Opened 4 years ago

Closed 4 years ago

#5875 closed defect (can't reproduce)

Crash during or after session close, possibly in check_for_changes

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core 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-10-10.0.19043
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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\guiWindows fatal exception: code 0x.py8001010e", line 

301 in evWindows fatal exception: code 0x8001010e

enWindows fatal exception: code 0xt_8001010e

loWindows fatal exception: code 0x8001010e

op
  File "CWindows fatal exception: :code 0x\8001010eP

rogram Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program FiWindows fatal exception: lcode 0xe8001010es

\ChimeWindows fatal exception: rcode 0xa8001010eX

 1.3\Windows fatal exception: bcode 0xi8001010en

\libWindows fatal exception: \code 0xs8001010ei

te-pWindows fatal exception: acode 0xc8001010ek

ages\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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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\lWindows fatal exception: icode 0xb8001010e\

runpy.Windows fatal exception: pcode 0xy8001010e"

, line 87 in _Windows fatal exception: rcode 0xu8001010en

_coWindows fatal exception: dcode 0xe8001010e


  File "C:Windows fatal exception: \code 0xP8001010er

ogram Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  File Windows fatal exception: "code 0xC8001010e:

\ProgrWindows fatal exception: acode 0xm8001010e 

FilesWindows fatal exception: \code 0xC8001010eh

imeraWindows fatal exception: Xcode 0x 8001010e1

.3\bWindows fatal exception: icode 0xn8001010e\

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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-Windows fatal exception: pcode 0xa8001010ec

kages\Windows fatal exception: ccode 0xh8001010ei

meraxWindows fatal exception: \code 0xo8001010ep

en_coWindows fatal exception: mcode 0xm8001010ea

nd\diWindows fatal exception: acode 0xl8001010eo

g.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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-packagesWindows fatal exception: \code 0xc8001010eh

imeraWindows fatal exception: xcode 0x\8001010eo

pen_Windows fatal exception: ccode 0xo8001010em

mandWindows fatal exception: \code 0xd8001010ei

aloWindows fatal exception: gcode 0x.8001010ep

y", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimerWindows fatal exception: acode 0xX8001010e 

1.3\bin\lWindows fatal exception: icode 0xb8001010e\

site-pacWindows fatal exception: kcode 0xa8001010eg

es\ChimWindows fatal exception: ecode 0xr8001010ea

X_main.Windows fatal exception: pcode 0xy8001010e"

, 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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (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\open_command\dialog.py", line 107 in 
  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 0x8001010e

Thread 0x000041b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\changes.py", line 21 in check_for_changes
Windows fatal exception: access violation

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

===== 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 "E:\GST Review Paper Sonu\dmdelta1 - 1.cxs" format session

opened ChimeraX session  

> select ::name="GSH"

40 atoms, 38 bonds, 2 residues, 2 models selected  

> show sel target ab

> color sel byelement

> select #1.1/A

1950 atoms, 1739 bonds, 466 residues, 1 model selected  

> color sel dark gray

> select ::name="GSH"

40 atoms, 38 bonds, 2 residues, 2 models selected  

> color sel byelement

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A #1.2/A

Alignment identifier is 1  

> select #1.1/A:3 #1.2/A:3

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1.1/A:3-6 #1.2/A:3-6

86 atoms, 90 bonds, 8 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [2-5] RMSD: 40.678  
  

> hide #1.1 models

> show #1.1 models

> select #1.1

1950 atoms, 1739 bonds, 466 residues, 1 model selected  

> ~select #1.1

Nothing selected  

> select #1.1/A:3-4 #1.2/A:3-4

38 atoms, 38 bonds, 4 residues, 2 models selected  

> select #1.1/A:3-7 #1.2/A:3-7

102 atoms, 106 bonds, 10 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [2-6] RMSD: 40.756  
  

> select #1.1/A:10 #1.2/A:10

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1.1/A:10-24 #1.2/A:10-24

204 atoms, 204 bonds, 30 residues, 2 models selected  
Seqview [ID: 1] region 2 chains [9-23] RMSD: 32.949  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

Alignment identifier is 1.1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.2/A

Alignment identifier is 1.2/A  

> select #1.1/A:3

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

> select #1.1/A:3-6

43 atoms, 45 bonds, 4 residues, 1 model selected  

> color sel red

> select #1.1/A:28

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

> select #1.1/A:28-31

34 atoms, 33 bonds, 4 residues, 1 model selected  

> color sel red

> select #1.1/A:55

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

> select #1.1/A:55-58

30 atoms, 29 bonds, 4 residues, 1 model selected  

> color sel red

> select #1.1/A:61

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

> select #1.1/A:61-64

38 atoms, 40 bonds, 4 residues, 1 model selected  

> color sel red

> select #1.2/A:3

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

> select #1.2/A:3-6

43 atoms, 45 bonds, 4 residues, 1 model selected  

> color sel orange

> select #1.2/A:28

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

> select #1.2/A:28-31

34 atoms, 33 bonds, 4 residues, 1 model selected  

> color sel orange

> select #1.2/A:55

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

> select #1.2/A:55-58

30 atoms, 29 bonds, 4 residues, 1 model selected  

> color sel orange

> select #1.2/A:61

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

> select #1.2/A:61-64

38 atoms, 40 bonds, 4 residues, 1 model selected  

> color sel orange

> select #1.2/A:10

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

> select #1.2/A:10

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

> select #1.1/A:10

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

> select #1.1/A:10-24

102 atoms, 102 bonds, 15 residues, 1 model selected  

> color sel blue

> select #1.1/A:33

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

> select #1.1/A:33-46

114 atoms, 116 bonds, 14 residues, 1 model selected  

> select #1.1/A:10-24,33-46,65-78,87-120,124-142,154-170,173-191,193-208

1205 atoms, 1230 bonds, 148 residues, 1 model selected  

> select #1.1/A:33

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

> select #1.1/A:33-36

30 atoms, 29 bonds, 4 residues, 1 model selected  

> select #1.1/A:33

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

> select #1.1/A:33-41

70 atoms, 70 bonds, 9 residues, 1 model selected  

> select #1.1/A:33

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

> select #1.1/A:33-40

61 atoms, 61 bonds, 8 residues, 1 model selected  

> select #1.1/A:33

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

> select #1.1/A:33-39

53 atoms, 53 bonds, 7 residues, 1 model selected  

> select #1.1/A:33

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

> select #1.1/A:33-41

70 atoms, 70 bonds, 9 residues, 1 model selected  

> color sel blue

> select #1.1/A:42

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

> select #1.1/A:42-46

44 atoms, 45 bonds, 5 residues, 1 model selected  

> color sel blue

> select #1.1/A:42

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

> select #1.1/A:42

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

> select #1.1/A:41

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

> select #1.1/A:41

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

> select #1.1/A:61

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

> select #1.1/A:61-64

38 atoms, 40 bonds, 4 residues, 1 model selected  

> select #1.1/A:65

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

> select #1.1/A:65-78

116 atoms, 117 bonds, 14 residues, 1 model selected  

> color sel blue

> select #1.1/A:87

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

> select #1.1/A:87-120

291 atoms, 300 bonds, 34 residues, 1 model selected  

> color sel blue

> select #1.1/A:124

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

> select #1.1/A:124-142

158 atoms, 162 bonds, 19 residues, 1 model selected  

> save "E:/GST Review Paper Sonu/dmdelta2 - 1.cxs"

> close session


===== 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  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GT 740/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Microsoft Windows 10 Education (Build 19043)
Memory: 34,301,300,736
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
OSLanguage: en-US
Locale: ('en_US', '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 Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash during or after session close, possibly in check_for_changes

comment:2 by Eric Pettersen, 4 years ago

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