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#6390 accepted defect

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

Reported by:	adrian.young@…	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-10-10.0.19042
ChimeraX Version: 1.3rc202112010754 (2021-12-01 07:54:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commaWindows fatal exception: code 0x8001010e

nds\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX Windows fatal exception: code 0x8001010e

1Windows fatal exception: code 0x8001010e

.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

2447 in _parsWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

e_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\binWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010eWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _procesWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

s_positional_arguments
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\ProgWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

ram Files\ChimeraXWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-pWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

ackages\ChimeraX_mWindows fatal exception: code 0x8001010e

ain.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\ProWindows fatal exception: code 0x8001010e

gram Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\clWindows fatal exception: code 0x8001010e

i.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimerWindows fatal exception: code 0x8001010e

aX_Windows fatal exception: code 0x8001010e

main.Windows fatal exception: code 0x8001010e

py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\sitWindows fatal exception: code 0x8001010e

e-packages\chimerax\core\commands\Windows fatal exception: code 0x8001010e

cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\libWindows fatal exception: code 0x8001010e

\site-packages\chimerax\core\cWindows fatal exception: code 0x8001010e

ommands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX Windows fatal exception: code 0x8001010e

1.3rc202112010754\bin\lib\site-packages\ChimeraX_Windows fatal exception: code 0x8001010e

main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\PWindows fatal exception: rogramWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

 Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\cocode 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

re\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py"Windows fatal exception: code 0x8001010e

, line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rcWindows fatal exception: code 0xWindows fatal exception: code 0x8001010e

8001010e

202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packagWindows fatal exception: code 0x8001010e

es\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program FWindows fatal exception: code 0x8001010e

iWindows 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 0xWindows 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: les\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\sitcode 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

e-packages\CWindows 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: 8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

code 0x8001010e

Windows fatal exception: code 0x8001010e

himeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraWindows fatal exception: code 0x8001010e

X 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\ProgrWindows fatal exception: code 0x8001010e

am Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program FilWindows fatal exception: code 0x8001010e

es\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc20211201Windows fatal exception: code 0x8001010e

0754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commandWindows fatal exception: code 0x8001010e

s\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Windows fatal exception: code 0x8001010e

Program Files\ChimeraX 1.3rc202112010754\bin\lib\siWindows fatal exception: code 0x8001010e

te-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc20211Windows fatal exception: code 0x8001010e

2010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 1028 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\sWindows fatal exception: code 0x8001010e

ite-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1210 in parse
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-Windows fatal exception: code 0x8001010e

packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\cWindows fatal exception: code 0x8001010e

ore\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimeraxWindows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

\ui\gui.pWindows fatal exception: code 0x8001010e

y", line 1028 in 
  File "C:\Program Files\Windows fatal exception: code 0x8001010e

ChimWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

eraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\ProWindows fatal exception: code 0x8001010e

gram Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.pWindows 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

y", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\Windows fatal exception: code 0x8001010e

ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_Windows fatal exception: code 0x8001010e

as_main
Windows fatal exception: code 0x8001010e

Thread 0x00003530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\libWindows fatal exception: code 0x8001010e

\json\__init__.py", line 180 in dump
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\siteWindows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

-packWindows fatal exception: code 0x8001010e

ages\chimerax\core\history.py", line 109 in save
Windows fatal exception: code 0x8001010e

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: Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

code 0x8001010e

Windows fatal exception: 8001010e

Windows fatal exception: code 0x8001010e

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 0x8001010eWindows 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: 1.3rc202112010754 (2021-12-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\alyou\OneDrive - McGill
> University\Documents\Liturature\Chantal
> Autexier\Telomerase\Structures\PDBs\Telomerase-TPP1 highlighted
> interactions.cxs" format session

registering illegal selector name "Motif 3"  

registering illegal selector name "TEN -B"  

registering illegal selector name "Motif 3-B"  

registering illegal selector name "IFD_B"  

opened ChimeraX session  

> select IFDS

760 atoms, 776 bonds, 95 residues, 1 model selected  

> show sel cartoons

> select #3/A:721

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

> show sel atoms

> style sel ball

Changed 7 atom styles  

> select #3/A:735

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

> show sel atoms

> style sel ball

Changed 7 atom styles  

> select #3/A:800

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

> style sel ball

Changed 9 atom styles  

> show sel atoms

> hide sel atoms

> select #3/A:772

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/A:771

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

> show sel atoms

> style sel ball

Changed 7 atom styles  

> select #3/A:785

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

> style sel ball

Changed 7 atom styles  

> show sel atoms

> select #3/A:726

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

> show sel atoms

> style sel ball

Changed 7 atom styles  

> color (#!3 & sel) byelement

> select #3/A:813

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

> show sel atoms

> style sel ball

Changed 8 atom styles  

> color (#!3 & sel) byelement

> select #3/A:722

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

> style sel ball

Changed 9 atom styles  

> show sel atoms

> color (#!3 & sel) byelement

> ui tool show H-Bonds

> hbonds sel showDist true interModel false twoColors true intraRes false
> select true reveal true

3 hydrogen bonds found  
1 strict hydrogen bonds found  

> select #3/A:813

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

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

2 hydrogen bonds found  
1 strict hydrogen bonds found  

> select #3/A:813

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

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

2 hydrogen bonds found  
1 strict hydrogen bonds found  

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

> select #3/A:781

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

> select #3/A:733

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

> select #3/A:729

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

> select #3/A:730

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

> select #3/A:731

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

> select #3/A:732

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

> select #3/A:729

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

> select #3/A:728

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

> select #3/A:727

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

> show sel atoms

> style sel ball

Changed 9 atom styles  

> select #3/A:724

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

> style sel ball

Changed 11 atom styles  

> show sel atoms

> select #3/A:725

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

> select #3/A:724

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

> select add #3/A:727@CB

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

> color (#!3 & sel) byelement

> select #3/A:727

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

> color (#!3 & sel) byelement

> select #3/A:810

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

> select #3/A:807

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

> style sel ball

Changed 8 atom styles  

> show sel atoms

> color (#!3 & sel) byelement

> select #3/A:814

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

> show sel atoms

> color (#!3 & sel) byelement

> style sel ball

Changed 6 atom styles  

> select #3/A:810

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

> select #3/A:803

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

> show sel atoms

> style sel ball

Changed 6 atom styles  

> color (#!3 & sel) byelement

> select #3/O

955 atoms, 968 bonds, 3 pseudobonds, 120 residues, 2 models selected  

> show sel cartoons

> select #3/A:807

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

> select add #3/A:803

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

> select add #3/A:727

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #3/A:724

34 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #3/A:722

43 atoms, 38 bonds, 5 residues, 2 models selected  

> select add #3/A:814

49 atoms, 43 bonds, 6 residues, 2 models selected  

> select add #3/A:726

56 atoms, 49 bonds, 7 residues, 2 models selected  

> select add #3/A:813

64 atoms, 56 bonds, 8 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

16 hydrogen bonds found  
7 strict hydrogen bonds found  

> hbonds sel dashes 6 showDist true interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

16 hydrogen bonds found  
7 strict hydrogen bonds found  

> select #3/A:893@N

1 atom, 1 residue, 1 model selected  

> select add #3/A:893@CA

2 atoms, 1 residue, 2 models selected  

> select add #3/A:893@C

3 atoms, 1 residue, 2 models selected  

> select add #3/A:893@O

4 atoms, 1 residue, 2 models selected  

> style sel ball

Changed 4 atom styles  

> color (#!3 & sel) byelement

> select #3/A:731@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select #3/A:731

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

> style sel ball

Changed 6 atom styles  

> color (#!3 & sel) byelement

> ui mousemode right "move label"

> select #2/A

7626 atoms, 7811 bonds, 3 pseudobonds, 951 residues, 2 models selected  

> show sel cartoons

> color (#!2 & sel) #ffff7fff

> color (#!2 & sel) #aaffffff

> color (#!2 & sel) #aaffff01

> color (#!2 & sel) #aaffff0f

> color (#!2 & sel) #00007f0f

> color (#!2 & sel) #0055000f

> color (#!2 & sel) #00aa7f0f

> color (#!2 & sel) #aa557f0f

> color (#!2 & sel) #ff00ff0f

> color (#!2 & sel) #5555ff0f

> color (#!2 & sel) #5500ff0f

> color (#!2 & sel) #0000000f

> select #2/A:893

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

> select Motif3A

400 atoms, 406 bonds, 49 residues, 1 model selected  

> show sel cartoons

> color (#!3 & sel) red

> select #3/N

461 atoms, 517 bonds, 1 pseudobond, 22 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:543

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

> select #3/A:543-610

602 atoms, 617 bonds, 68 residues, 1 model selected  

> select #3/A:543-544

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:543-545

28 atoms, 28 bonds, 3 residues, 1 model selected  

> select #3/A:543-544

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:543-594

462 atoms, 476 bonds, 52 residues, 1 model selected  

> name frozen MotifT sel

> show sel cartoons

> show sel atoms

> hide sel atoms

> color (#!3 & sel) magenta

> select clear

> select #2/A:570

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

> select add #3/A:570

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

> select add #3/A:571

26 atoms, 23 bonds, 3 residues, 3 models selected  

> select add #2/A:569

35 atoms, 31 bonds, 4 residues, 3 models selected  

> select add #3/A:568

46 atoms, 42 bonds, 5 residues, 3 models selected  

> select add #3/A:569

55 atoms, 50 bonds, 6 residues, 3 models selected  

> show sel atoms

> style sel ball

Changed 55 atom styles  

> color (#!2-3 & sel) byelement

> select #3/A:570

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

> ui tool show H-Bonds

> hbonds sel dashes 6 showDist true interModel false twoColors true intraRes
> false select true reveal true retainCurrent true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:1021

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

> select #3/A:940-1021

671 atoms, 683 bonds, 82 residues, 1 model selected  

> name frozen MotifEI sel

> show sel cartoons

> color (#!3 & sel) white

> color (#!3 & sel) black

> select #3/A:1028

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

> select #3/A:1028-1051

189 atoms, 192 bonds, 24 residues, 1 model selected  

> name frozen MotifEII sel

> show sel cartoons

> color (#!3 & sel) dim gray

> select #3/A:1060

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:1060-1077

128 atoms, 132 bonds, 18 residues, 1 model selected  

> select #3/A:1060-1061

9 atoms, 8 bonds, 2 residues, 1 model selected  

> select #3/A:1060-1099

308 atoms, 316 bonds, 40 residues, 1 model selected  

> select #3/A:1063

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:1063-1099

294 atoms, 302 bonds, 37 residues, 1 model selected  

> name frozen MotifEIII sel

> show sel cartoons

> color (#!3 & sel) gray

> color (#!3 & sel) dark gray

> select #3/A:1119

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

> select #3/A:1119-1123

33 atoms, 33 bonds, 5 residues, 1 model selected  

> name frozen MotifEIV sel

> color (#!3 & sel) light gray

> show sel cartoons

> save "C:/Users/alyou/Documents/Telomerase - Labeled Motifs.cxs"

> cd "C:/Users/alyou/OneDrive - McGill University/Documents/Liturature/Chantal
> Autexier/Telomerase/Structures/PDBs"

Current working directory is: C:\Users\alyou\OneDrive - McGill
University\Documents\Liturature\Chantal Autexier\Telomerase\Structures\PDBs  


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

Log:
UCSF ChimeraX version: 1.3rc202112010754 (2021-12-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.8682
OpenGL renderer: Intel(R) HD Graphics 615
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Go
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 8,468,795,392
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Pentium(R) CPU 4415Y @ 1.60GHz
OSLanguage: en-US
Locale: ('en_CA', '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: 2.0.8
    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: 1.3rc202112010754
    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: 2.7.3
    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: 1.11.2
    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 → 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

Hi Adrian,

Thanks for reporting this problem. Were you using the File→Open dialog when this crash occurred? If so, is this the first time it's happened or has it happened before?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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