Crash drawing side view during alphafold prediction

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.4.dev202202090150 (2022-02-09 01:50:51 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x000044c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: access violation

Current thread 0x000044c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\graphics\opengl.py", line 111 in make_current
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\graphics\opengl.py", line 490 in make_current
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\graphics\opengl.py", line 536 in use_shared_context
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\sideview\tool.py", line 282 in render
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\sideview\tool.py", line 116 in exposeEvent
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202090150\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202202090150 (2022-02-09)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> IRGLSGGQKVKLVLAAGTWQRPHLIVLDEPTNYLDRDSLGALSKALKEFEGGVIIITHSAEFTKNLTEEVWAVKDGRMTPSGHNWVSGQGAGPRIEKKEDEEDKFDAMGNKIAGGKKKKKLSSAELRKKKKERMKKKKELGDAYVSSDEEF

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\mniak/Downloads\ChimeraX\AlphaFold\prediction_1  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1

2393 atoms, 2411 bonds, 151 residues, 1 model selected  

> ~select #1

Nothing selected  

> hide #1 models

> show #1 models

> alphafold predict
> IRGLSGGQKVKLVLAAGTWQRPHLIVLDEPTNYLDRDSLGALSKALKEFEGGVIIITHSAEFTKNLTEEVWAVKDGRMTPSGHNWVSGQGAGPRIEKKEDEEDKFDAMGNKIAGGKKKKKLSSAELRKKKKERMKKKKELGDAYVEEDEEF

Running AlphaFold prediction  

> select #1

2393 atoms, 2411 bonds, 151 residues, 1 model selected  

> ~select #1

Nothing selected  

> ui mousemode right swapaa

> swapaa mousemode /A:139 GLU

> undo

Undo failed, probably because structures have been modified.  

> ui mousemode right swapaa

> swapaa mousemode /A:146 MET

> swapaa mousemode /A:146 LYS

> swapaa mousemode /A:146 ALA

> ui mousemode right swapaa

> swapaa mousemode /A:146 ALA

> ui mousemode right "bond rotation"

> ui mousemode right swapaa

> swapaa mousemode /A:139 GLY

> swapaa mousemode /A:146 ALA

> swapaa mousemode /A:146 VAL

> swapaa mousemode /A:146 ALA

> swapaa mousemode /A:146 ARG

> swapaa mousemode /A:146 ASP

> swapaa mousemode /A:146 GLY

> ui mousemode right swapaa

> swapaa mousemode /A:146 GLY

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> ~select #1

Nothing selected  

> view clip false

> show target m

> hide target m

> show target m

> style stick

Changed 2381 atom styles  

> style stick

Changed 2381 atom styles  

> ui tool show "Side View"

> graphics silhouettes true

> graphics silhouettes false

> color bychain

> ui mousemode right "contour level"

> volume style surface

No volumes specified  

> volume style surface

No volumes specified  

> color byhetero

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -12.68, mean
1.59, maximum 14.41  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -29.45, mean
-3.129, maximum 23.36  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -12.68, mean
1.59, maximum 14.41  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color byhetero

> color bychain

> style stick

Changed 2381 atom styles  

> rainbow

> color bychain

> show cartoons

> cartoon

> style stick

Changed 2381 atom styles  

> hide surfaces

> coulombic

Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -12.68, mean
1.59, maximum 14.41  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -12.68, mean
1.59, maximum 14.41  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> mlp

Map values for surface "best_model.pdb_A SES surface": minimum -29.45, mean
-3.129, maximum 23.36  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> show atoms

> hide atoms

> color bfactor

2381 atoms, 151 residues, 1 surfaces, atom bfactor range 33.1 to 96.2  
Alignment identifier is 1/A  

> select /A:139,146

14 atoms, 12 bonds, 2 residues, 1 model selected  

> hbonds sel reveal true

2 hydrogen bonds found  

> hbonds sel reveal true

2 hydrogen bonds found  

> ~hbonds

> hbonds sel reveal true

2 hydrogen bonds found  

> ~hbonds

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> ~select #1

1 model selected  

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> ~select #1

1 model selected  

> show #!1 target m

> style stick

Changed 2381 atom styles  

> style ball

Changed 2381 atom styles  
Alignment identifier is 1/A  

> select /A:115-116

29 atoms, 28 bonds, 2 residues, 1 model selected  

> select /A:115-119

95 atoms, 94 bonds, 5 residues, 1 model selected  

> select /A:116

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select /A:116-120

110 atoms, 109 bonds, 5 residues, 1 model selected  

> select /A:99

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:99-103

69 atoms, 68 bonds, 5 residues, 1 model selected  

> hide #!1 target m

> show #!1 models

> select /A:6-18,36-48,60-63,85-88,123-143

870 atoms, 868 bonds, 55 residues, 1 model selected  

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> ~select #1

1 model selected  

> select /A:127

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:127-131

112 atoms, 111 bonds, 5 residues, 1 model selected  

> select /A:120-121

41 atoms, 40 bonds, 2 residues, 1 model selected  

> select /A:116-121

129 atoms, 128 bonds, 6 residues, 1 model selected  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> ui mousemode right "next docked"

AlphaFold prediction finished  
Results in C:\Users\mniak/Downloads\ChimeraX\AlphaFold\prediction_2  
Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select #2

2401 atoms, 2419 bonds, 151 residues, 1 model selected  

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> select #2

2401 atoms, 2419 bonds, 151 residues, 1 model selected  
Alignment identifier is 2/A  

> select #1

2381 atoms, 2399 bonds, 151 residues, 1 model selected  

> color #1 red transparency 0

> color #2 #55007f transparency 0

> mmaker #2 to #1 showAlignment true

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 best_model.pdb, chain A (#1) with best_model.pdb, chain A (#2),
sequence alignment score = 744.8  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 41 pruned atom pairs is 0.933 angstroms; (across all 151 pairs:
6.766)  
  

> alphafold predict
> MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAPVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD,MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEESEESDDDMGFGLFD,MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAGGPAPAAGAAPAGGPAPSTAAAPAEEKKVEAKKEESEESDDDMGFGLFD,MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD,MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD

Running AlphaFold prediction  

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_2/model_1_unrelaxed.pdb

Chain information for model_1_unrelaxed.pdb #3  
---  
Chain | Description  
A | No description available  
  
Associated model_1_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A  

> hide #3 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_2/model_2_unrelaxed.pdb

Chain information for model_2_unrelaxed.pdb #4  
---  
Chain | Description  
A | No description available  
  
Associated model_2_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A  

> hide #4 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_2/model_3_unrelaxed.pdb

Chain information for model_3_unrelaxed.pdb #5  
---  
Chain | Description  
A | No description available  
  
Associated model_3_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A  

> hide #2 models

> mmaker #5 to #1 showAlignment true

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 best_model.pdb, chain A (#1) with model_3_unrelaxed.pdb, chain A
(#5), sequence alignment score = 726.8  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 80 pruned atom pairs is 0.422 angstroms; (across all 151 pairs:
7.443)  
  

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_2/model_4_unrelaxed.pdb

Chain information for model_4_unrelaxed.pdb #6  
---  
Chain | Description  
A | No description available  
  
Associated model_4_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A  
Associated model_4_unrelaxed.pdb chain A to model_3_unrelaxed.pdb, chain A
with 0 mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A  

> hide #6 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_2/model_5_unrelaxed.pdb

Chain information for model_5_unrelaxed.pdb #7  
---  
Chain | Description  
A | No description available  
  
Associated model_5_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A  
Associated model_5_unrelaxed.pdb chain A to model_3_unrelaxed.pdb, chain A
with 0 mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A  

> hide #7 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_1/model_1_unrelaxed.pdb

Chain information for model_1_unrelaxed.pdb #8  
---  
Chain | Description  
A | No description available  
  
Associated model_1_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A  
Associated model_1_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A  

> hide #8 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_1/model_2_unrelaxed.pdb

Chain information for model_2_unrelaxed.pdb #9  
---  
Chain | Description  
A | No description available  
  
Associated model_2_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A  
Associated model_2_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A  

> hide #9 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_1/model_3_unrelaxed.pdb

Chain information for model_3_unrelaxed.pdb #10  
---  
Chain | Description  
A | No description available  
  
Associated model_3_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A  
Associated model_3_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A  

> hide #10 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_1/model_4_unrelaxed.pdb

Chain information for model_4_unrelaxed.pdb #11  
---  
Chain | Description  
A | No description available  
  
Associated model_4_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A, model_4_unrelaxed.pdb #11/A  
Associated model_4_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A, model_4_unrelaxed.pdb #11/A  

> hide #11 models

> open
> C:/Users/mniak/Downloads/ChimeraX/AlphaFold/prediction_1/model_5_unrelaxed.pdb

Chain information for model_5_unrelaxed.pdb #12  
---  
Chain | Description  
A | No description available  
  
Associated model_5_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 1: best_model.pdb #1/A,
best_model.pdb #2/A, model_1_unrelaxed.pdb #3/A, model_2_unrelaxed.pdb #4/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A, model_4_unrelaxed.pdb #11/A,
model_5_unrelaxed.pdb #12/A  
Associated model_5_unrelaxed.pdb chain A to best_model.pdb, chain A with 0
mismatches  
Chains used in RMSD evaluation for alignment 2: best_model.pdb #1/A,
model_3_unrelaxed.pdb #5/A, model_4_unrelaxed.pdb #6/A, model_5_unrelaxed.pdb
#7/A, model_1_unrelaxed.pdb #8/A, model_2_unrelaxed.pdb #9/A,
model_3_unrelaxed.pdb #10/A, model_4_unrelaxed.pdb #11/A,
model_5_unrelaxed.pdb #12/A  

> hide #12 models

> ui mousemode right "move picked models"

> view orient

> ~select #1

1 model selected  

> ui tool show "Side View"

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> ui tool show "Build Structure"

> build start peptide "custom built" KKKKELGDAYVSSDEEF -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack

Chain information for custom built #13  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" KKKKELGDAYVSSDEEF -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack

Chain information for custom built #14  
---  
Chain | Description  
A | No description available  
  

> hide #14 models

> hide #!1 models

> hide #5 models

> build start peptide "custom built" KKKKELGDAYVSSDEEF -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack

Chain information for custom built #15  
---  
Chain | Description  
A | No description available  
  

> close #15

> close #14

> build start peptide "custom built" KKKKELGDAYVSSDEEF -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack

Chain information for custom built #14  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" KKKKELGDAYVSSDEEF -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack

Chain information for custom built #15  
---  
Chain | Description  
A | No description available  
  
You must select exactly one atom to modify.  

> show #!1 models

> show #5 models

> hide #15 models

> hide #14 models

> hide #13 models


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4.dev202202090150 (2022-02-09)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.9365
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Locale: pl_PL.cp1250
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 3593
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 8,346,107,904
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.11
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36
    ChimeraX-AtomicLibrary: 6.0.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202090150
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.27
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1