.7 size
> 14
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels delete
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.7 ypos 0.7 size 14
[Repeated 1 time(s)]
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.4 ypos 0.7 size 14
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.35 ypos 0.7 size
> 14
> 2dlabels text "Model 1:Tandem RBD3+4 withRNA " xpos 0 ypos 0.7 size 14
> 2dlabels delete
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.7 ypos 0.7 size 14
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.6 ypos 0.7 size 14
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65ypos 0.7 size 14
Invalid "xpos" argument: Expected a number
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 14
> 2dlabels delete
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 14
> 2dlabels text "Model 2: Bound Tandem RBD3+4 no RNA" xpos 0.35 ypos 0.7 size
> 14
> 2dlabels delete
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.35 ypos 0.7 size
> 14
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 14
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 12
> 2dlabels delete
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 12
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.35 ypos 0.7 size
> 12
> 2dlabels delete
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.3 ypos 0.7 size 12
> 2dlabels text "Model 3: Tandem RBD3+4 not bound" xpos 0.65 ypos 0.7 size 12
> 2dlabels text "Model 1:Tandem RBD3+4 withRNA " xpos 0 ypos 0.7 size 12
> 2dlabels text "Model 2: Bound Tandem RBD3+4 noRNA" xpos 0.3 ypos 0.7 size 12
> 2dlabels delete
> 2dlabels text ARF1 xpos 0.06 ypos 0.3 size 18
> 2dlabels text ARF1 xpos 0.06 ypos 0.3 size 8
> 2dlabels text ARF1 xpos 0 ypos 0.3 size 8
> 2dlabels delete
> movie record
> 2dlabels text "Human Staufen Conformational Change Comparison" xpos 0.1 ypos
> 0.9 size 25
> 2dlabels text "Model 1:Tandem RBD3+4 withRNA " xpos 0 ypos 0.7 size 1225
An OpenGL graphics error occurred. Most often this is caused by a graphics
driver bug. The only way to fix such bugs is to update your graphics driver.
Redrawing graphics is now stopped to avoid a continuous stream of error
messages. To restart graphics use the command "graphics restart" after
changing the settings that caused the error.
Texture size (31820,2280) exceeds OpenGL driver maximum 16384
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\view.py", line 195, in draw
draw_overlays(odrawings, r)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\label\label2d.py", line 605, in draw
Model.draw(self, renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3174, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3217, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3077, in initialize_texture
self._check_maximum_texture_size(size)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3157, in
_check_maximum_texture_size
raise OpenGLError('Texture size (%s) exceeds OpenGL driver maximum %d' %
chimerax.graphics.opengl.OpenGLError: Texture size (31820,2280) exceeds OpenGL
driver maximum 16384
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\movie\movie.py", line 170, in capture_image
rgba = v.image_rgba(width, height, supersample = self.supersample,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\view.py", line 513, in image_rgba
self.draw(c, drawings, swap_buffers = False)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\view.py", line 195, in draw
draw_overlays(odrawings, r)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\label\label2d.py", line 605, in draw
Model.draw(self, renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self
self._draw_geometry(renderer, transparent_only = any_opaque)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry
t.bind_texture()
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3174, in bind_texture
self.fill_opengl_texture()
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3217, in fill_opengl_texture
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3077, in initialize_texture
self._check_maximum_texture_size(size)
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3157, in
_check_maximum_texture_size
raise OpenGLError('Texture size (%s) exceeds OpenGL driver maximum %d' %
chimerax.graphics.opengl.OpenGLError: Texture size (31805,2279) exceeds OpenGL
driver maximum 16384
Error processing trigger "frame drawn":
chimerax.graphics.opengl.OpenGLError: Texture size (31805,2279) exceeds OpenGL
driver maximum 16384
File "C:\Program Files\ChimeraX 1.12.dev202601050431\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3157, in
_check_maximum_texture_size
raise OpenGLError('Texture size (%s) exceeds OpenGL driver maximum %d' %
See log for complete Python traceback.
Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable
[Repeated 1 time(s)]
OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_GB.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: HUAWEI
Model: BoDE-WXX9
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 8,362,713,088
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1155G7 @ 2.50GHz
OSLanguage: en-GB
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.5
ChimeraX-AtomicLibrary: 14.2.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202601050431
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.7
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.15.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.4
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.1
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.1.2
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.13.3
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.40.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
File attachment: STAU1 and ARF1 1 copy Conformational Changes_1.cxs
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| Attachment: | STAU1 and ARF1 1 copy Conformational Changes_1.cxs added |
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