Opened 2 years ago

Closed 2 years ago

#8899 closed defect (can't reproduce)

Crash using File→Open on Windows and/or in return statement

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x80040155

Current thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x80040155

Thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x80040155

Current thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x80040155

Thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x80040155

Current thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x80040155

Thread 0x00001978 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 17 in _file_open
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\providers.py", line 45 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\__init__.py", line 37 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\__init__.py", line 1284 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 381 in run_provider
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\toolbar\tool.py", line 165 in callback
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7zh3

7zh3 title:  
USP1 bound to ubiquitin conjugated to FANCD2 (focused refinement) [more
info...]  
  
Chain information for 7zh3 #1  
---  
Chain | Description | UniProt  
C | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN  
D | Ubiquitin carboxyl-terminal hydrolase 1 | UBP1_HUMAN  
  
Non-standard residues in 7zh3 #1  
---  
ZN — zinc ion  
  

> open 7zh4

7zh4 title:  
USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement)
[more info...]  
  
Chain information for 7zh4 #2  
---  
Chain | Description | UniProt  
C | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN  
D | Ubiquitin carboxyl-terminal hydrolase 1 | UBP1_HUMAN  
  
Non-standard residues in 7zh4 #2  
---  
JDA —
5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine  
ZN — zinc ion  
  

> hide #!2 models

> open C:/Users/marti/Downloads/cryosparc_P38_J1091_007_volume_map_sharp.mrc

Opened cryosparc_P38_J1091_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.83, shown at level 0.0516, step 2, values float32  

> volume #3 level 0.1748

> volume #3 step 1

> ui mousemode right "rotate selected models"

> select #3

2 models selected  

> ~select #3

Nothing selected  

> select #1

3301 atoms, 3317 bonds, 9 pseudobonds, 446 residues, 3 models selected  

> view matrix models
> #1,-0.99742,-0.065034,-0.030245,352.18,-0.064456,0.62782,0.77569,-33.361,-0.031457,0.77564,-0.63039,99.408

> delete /C

> view matrix models
> #1,-0.84506,-0.28003,0.45547,296.02,0.33064,0.39576,0.85677,-77.949,-0.42018,0.87462,-0.24185,103.12

> view matrix models
> #1,-0.86558,0.029085,0.49993,250.51,0.45077,0.48012,0.75252,-97.227,-0.21814,0.87672,-0.42869,91.783

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.86558,0.029085,0.49993,211.46,0.45077,0.48012,0.75252,-133.76,-0.21814,0.87672,-0.42869,87.008

> view matrix models
> #1,-0.86558,0.029085,0.49993,212.9,0.45077,0.48012,0.75252,-134.42,-0.21814,0.87672,-0.42869,84.295

> fitmap #1 inMap #3

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) using 2688 atoms  
average map value = 0.1004, steps = 196  
shifted from previous position = 1.81  
rotated from previous position = 23.9 degrees  
atoms outside contour = 1924, contour level = 0.1748  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.65517252 0.05552141 0.75343635 142.55885536  
0.58106810 0.67438789 0.45558844 -147.40023574  
-0.48281344 0.73628686 -0.47410214 154.86122358  
Axis 0.20454068 0.90083647 0.38295791  
Axis point 125.89774478 0.00000000 75.33293930  
Rotation angle (degrees) 136.67248992  
Shift along axis -44.31909320  
  

> select clear

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7zh3, chain D (#1) with 7zh4, chain D (#2), sequence alignment
score = 3251.3  
RMSD between 269 pruned atom pairs is 0.398 angstroms; (across all 285 pairs:
1.362)  
  

> select #1

2688 atoms, 2704 bonds, 9 pseudobonds, 363 residues, 3 models selected  

> view matrix models
> #1,-0.65517,0.055521,0.75344,142.5,0.58107,0.67439,0.45559,-144.67,-0.48281,0.73629,-0.4741,156.63

> fitmap #1 inMap #3

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) using 2688 atoms  
average map value = 0.1091, steps = 116  
shifted from previous position = 1.65  
rotated from previous position = 9.12 degrees  
atoms outside contour = 1861, contour level = 0.1748  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.63252643 0.18346282 0.75249698 120.79956352  
0.60309117 0.72626805 0.32987231 -141.55108131  
-0.48599522 0.66247725 -0.57002854 179.18370736  
Axis 0.24650411 0.91788603 0.31099994  
Axis point 120.21323660 0.00000000 85.71597367  
Rotation angle (degrees) 137.57350589  
Shift along axis -44.42404749  
  

> view matrix models
> #1,-0.63253,0.18346,0.7525,123.65,0.60309,0.72627,0.32987,-143.17,-0.486,0.66248,-0.57003,176.06

> fitmap #1 inMap #3

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) using 2688 atoms  
average map value = 0.1091, steps = 128  
shifted from previous position = 4.53  
rotated from previous position = 0.0107 degrees  
atoms outside contour = 1862, contour level = 0.1748  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.63257008 0.18351722 0.75244702 120.80084569  
0.60316988 0.72615849 0.32996959 -141.55315322  
-0.48584069 0.66258227 -0.57003820 179.13839919  
Axis 0.24654242 0.91785571 0.31105905  
Axis point 120.20250868 0.00000000 85.70265329  
Rotation angle (degrees) 137.58042262  
Shift along axis -44.42021767  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.57599,0.25395,0.77701,98.23,0.63763,0.73437,0.23265,-136.44,-0.51153,0.62945,-0.58492,190.01

> fitmap #1 inMap #3

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) using 2688 atoms  
average map value = 0.3103, steps = 84  
shifted from previous position = 2.56  
rotated from previous position = 10 degrees  
atoms outside contour = 1109, contour level = 0.1748  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1091_007_volume_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
-0.45479562 0.18023996 0.87216655 75.44247759  
0.63997845 0.74717842 0.17930978 -130.64245651  
-0.61934524 0.63971710 -0.45516316 188.59507227  
Axis 0.28293587 0.91658442 0.28252485  
Axis point 114.39375582 0.00000000 89.67545768  
Rotation angle (degrees) 125.54838015  
Shift along axis -45.11666454  
  

> select clear

> save C:\Users\marti/Downloads/7zh3_aligned2.pdb models #1

> ui mousemode right translate

> volume #3 level 0.3721

> volume #3 level 0.2771

> show #!3 models

> open C:/Users/marti/Downloads/cryosparc_P38_J1085_007_volume_map_sharp.mrc

Opened cryosparc_P38_J1085_007_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.83, shown at level 0.04, step 2, values float32  

> volume #4 level 0.1563

> volume #4 step 1

> volume #4 level 0.2517

> hide #!1 atoms

> show #!1 atoms

> hide #!1 cartoons

> view /D:583

> volume #3 color #b2b2b296

> volume #4 color #ffffb296

> open C:/Users/marti/Downloads/cryosparc_P38_J1082_007_volume_map_sharp.mrc

Opened cryosparc_P38_J1082_007_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.83, shown at level 0.0433, step 2, values float32  

> volume #5 level 0.25

> volume #5 step 1

> volume #5 color #b2ffff96

> volume #5 level 0.3073

> open C:/Users/marti/Downloads/cryosparc_P38_J950_008_volume_map_sharp.mrc

Opened cryosparc_P38_J950_008_volume_map_sharp.mrc as #6, grid size
320,320,320, pixel 0.83, shown at level 0.0514, step 2, values float32  

> volume #6 level 0.2948

> volume #6 step 1

> volume #6 color #b2b2ff96

> open C:/Users/marti/Downloads/cryosparc_P38_J1095_005_volume_map_sharp.mrc

Opened cryosparc_P38_J1095_005_volume_map_sharp.mrc as #7, grid size
320,320,320, pixel 0.83, shown at level 0.0409, step 2, values float32  

> volume #7 level 0.1175

> volume #7 step 1

> volume #7 level 0.1893

> volume #7 color #ffb2ff96

> view /D:583

> volume #7 level 0.2676

> hide #!7 models

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  

> open C:/Users/marti/Downloads/cryosparc_P38_J1096_006_volume_map_sharp.mrc

Opened cryosparc_P38_J1096_006_volume_map_sharp.mrc as #8, grid size
320,320,320, pixel 0.83, shown at level 0.043, step 2, values float32  

> volume #8 level 0.2112

> volume #8 step 1

> volume #8 color #ffb2b296

> view /D:583

> volume #8 level 0.252

> show #!6 models

> hide #!8 models

> hide #!6 models

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7zh3, chain D (#1) with 7zh4, chain D (#2), sequence alignment
score = 3251.3  
RMSD between 269 pruned atom pairs is 0.398 angstroms; (across all 285 pairs:
1.362)  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 cartoons

> show #!2 atoms

> hide #!2 models

> open C:/Users/marti/Downloads/cryosparc_P38_J1091_007_volume_map.mrc
> C:/Users/marti/Downloads/cryosparc_P38_J1085_007_volume_map.mrc
> C:/Users/marti/Downloads/cryosparc_P38_J950_008_volume_map.mrc

Opened cryosparc_P38_J1091_007_volume_map.mrc as #9.1, grid size 320,320,320,
pixel 0.83, shown at level 0.0192, step 2, values float32  
Opened cryosparc_P38_J1085_007_volume_map.mrc as #9.2, grid size 320,320,320,
pixel 0.83, shown at level 0.0185, step 2, values float32  
Opened cryosparc_P38_J950_008_volume_map.mrc as #9.3, grid size 320,320,320,
pixel 0.83, shown at level 0.0192, step 2, values float32  

> volume #9 level 0.2

> volume #9 level 0.1

> volume #9 step 1

> hide #!9.3 models

> hide #!9.2 models

> show #!9.2 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.2 models

> show #!9.2 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.2 models

> show #!9.2 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.2 models

> show #!9.2 models

> show #!9.3 models

> hide #!9.2 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.3 models

> show #!9.3 models

> show #!1 models

> hide #!9.3 models

> hide #!9.1 models

> show #!1 cartoons

> show #!9.1 models

> hide #!1 models

> show #!9.3 models

> hide #!9.3 models

> show #!9.3 models

> show #!1 models

> hide #!9.3 models

> show #!9.3 models

> hide #!9.3 models

> show #!9.3 models

> hide #!9.3 models

> show #!9.3 models

> hide #!9.3 models

> show #!9.3 models

> hide #!9.3 models

> show #!9.3 models

> open C:/Users/marti/Downloads/cryosparc_P38_J1096_006_volume_map.mrc

Opened cryosparc_P38_J1096_006_volume_map.mrc as #10, grid size 320,320,320,
pixel 0.83, shown at level 0.00675, step 2, values float32  

> volume #10 step 1

> volume #10 level 0.1

> hide #!9.3 models

> hide #!10 models

> show #!10 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.1 models

> show #!9.1 models

> hide #!9.1 models

> show #!9.1 models

> hide #!10 models

> show #!10 models

> hide #!9.1 models

> show #!9.1 models

> hide #!10 models

> show #!10 models

> hide #!9.1 models

> show #!9.1 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!9.1 models

> hide #!1 models

> show #!2 models

> volume #10 color #cccc9996

> view ligand

> show #!9.1 models

> hide #!10 models

> show #!10 models

> hide #!9.1 models

> hide #!10 models

> open C:/Users/marti/Downloads/cryosparc_P38_J1102_005_volume_map.mrc
> C:/Users/marti/Downloads/cryosparc_P38_J1101_005_volume_map.mrc

Opened cryosparc_P38_J1102_005_volume_map.mrc as #11.1, grid size 320,320,320,
pixel 0.83, shown at level 0.0063, step 2, values float32  
Opened cryosparc_P38_J1101_005_volume_map.mrc as #11.2, grid size 320,320,320,
pixel 0.83, shown at level 0.00593, step 2, values float32  

> volume #11 level 0.1

> volume #11 step 1

> hide #!11.2 models

> show #!11.2 models

> hide #!11.2 models

> show #!11.2 models

> hide #!11.1 models

> show #!11.1 models

> hide #!11.2 models

> show #!1 models

> hide #!2 models

> fitmap #1 inMap #11.1

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1102_005_volume_map.mrc (#11.1)
using 2688 atoms  
average map value = 0.141, steps = 48  
shifted from previous position = 0.289  
rotated from previous position = 0.392 degrees  
atoms outside contour = 1157, contour level = 0.1  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1102_005_volume_map.mrc
(#11.1) coordinates:  
Matrix rotation and translation  
-0.45043221 0.18391940 0.87366153 73.89341423  
0.64045007 0.74833999 0.17265850 -129.88796733  
-0.62204062 0.63730754 -0.45486763 189.53620947  
Axis 0.28481731 0.91682503 0.27984097  
Axis point 114.08601366 0.00000000 90.15423330  
Rotation angle (degrees) 125.34369946  
Shift along axis -44.99841912  
  

> hide #!10 models

> show #!10 models

> hide #!11.1 models

> show #!11.1 models

> hide #!11 models

> show #!11.2 models

> hide #!11.2 models

> hide #!10 models

> hide #!1 atoms

> color #11 #b2b2b296 models

> show #!11.1 models

> hide #!11.2 models

> show #!11.2 models

> hide #!11.1 models

> volume #11.2 level 0.02703

> volume #11.2 level 0.01834

> hide #!11.2 models

> show #!11.1 models

> show #!11.2 models

> hide #!11.1 models

> close #9-11#9.1-3

> open C:/Users/marti/Downloads/cryosparc_P38_J1101_005_volume_map_sharp.mrc
> C:/Users/marti/Downloads/cryosparc_P38_J1102_005_volume_map_sharp.mrc

Opened cryosparc_P38_J1101_005_volume_map_sharp.mrc as #9.1, grid size
320,320,320, pixel 0.83, shown at level 0.0428, step 2, values float32  
Opened cryosparc_P38_J1102_005_volume_map_sharp.mrc as #9.2, grid size
320,320,320, pixel 0.83, shown at level 0.0403, step 2, values float32  

> volume #9.1 level 0.04275

> volume #9.1 step 1

> volume #9.2 step 1

> volume #9 level 0.1

> volume #9 level 0.2

> volume #9 level 0.25

> color #9 #b2b2b296 models

> show #!1 atoms

> hide #!1 cartoons

> fitmap #1 inMap #9.1

Fit molecule 7zh3 (#1) to map cryosparc_P38_J1101_005_volume_map_sharp.mrc
(#9.1) using 2688 atoms  
average map value = 0.3023, steps = 48  
shifted from previous position = 0.0708  
rotated from previous position = 0.518 degrees  
atoms outside contour = 1403, contour level = 0.25  
  
Position of 7zh3 (#1) relative to cryosparc_P38_J1101_005_volume_map_sharp.mrc
(#9.1) coordinates:  
Matrix rotation and translation  
-0.45365540 0.17754259 0.87331289 75.36096007  
0.64076157 0.74605479 0.18118186 -130.70110349  
-0.61937177 0.64177946 -0.45221425 188.07835037  
Axis 0.28268539 0.91611449 0.28429422  
Axis point 114.37496909 0.00000000 89.53277362  
Rotation angle (degrees) 125.44403240  
Shift along axis -44.96414487  
  

> view /D:583

> show #!2 models

> hide #!1 models

> fitmap #2 inMap #9.2

Fit molecule 7zh4 (#2) to map cryosparc_P38_J1102_005_volume_map_sharp.mrc
(#9.2) using 2339 atoms  
average map value = 0.3247, steps = 52  
shifted from previous position = 0.311  
rotated from previous position = 0.717 degrees  
atoms outside contour = 1134, contour level = 0.25  
  
Position of 7zh4 (#2) relative to cryosparc_P38_J1102_005_volume_map_sharp.mrc
(#9.2) coordinates:  
Matrix rotation and translation  
-0.44342644 0.18858382 0.87624719 71.84219733  
0.65361626 0.73698696 0.17215109 -130.39454127  
-0.61331784 0.64906576 -0.45006096 185.88209079  
Axis 0.29227746 0.91288088 0.28499543  
Axis point 113.06139396 0.00000000 89.22506283  
Rotation angle (degrees) 125.32756594  
Shift along axis -45.06128304  
  

> close #9

> open C:/Users/marti/Downloads/cryosparc_P38_J1124_003_volume_map_sharp.mrc

Opened cryosparc_P38_J1124_003_volume_map_sharp.mrc as #9, grid size
320,320,320, pixel 0.83, shown at level 0.0496, step 2, values float32  

> volume #9 level 0.2124

> volume #9 step 1

> volume #9 color #ffb2ff96

> volume #9 level 0.252

> volume #9 level 0.2

> open C:/Users/marti/Downloads/cryosparc_P38_J1127_cluster_007.mrc

Opened cryosparc_P38_J1127_cluster_007.mrc as #10, grid size 128,128,128,
pixel 2.08, shown at level 0.0831, step 1, values float32  

> hide #!9 models

> volume #10 level 0.2504

> volume #10 color #ffb2b296

> show #!1 models

> hide #!2 models


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\marti\\\Downloads\\\cryosparc_P38_J1135_004_volume_map_sharp.mrc

Opened cryosparc_P38_J1135_004_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.83, shown at level 0.0394, step 2, values float32  




OpenGL version: 3.3.0 - Build 27.20.100.8935
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: XPS 13 7390
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,362,000,384
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: en-US
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    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
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    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: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 years ago

Component: Unassigned → Platform
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash using File→Open on Windows and/or in return statement

comment:2 by pett, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

1.3

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