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#9324 assigned defect

Crash opening session

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

Description

The following bug report has been submitted:
Platform:        Linux-5.19.0-46-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6rc202304282142 (2023-04-28 21:42:26 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f0170618b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/pkg_resources/_vendor/packaging/version.py", line 518 in _cmpkey
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/pkg_resources/_vendor/packaging/version.py", line 212 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 696 in find_bundle
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 190 in class_of
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 720 in restore
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 1004 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 368 in thread_safe
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:1

3 atoms, 3 residues, 1 model selected  

> select /A

409 atoms, 3 bonds, 403 pseudobonds, 409 residues, 2 models selected  

> show sel surfaces

> select clear

> close session

> open
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb
> format pdb

No such file/path:
/home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb  

> open
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb
> format pdb

No such file/path:
/home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb  

> open
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb
> format pdb

No such file/path:
/home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/only_first_3/three_structure.pdb  

> open
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/session_all_clustertogethes.cxs
> format session


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

Log:
UCSF ChimeraX version: 1.6rc202304282142 (2023-04-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open session_all_clustertogethes.cxs

Log from Wed Jul 5 18:15:50 2023UCSF ChimeraX version: 1.6rc202304282142
(2023-04-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cluster_0001.pdb

Chain information for cluster_0001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open cluster_0002.pdb

Chain information for cluster_0002.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open cluster_0003.pdb

Chain information for cluster_0003.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open cluster_0004.pdb

Chain information for cluster_0004.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open cluster_0005.pdb

Chain information for cluster_0005.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open cluster_0006.pdb

Chain information for cluster_0006.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> show surfaces

> select #329-1118

Nothing selected  

> select :329-1118

Nothing selected  

> set bgColor white

> select #329-1118

Nothing selected  

> select @329-1118

Expected an objects specifier or a keyword  

> select @329-1118 #

Expected an objects specifier or a keyword  

> select @329-1118 #*

Expected an objects specifier or a keyword  

> select #* @329

Nothing selected  

> select #*

2730 atoms, 26 bonds, 2692 pseudobonds, 2730 residues, 12 models selected  

> select #* @329

Nothing selected  

> select @329 #*

2730 atoms, 26 bonds, 2692 pseudobonds, 2730 residues, 12 models selected  

> select clear

> select @329-1118 #*

Expected an objects specifier or a keyword  

> select :329-1118 & #*

Nothing selected  

> select @329-1118 & #*

Expected an objects specifier or a keyword  

> select atomid 329

Expected an objects specifier or a keyword  

> select atomid 329 #*

Expected an objects specifier or a keyword  

> select #* @21

Nothing selected  

> select #*

2730 atoms, 26 bonds, 2692 pseudobonds, 2730 residues, 12 models selected  

> select #* and @21

Expected a keyword  

> select #* & @21

Nothing selected  

> select :374.A

Expected an objects specifier or a keyword  

> select .A

Expected an objects specifier or a keyword  

> sel: .A

Unknown command: sel: .A  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #3/B #4/B #5/B #6/B

Alignment identifier is 1  

> select #1/B:1-2 #3/B:1-2 #4/B:1-2 #5/B:1-2 #6/B:1-2

10 atoms, 5 pseudobonds, 10 residues, 10 models selected  

> select #1/B:1-71 #3/B:1-71 #4/B:1-71 #5/B:1-71 #6/B:1-71

355 atoms, 8 bonds, 342 pseudobonds, 355 residues, 10 models selected  

> select clear

[Repeated 1 time(s)]

> select #1/B:1 #3/B:1 #4/B:1 #5/B:1 #6/B:1

5 atoms, 5 residues, 5 models selected  

> select #1/B:1-23 #3/B:1-23 #4/B:1-23 #5/B:1-23 #6/B:1-23

115 atoms, 5 bonds, 105 pseudobonds, 115 residues, 10 models selected  

> select #1/B:1-2 #3/B:1-2 #4/B:1-2 #5/B:1-2 #6/B:1-2

10 atoms, 5 pseudobonds, 10 residues, 10 models selected  

> select #1/B:1-300 #3/B:1-300 #4/B:1-300 #5/B:1-300 #6/B:1-300

1500 atoms, 16 bonds, 1479 pseudobonds, 1500 residues, 10 models selected  

> select #1/B #3/B #4/B #5/B #6/B

1590 atoms, 16 bonds, 1569 pseudobonds, 1590 residues, 10 models selected  

> set bgColor gray

[Repeated 3 time(s)]

> color blue sele

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> set bgColor white

> ui tool show "Color Actions"

> color sel dodger blue

> color sel medium purple

> color sel cornflower blue

> select clear

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting full

[Repeated 2 time(s)]

> lighting soft

> lighting simple

> lighting soft

> ui tool show "Color Actions"

> color medium slate blue

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A

Alignment identifier is 2  

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1 #6/A:1

6 atoms, 6 residues, 6 models selected  

> select #1/A:1-9 #2/A:1-9 #3/A:1-9 #4/A:1-9 #5/A:1-9 #6/A:1-9

54 atoms, 48 pseudobonds, 54 residues, 12 models selected  

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1 #6/A:1

6 atoms, 6 residues, 6 models selected  

> select #1/A:1-12 #2/A:1-12 #3/A:1-12 #4/A:1-12 #5/A:1-12 #6/A:1-12

72 atoms, 66 pseudobonds, 72 residues, 12 models selected  

> select #1/A:1-2 #2/A:1-2 #3/A:1-2 #4/A:1-2 #5/A:1-2 #6/A:1-2

12 atoms, 6 pseudobonds, 12 residues, 12 models selected  

> select #1/A #2/A #3/A #4/A #5/A #6/A

822 atoms, 4 bonds, 812 pseudobonds, 822 residues, 12 models selected  

> color (#!1-6 & sel) orange red

> select clear

> select #1/A:1-2 #2/A:1-2 #3/A:1-2 #4/A:1-2 #5/A:1-2 #6/A:1-2

12 atoms, 6 pseudobonds, 12 residues, 12 models selected  

> select #1/A #2/A #3/A #4/A #5/A #6/A

822 atoms, 4 bonds, 812 pseudobonds, 822 residues, 12 models selected  

> color (#!1-6 & sel) orange

> ui tool show "Color Actions"

> color sel tomato

> select clear

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1 #6/A:1

6 atoms, 6 residues, 6 models selected  

> select #1/A:1-11 #2/A:1-11 #3/A:1-11 #4/A:1-11 #5/A:1-11 #6/A:1-11

66 atoms, 60 pseudobonds, 66 residues, 12 models selected  

> color (#!1-6 & sel) yellow

> color (#!1-6 & sel) lime

> color (#!1-6 & sel) yellow

> select clear

> select #1/A:129 #2/A:129 #3/A:129 #4/A:129 #5/A:129 #6/A:129

6 atoms, 6 residues, 6 models selected  

> select #1/A:129-137 #2/A:129-137 #3/A:129-137 #4/A:129-137 #5/A:129-137
> #6/A:129-137

54 atoms, 48 pseudobonds, 54 residues, 12 models selected  

> ui tool show "Color Actions"

> color sel fire brick

> select #1/A:128 #2/A:128 #3/A:128 #4/A:128 #5/A:128 #6/A:128

6 atoms, 6 residues, 6 models selected  

> select #1/A:13-128 #2/A:13-128 #3/A:13-128 #4/A:13-128 #5/A:13-128
> #6/A:13-128

696 atoms, 4 bonds, 686 pseudobonds, 696 residues, 12 models selected  

> color sel salmon

> select #1/A:12-128 #2/A:12-128 #3/A:12-128 #4/A:12-128 #5/A:12-128
> #6/A:12-128

702 atoms, 4 bonds, 692 pseudobonds, 702 residues, 12 models selected  

> ui tool show "Color Actions"

> color sel tomato

> color sel indian red

> color sel chocolate

> color sel tomato

> select clear

> select #1/A:129-130 #2/A:129-130 #3/A:129-130 #4/A:129-130 #5/A:129-130
> #6/A:129-130

12 atoms, 6 pseudobonds, 12 residues, 12 models selected  

> select #1/A:129-137 #2/A:129-137 #3/A:129-137 #4/A:129-137 #5/A:129-137
> #6/A:129-137

54 atoms, 48 pseudobonds, 54 residues, 12 models selected  

> color sel blanched almond

> color sel black

> color sel fire brick

> color sel red

> select #1/A:98-128 #2/A:98-128 #3/A:98-128 #4/A:98-128 #5/A:98-128
> #6/A:98-128

186 atoms, 1 bond, 179 pseudobonds, 186 residues, 12 models selected  

> select #1/A:10-128 #2/A:10-128 #3/A:10-128 #4/A:10-128 #5/A:10-128
> #6/A:10-128

714 atoms, 4 bonds, 704 pseudobonds, 714 residues, 12 models selected  

> select #1/A:10-128 #2/A:10-128 #3/A:10-128 #4/A:10-128 #5/A:10-128
> #6/A:10-128

714 atoms, 4 bonds, 704 pseudobonds, 714 residues, 12 models selected  

> color sel light green

> color sel violet

> color sel pale goldenrod

> color sel khaki

> color sel light steel blue

> color sel burly wood

> color sel tan

> color sel lime

> color sel chartreuse

> color sel spring green

> color sel lime green

> color sel medium sea green

> color sel sea green

> color sel forest green

> color sel orange

> color sel dark orange

> select clear

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1 #6/A:1

6 atoms, 6 residues, 6 models selected  

> select #1/A:1-10 #2/A:1-10 #3/A:1-10 #4/A:1-10 #5/A:1-10 #6/A:1-10

60 atoms, 54 pseudobonds, 60 residues, 12 models selected  

> color sel yellow

[Repeated 1 time(s)]

> select clear

> select #1/A:130 #2/A:130 #3/A:130 #4/A:130 #5/A:130 #6/A:130

6 atoms, 6 residues, 6 models selected  

> select #1/A:130-131 #2/A:130-131 #3/A:130-131 #4/A:130-131 #5/A:130-131
> #6/A:130-131

12 atoms, 6 pseudobonds, 12 residues, 12 models selected  

> select #1/A:129 #2/A:129 #3/A:129 #4/A:129 #5/A:129 #6/A:129

6 atoms, 6 residues, 6 models selected  

> select #1/A:129-137 #2/A:129-137 #3/A:129-137 #4/A:129-137 #5/A:129-137
> #6/A:129-137

54 atoms, 48 pseudobonds, 54 residues, 12 models selected  

> color sel crimson

> color sel green

> color sel lime

> color sel tomato

> color sel chocolate

> color sel coral

> color sel yellow

> color sel lawn green

> color sel green

> color sel lawn green

> color sel forest green

> color sel medium sea green

> color sel olive drab

> color sel sea green

> color sel forest green

> color sel dark salmon

> color sel lime

> color sel red

> select clear

> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1 #6/A:1

6 atoms, 6 residues, 6 models selected  

> select #1/A:1-10 #2/A:1-10 #3/A:1-10 #4/A:1-10 #5/A:1-10 #6/A:1-10

60 atoms, 54 pseudobonds, 60 residues, 12 models selected  

> color (#!1-6 & sel) lime

> select clear

> select #1/B:1 #3/B:1 #4/B:1 #5/B:1 #6/B:1

5 atoms, 5 residues, 5 models selected  

> select #1/B:1-30 #3/B:1-30 #4/B:1-30 #5/B:1-30 #6/B:1-30

150 atoms, 8 bonds, 137 pseudobonds, 150 residues, 10 models selected  

> color (#!1,3-6 & sel) magenta

> ui tool show "Color Actions"

> color sel purple

> select clear

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:1-2

2 atoms, 1 pseudobond, 2 residues, 2 models selected  

> select #2/B:1-30

30 atoms, 2 bonds, 27 pseudobonds, 30 residues, 2 models selected  

> color (#!2 & sel) purple

> select clear

> lighting soft

[Repeated 1 time(s)]

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 2 time(s)]

> lighting full

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/all_6_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!6 models

> hide #!5 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/1_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/2_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!3 models

> hide #!2 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/3_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!4 models

> hide #!3 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/4_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!5 models

> hide #!4 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/5_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!6 models

> hide #!5 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/6_front.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/all_6_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/1_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!2 models

> hide #!1 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/2_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!3 models

> hide #!2 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/4_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/3_retro.png
> width 1339 height 734 supersample 3

> show #!4 models

> hide #!3 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/4_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!5 models

> hide #!4 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/5_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!6 models

> hide #!5 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/6_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> show #!3 models

> hide #!6 models

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/3_retro.png
> width 1339 height 734 supersample 3 transparentBackground true

> save
> /home/aria/Documents/CCRL2_BIOINFO/ritorno_da_Verona/clustering_analysis/clustering_only_bound/prova_cutframe_MD/session_all_clustertogethes.cxs

——— End of log from Wed Jul 5 18:15:50 2023 ———

opened ChimeraX session  




OpenGL version: 4.6 (Core Profile) Mesa 22.2.5-0ubuntu0.1~22.04.3
OpenGL renderer: RENOIR (renoir, LLVM 15.0.7, DRM 3.47, 5.19.0-46-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 20YGCTO1WW
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           6.6Gi       4.1Gi       118Mi        91Mi       2.4Gi       2.1Gi
	Swap:          2.0Gi       212Mi       1.8Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Lucienne [1002:164c] (rev c1)	
	Subsystem: Lenovo Lucienne [17aa:5097]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304282142
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (1)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Sessions
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash opening session

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