Opened 4 years ago

Last modified 4 years ago

#6379 feedback defect

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

Reported by: martti.tolvanen@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.4.dev202202030703 (2022-02-03 07:03:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202030703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0xe0000002

Thread 0x00001998 (most recent call first):
  File "", line 1067 in _handle_fromlist
Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: access violation

Windows fatal exception: stack overflow

Windows fatal exception: access violation

Windows fatal exception: access violation

===== Log before crash start =====
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7262 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.4.dev202202030703 (2022-02-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\meetol\Dropbox\CA_projects_Martti\00 G. salaris CAs\Gs BCA
> alone.fasta" format fasta

Summary of feedback from opening C:\Users\meetol\Dropbox\CA_projects_Martti\00
G. salaris CAs\Gs BCA alone.fasta  
---  
note | Alignment identifier is Gs BCA alone.fasta  
  
Opened 1 sequences from Gs BCA alone.fasta  

> open 1ekj format mmcif fromDatabase pdb

Non-standard residues in 1ekj #1  
---  
ACT — acetate ion  
AZI — azide ion  
CIT — citric acid  
CL — chloride ion  
CU — copper (II) ion  
EDO — 1,2-ethanediol (ethylene glycol)  
ZN — zinc ion  
  
1ekj mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete #2/D-h

> delete #1/D-h

> delete #1/a-b

> delete #1/D-h

> delete #1:hoh

> select ::name="CL"

1 atom, 1 residue, 1 model selected  

> delete #1:cl

> delete #1:cu

> open
> C:/Users/meetol/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb
> format pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #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 1ekj, chain C (#1) with best_model.pdb, chain A (#2), sequence
alignment score = 249  
RMSD between 113 pruned atom pairs is 1.042 angstroms; (across all 200 pairs:
5.616)  
  

> hide target a

> ribbon #1

> ui tool show Matchmaker

> select #2:31-500

3158 atoms, 3192 bonds, 199 residues, 1 model selected  

> matchmaker #2 & sel to #1 cutoffDistance 1.3

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 | 1.3  
  
Matchmaker 1ekj, chain C (#1) with best_model.pdb, chain A (#2), sequence
alignment score = 222.6  
RMSD between 85 pruned atom pairs is 0.753 angstroms; (across all 170 pairs:
5.458)  
  
Alignment identifier is 2/A  

> select clear

> ui mousemode right zoom

> lighting shadows false

> lighting full

> lighting shadows false

Alignment identifier is 1/C  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/af model
> and pea ca.cxs"

> select #1/C:160

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/C:160

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/C:162

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/C:162

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/C:160,162

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

> select #1/C:160,162,164

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select #1/C:160,162,164,220

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/C:160,162,164,220,223

41 atoms, 37 bonds, 5 residues, 1 model selected  

> select #2/A:37

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:37

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:37,39

23 atoms, 21 bonds, 2 residues, 1 model selected  

> select #2/A:37,39,41

47 atoms, 44 bonds, 3 residues, 1 model selected  

> select #2/A:37,39,41,102

64 atoms, 61 bonds, 4 residues, 1 model selected  

> select #2/A:37,39,41,102,105

75 atoms, 71 bonds, 5 residues, 1 model selected  

> show sel target ab

> select H

1823 atoms, 229 residues, 1 model selected  

> hide sel target a

> select #1/C:160,162,164,220

35 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel target ab

> style sel stick

Changed 35 atom styles  

> cofr #1

> select clear

> select #1/C:160,162,164,220

35 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/C:160,162,164,220,223

41 atoms, 37 bonds, 5 residues, 1 model selected  

> show sel target ab

> style sel stick

Changed 41 atom styles  

> color sel byhetero

> select clear

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/af model
> and pea ca.cxs"

> color #1 forest green

> color #1 byhetero

> toolshed show

> color bfactor

5323 atoms, 449 residues, atom bfactor range 18.7 to 98.5  

> select #2

3648 atoms, 3684 bonds, 229 residues, 1 model selected  

> color #1 forest green

> color #1 byhetero

> color bfactor sel

3648 atoms, 229 residues, atom bfactor range 50.3 to 98.5  

> color #2 gold

> color #2 byhetero

> select :zn

1 atom, 1 residue, 1 model selected  

> show sel target ab

> ui tool show "Selection Inspector"

> size sel atomRadius 0.01

Changed 1 atom radii  

> size sel atomRadius 0.8

Changed 1 atom radii  

> size sel atomRadius 0.9

Changed 1 atom radii  

> select clear

> set bgColor white

> graphics silhouettes true

> ui tool show "Selection Inspector"

> select :zn

1 atom, 1 residue, 1 model selected  

> size sel atomRadius 0.8

Changed 1 atom radii  

> ui tool show "Side View"

> select clear

> graphics depthcue false

Expected a keyword  

> lighting depthCue false

> lighting full

> lighting shadows false

Destroying pre-existing alignment with identifier 1/C  
Alignment identifier is 1/C  
Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> select #1/C:329

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/C:113-329

1666 atoms, 1711 bonds, 217 residues, 1 model selected  

> select #1/C:329

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/C:113-329

1666 atoms, 1711 bonds, 217 residues, 1 model selected  

> select #1/C:329

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/C:113-329

1666 atoms, 1711 bonds, 217 residues, 1 model selected  

> select #1/C:259

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/C:259

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/C:259

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/C:259-261

24 atoms, 24 bonds, 3 residues, 1 model selected  

> select #2/A:92

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2/A:92

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2/A:102

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:102-106

73 atoms, 73 bonds, 5 residues, 1 model selected  

> select #2/A:106

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

> select #2/A:106-112

117 atoms, 116 bonds, 7 residues, 1 model selected  

> select #2/A:113

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

> select #2/A:113-120

126 atoms, 125 bonds, 8 residues, 1 model selected  

> ui mousemode right translate

> select clear

> ui mousemode right zoom

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/af model
> and pea ca v2.cxs"

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA.png" width 1280 height 720 supersample 3

> select #1

1675 atoms, 1717 bonds, 3 pseudobonds, 220 residues, 2 models selected  

> ui tool show "Color Actions"

> color #1 sky blue

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA.png" width 1280 height 720 supersample 3

> color #1 heteroatom

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #1 byhetero

> color :zn red

> select clear

> ui mousemode right translate

> windowsize 900 900

QWindowsWindow::setGeometry: Unable to set geometry 1702x1116+9+38 (frame:
1720x1163+0+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1702x1055+9+38 (frame: 1720x1102+0+0) margins: 9, 38, 9, 9
minimum size: 470x568 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,615
maxtrack=0,0)  

> ui mousemode right zoom

> ui mousemode right translate

> select #2/A:1

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select #2/A:1

26 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA.png" width 900 height 839 supersample 3

> select #2/A:2-7,11-26,44-47,69-72,80-91,106-121,130-144,173-195

1564 atoms, 1569 bonds, 96 residues, 1 model selected  

> select #2/A:141-142

31 atoms, 30 bonds, 2 residues, 1 model selected  

> select #2/A:141-145

88 atoms, 88 bonds, 5 residues, 1 model selected  

> select #2/A:141-145

88 atoms, 88 bonds, 5 residues, 1 model selected  

> select clear

> select #2/A:2-7,11-26,44-47,69-72,80-91,106-121,130-144,173-195

1564 atoms, 1569 bonds, 96 residues, 1 model selected  

> select #2/A:106

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

> select #2/A:106-121

258 atoms, 257 bonds, 16 residues, 1 model selected  

> select #2/A:2-7,11-26,44-47,69-72,80-91,106-121,130-144,173-195

1564 atoms, 1569 bonds, 96 residues, 1 model selected  

> select #2/A:92

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2/A:80-92

195 atoms, 196 bonds, 13 residues, 1 model selected  

> select #2/A:176

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

> select #2/A:176

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

> select #2/A:2-7,11-26,44-47,69-72,80-91,106-121,130-144,173-195

1564 atoms, 1569 bonds, 96 residues, 1 model selected  

> select #2/A:176

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

> select #2/A:176-196

340 atoms, 341 bonds, 21 residues, 1 model selected  

> select clear

> ui mousemode right zoom

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/af model
> and pea ca v3.cxs"

> windowsize 900 700

> windowsize 700 900

QWindowsWindow::setGeometry: Unable to set geometry 1502x1116+0+29 (frame:
1520x1163-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1502x1055+0+29 (frame: 1520x1102-9-9) margins: 9, 38, 9, 9
minimum size: 470x568 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,615
maxtrack=0,0)  

> windowsize 700 900

QWindowsWindow::setGeometry: Unable to set geometry 1502x1116+0+29 (frame:
1520x1163-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1502x1055+0+29 (frame: 1520x1102-9-9) margins: 9, 38, 9, 9
minimum size: 470x568 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,615
maxtrack=0,0)  

> ui mousemode right translate

> ui mousemode right zoom

> windowsize 650 850

QWindowsWindow::setGeometry: Unable to set geometry 1452x1066+0+29 (frame:
1470x1113-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1452x1055+0+29 (frame: 1470x1102-9-9) margins: 9, 38, 9, 9
minimum size: 470x568 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=488,615
maxtrack=0,0)  

> ui mousemode right translate

> windowsize 650 800

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA 2.png" width 900 height 839 supersample 3

> windowsize 650 800

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA 2.png" width 650 height 800 supersample 3

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA 2 HR.png" width 900 height 1108 supersample 3

> windowsize 650 800

> ui tool show Matchmaker

> matchmaker #2 to #1 cutoffDistance 1.5 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 | 1.5  
  
Matchmaker 1ekj, chain C (#1) with best_model.pdb, chain A (#2), sequence
alignment score = 249  
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: 1ekj #1/C, best_model.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 97 pruned atom pairs is 0.858 angstroms; (across all 200 pairs:
5.584)  
  

> windowsize 650 800

> lighting full

> lighting shadows false

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/GsBCA and
> pea BCA 2 HR.png" width 1000 height 1231 supersample 3

> ui mousemode right zoom

> ui mousemode right translate

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/chimerax
> test.png" width 1118 height 785 supersample 3

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting shadows false

> save "C:/Users/meetol/Dropbox/CA_projects_Martti/00 G. salaris CAs/af model
> and pea ca v4.cxs"

> close session


===== Log before crash end =====
I had just closed everything and was preparing to try a command file. The crash happened when I pressed Browse in the file-open dialog. Could be a problem in my Windows too

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7262 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.4.dev202202030703 (2022-02-03)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 26.20.100.7262
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel

Locale: fi_FI.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 840 G3
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 8,464,723,968
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: en-US

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: 1.35
    ChimeraX-AtomicLibrary: 5.0
    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
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202030703
    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: 2.6
    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: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.7.5
    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: 3.0.26
    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

Attachments (3)

00a_file_explorer_windows_10_style.png​ (39.2 KB ) - added by Eric Pettersen 4 years ago.
Added by email2trac
00a_file_explorer_windows_10_style-1.png​ (39.2 KB ) - added by martti.tolvanen@… 4 years ago.
Added by email2trac
image.png​ (76.2 KB ) - added by martti.tolvanen@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (13)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Owner: set to Eric Pettersen
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 Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Martti,

Thanks for reporting this problem. Would you using the file dialog to open or save a file when this happened?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by martti.tolvanen@…, 4 years ago 

Hi Eric,

I think I was trying to change folders using the Windows frequently
accessed folders quick link, and it was for opening a file.

-Martti

ti 15. maalisk. 2022 klo 18.59 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

in reply to:  4 ; comment:4 by Eric Pettersen, 4 years ago 

Hi Martti,
	I finally got ChimeraX to crash once, after many, many tries by clicking on a path element to go to a parent directory (the "[star] > Quick access >” part of the dialog in the image below).  Is that what you did, or were you using the dropdown arrow to the right of that?

—Eric

Added by email2trac

by Eric Pettersen, 4 years ago

Attachment: 00a_file_explorer_windows_10_style.png​ added

Added by email2trac

in reply to:  6 comment:5 by martti.tolvanen@…, 4 years ago 

I was able to reproduce the crash on a first try, and this time it was the
first thing I did in a ChimeraX session (same build of 1.14 as in the bug
report). Here's the pic. What happened was that I just clicked on the
folder quick link and after maybe 5 seconds of trying to load the folder
contents ChimeraX crashed. The link is not a pinned one, just one that
Windows has created automatically due to frequent file access recently. The
folder contains only 90 files and no subfolders, and the Dropbox folder you
see in the address bar is right below C:\Users\[my_username]\. As a
non-expert guess, maybe these quick links contain the pathname of ~
implicitly in a way that is not passed on to ChimeraX?

[image: image.png]
I have a new laptop waiting to be taken into use, with a newer version of
Windows 10 which might remove the problem. I also get occasional crashes of
the File Explorer outside of any application in this computer, not related
to these quick links for frequently used folders, but some other random
events that I haven't really tried to follow up. What happens is that all
File Explorer (Windows Explorer?) windows are closed but Windows keeps
running, and I can reopen whichever folders I need and go on working
without needing to reboot.

BTW while I'm at it, I could report a bug (or feature) in Chimera (not X)
new installations which replace a previous version. When I install a new
version of Chimera, opening a file (of a type registered to Chimera) stops
working by double-clicking from a Windows folder, or by choosing Chimera
from the "open with" dialog. What is more, trying to teach Windows to use
the new version of Chimera ("use this application for opening files of this
type") didn't work either. This is because the registry entry
Computer\HKEY_USERS\S-1-5-21-1004336348-152049171-1801674531-111748_Classes\Applications\chimera.exe\shell\open\command
is left behind with a pointer to the previous installation folder of
Chimera. In my case the value was "C:\Program Files\Chimera
1.15\bin\chimera.exe" "%1" until a few minutes ago, pointing to the
previous location which is a non-existent folder now. After editing it (in
regedit) into "C:\Program Files\Chimera 1.16\bin\chimera.exe" "%1", just
changing 1.15 to 1.16 in the pathname, Chimera starts launching as
expected. This annoyance has been around at least since Chimera 1.12, and
I've just resigned to opening files only from inside of Chimera until I get
the inspiration to dig into the registry (as I did now).

Cheers,
-Martti


pe 18. maalisk. 2022 klo 2.36 Eric Pettersen (pett@cgl.ucsf.edu) kirjoitti:

Added by email2trac

Added by email2trac

by martti.tolvanen@…, 4 years ago

Attachment: 00a_file_explorer_windows_10_style-1.png​ added

Added by email2trac

by martti.tolvanen@…, 4 years ago

Attachment: image.png​ added

Added by email2trac

comment:6 by Eric Pettersen, 4 years ago

Hi Martti,

We recently upgraded the version of Python that ChimeraX uses (3.9.6→3.9.11) and are hopeful that certain specific bug fixes that are included with that upgrade may remedy this problem. We are hoping you can try out the latest daily build and see if the Open dialog seems more stable...

--Eric

in reply to:  10 ; comment:7 by martti.tolvanen@…, 4 years ago 

Hi Eric,

I finally had a chance to try the latest daily version, and now file-open
from those quick link folders works, from the same old laptop. Thanks! I
was also excited to find the alphafold error plot tool, and happy to see
"show all colors" in the color action menu.

I can also see that those JSON files are a new thing from AlphaFold, they
were not downloaded with a prediction ~3 weeks ago but were there two days
ago. Did you ask for them?

Cheers,
-Martti

ke 6. huhtik. 2022 klo 21.30 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

in reply to:  11 comment:8 by goddard@…, 4 years ago 

I updated ChimeraX AlphaFold predictions using Colab to use AlphaFold 2.2.0 earlier this week, and I made it use the "monomer_ptm" preset instead of the "monomer" preset since the the latter does not compute PAE and the json files.  Those changes were in the ChimeraX Colab script which ChimeraX fetches from GitHub when you make a prediction, so those updates even apply to older ChimeraX daily builds.  But the AlphaFold Error Plot button and ability to show those plots requires a daily build from this week.  Here's a web page explaining the new error plots and a video demonstrating them if you are interested in more info

	https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html <https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html>

	https://youtu.be/oxblwn0_PMM

in reply to:  7 comment:9 by Eric Pettersen, 4 years ago

Well, that's encouraging! Have my fingers crossed that it fixes it for everyone -- since we get this reported multiple times per day!

--Eric

Replying to martti.tolvanen@…:

Hi Eric,

I finally had a chance to try the latest daily version, and now file-open
from those quick link folders works, from the same old laptop. Thanks! I
was also excited to find the alphafold error plot tool, and happy to see
"show all colors" in the color action menu.

I can also see that those JSON files are a new thing from AlphaFold, they
were not downloaded with a prediction ~3 weeks ago but were there two days
ago. Did you ask for them?

Cheers,
-Martti

ke 6. huhtik. 2022 klo 21.30 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:

in reply to:  13 ; comment:10 by martti.tolvanen@…, 4 years ago 

I had the crash happen once again some days ago. I think it was when I
changed the folder display from icons into details. But I was too busy to
try to repeat that at the time. I'll let you know if I can repeat the
precise actions next week.

Happy Easter,
-Martti

ti 12. huhtik. 2022 klo 3.40 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
kirjoitti:
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