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

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.4.dev202203170703 (2022-03-17 07:03:24 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010eWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x

Windows fatal exception: Windows fatal exception: 8001010e

code 0xWindows fatal exception: code 0x8001010e

code 0x8001010e

Thread 0x00001c74 (most recent call first):
8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py"code 0xWindows fatal exception: code 0x8001010e

, line 1358001010e



Windows fatal exception: code 0xWindows fatal exception: code 0x in show_open_file_dialog
8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e8001010e

code 0x8001010e

  File 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

8001010eWindows fatal exception: code 0xC8001010e

:\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: Windows fatal exception: code 0x8001010e

Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\diWindows fatal exception: code 0xcode 0x8001010ecode 0x

8001010e

aWindows fatal exception: code 0xlo8001010e

8001010eWindows fatal exception: gcode 0x8001010e

.pyWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

", line Windows fatal exception: code 0x8001010e

107 in 

Windows fatal exception: code 0x8001010e


Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

CWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chWindows fatal exception: code 0ximerax\ui8001010e

\gui.py"Windows fatal exception: , line 318code 0x8001010e

 in Windows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

vWindows fatal exception: code 0x8001010e

eWindows fatal exception: code 0x8001010e

nWindows fatal exception: code 0x8001010e

tWindows fatal exception: code 0x8001010e

_Windows fatal exception: code 0x8001010e

lWindows fatal exception: code 0x8001010e

oWindows fatal exception: code 0x8001010e

op
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\Windows fatal exception: code 0xbin\lib\site-packages\ChimeraX_main.py"8001010e

, line 867Windows fatal exception: code 0x in 8001010e

init
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.4.devcode 0x8001010e

202203170703\bin\lib\site-packages\ChimeraX_main.py"Windows fatal exception: code 0x, line 1018 in 8001010e


  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.pWindows fatal exception: code 0x8001010e

y", line 87 in Windows fatal exception: code 0x8001010e

_Windows fatal exception: code 0x8001010e

rWindows fatal exception: code 0xun_c8001010eode


  File "C:\Program Files\ChimeraX 1.4.dev20220317Windows fatal exception: code 0x08001010e

703\bin\lib\runpy.py", line 197Windows fatal exception: code 0x in _run_module_as_8001010e

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

8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packageWindows fatal exception: code 0xs\chimerax\open_command\dialog.py", line 1358001010e

 in show_open_file_dialog
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.4.dev20220317code 0x8001010e0703\bin\lib\site-packages\chimerax\open_co

mmand\dialog.py"Windows fatal exception: , line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py"code 0x8001010e, line 

318 in event_loop
Windows fatal exception:   File "C:\Program Ficode 0x8001010e

les\ChimeraX 1.4.dev202203170703\bin\lib\siteWindows fatal exception: code 0x-8001010e

packages\ChimeraX_main.py", line Windows fatal exception: code 0x867 in 8001010e

init
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\Chimcode 0x8001010eeraX_main.py"

, line 1018 in Windows fatal exception: code 0x
8001010e  File 

"C:\Program FileWindows fatal exception: s\ChimeraX 1.4.code 0x8001010edev202203170703\bin\lib\runpy.py"

, line 87 in Windows fatal exception: code 0x8001010e

_Windows fatal exception: code 0x8001010e

run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py"Windows fatal exception: code 0x, line 1978001010e

 in _run_module_as_main
Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e8001010e

Thread 0x00001c74 (most recent call first):
  File 

"C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimeWindows fatal exception: code 0xra8001010e

x\open_command\dialog.py"Windows fatal exception: code 0x, line 8001010e

135 in Windows fatal exception: code 0x8001010e

show_open_file_dialog
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py"code 0x, line 107 in 8001010e


  File "C:\Program Files\ChWindows fatal exception: code 0xi8001010e

meraX 1.4.dev202203170703\bin\lib\site-pWindows fatal exception: code 0xa8001010eckages\chimerax\ui\gui.py", line 318 in 

eWindows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010event_loop
  File 

"C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py"Windows fatal exception: code 0x, line 8678001010e in 

init
Windows fatal exception: code 0x  File "C:\Program Files\Chime8001010eraX 1.4.dev202203170703\bin\lib

\site-Windows fatal exception: code 0xp8001010eackages\ChimeraX_main.py", line 1018 in 


Windows fatal exception: code 0x  File 8001010e

"C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py"Windows fatal exception: code 0x, line 878001010e in 

_run_code
  File "C:\Program Files\ChimeraX 1.4.dev2022031707Windows fatal exception: 03\bin\lib\runpy.py"code 0x8001010e, line 197 in 

_run_module_as_main
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Thread 0x00001c74Windows fatal exception:  (most recent call first):
code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

  File "Windows fatal exception: C:\Prcode 0xogram Files\C8001010e

hWindows fatal exception: code 0x8001010e

iWindows fatal exception: code 0x8001010e

meraX 1.4.dev202203170703\bin\lib\site-packagWindows fatal exception: code 0xes\chimerax\open_command\dialog.py8001010e

", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001c74 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\graphics\opengl.py", line 235 in swap_buffers
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\graphics\opengl.py", line 496 in swap_buffers
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\statusbar.py", line 152 in status
  File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-packages\chimerax\ui\statusbar.py", line 84 in _expose_event
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

===== Log before crash start =====
Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX
1.4.dev202203170703\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "", line 1030, in _gcd_import  
File "", line 1007, in _find_and_load  
File "", line 986, in _find_and_load_unlocked  
File "", line 680, in _load_unlocked  
File "", line 850, in exec_module  
File "", line 228, in _call_with_frames_removed  
File "C:\Users\mpapa\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 51, in   
__version__ = _version()  
File "C:\Users\mpapa\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\pkg_resources\\__init__.py", line 891, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\pkg_resources\\__init__.py", line 782, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 6.1.1
(c:\program files\chimerax 1.4.dev202203170703\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 359, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 6.1.1 (c:\program files\chimerax
1.4.dev202203170703\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=4.2'), {'ChimeraX-ISOLDE'})  
  

> lighting soft

> set bgColor white

> graphics silhouettes true

UCSF ChimeraX version: 1.4.dev202203170703 (2022-03-17)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "G:\\\My Drive\\\My_Projects\\\b2AR-
> Gs\\\Manuscripts\\\01_GTP_Dissociation\\\Figures\\\Figure_1\\\Combined_GTP\\\HighRes_with_Gaussian.cxs"

Opened map series Z785.mrc as #1, 20 images, grid size 328,328,328, pixel
0.868, shown at level 0.165, step 1, values float32  
Opened map series Frame_G_00.mrc as #6, 20 images, grid size 328,328,328,
pixel 0.868, shown at level 0.0369, step 2, values float32  
opened ChimeraX session  

> hide #!6 models

> ui tool show "Side View"

> save "G:/My Drive/My_Projects/b2AR-
> Gs/Manuscripts/01_GTP_Dissociation/Figures/Figure_2/Frame_1.png" width 798
> height 793 supersample 3 transparentBackground true

QAccessibleTable::child: Invalid index at: 2 0  

QAccessibleTable::child: Invalid index at: 2 1  

QAccessibleTable::child: Invalid index at: 2 2  

QAccessibleTable::child: Invalid index at: 2 3  

> save "G:/My Drive/My_Projects/b2AR-
> Gs/Manuscripts/01_GTP_Dissociation/Figures/Figure_2/Frame_1_Zoom.png" width
> 798 height 793 supersample 3 transparentBackground true

> save "G:/My Drive/My_Projects/b2AR-
> Gs/Manuscripts/01_GTP_Dissociation/Figures/Figure_2/Frame_10_Zoom.png" width
> 798 height 793 supersample 3 transparentBackground true

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> transparency sel 0

> select /R

3497 atoms, 3579 bonds, 9 pseudobonds, 492 residues, 4 models selected  

> color sel #cd5aff

> select /A

5155 atoms, 5244 bonds, 7 pseudobonds, 702 residues, 5 models selected  

> color sel #daa520

> select /L

34 atoms, 36 bonds, 2 residues, 2 models selected  

> color sel #ff8c00

> select /B

4846 atoms, 4939 bonds, 1 pseudobond, 663 residues, 3 models selected  

> color sel #89bdd5

> select /G

660 atoms, 670 bonds, 101 residues, 2 models selected  

> color sel #27706a

> select /N

64 atoms, 68 bonds, 2 residues, 2 models selected  

> color sel #00c85d

> show #!2 models

> hide #!2 models

> show #!3 models

> select /A:88-202

1609 atoms, 1641 bonds, 2 pseudobonds, 221 residues, 3 models selected  

> transparency sel 70

> transparency sel 70 target a

> select #2-3

13354 atoms, 13624 bonds, 17 pseudobonds, 1845 residues, 4 models selected  

> color zone #1 near sel distance 20

> hide #!3 models

> select up

13354 atoms, 13624 bonds, 17 pseudobonds, 1845 residues, 4 models selected  

> select up

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 7 models selected  

> select up

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 7 models selected  

> select down

13354 atoms, 13624 bonds, 17 pseudobonds, 1845 residues, 4 models selected  

> select down

17 pseudobonds, 2 models selected  

> select down

17 pseudobonds, 2 models selected  

> select up

13354 atoms, 13624 bonds, 17 pseudobonds, 1845 residues, 4 models selected  

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> transparency sel 0 target a

> select /A:88-202

1609 atoms, 1641 bonds, 2 pseudobonds, 221 residues, 3 models selected  

> transparency sel 70 target a

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> save "G:/My Drive/My_Projects/b2AR-
> Gs/Manuscripts/01_GTP_Dissociation/Figures/Figure_2/Frame_15_Zoom.png" width
> 798 height 793 supersample 3 transparentBackground true

> save "G:/My Drive/My_Projects/b2AR-
> Gs/Manuscripts/01_GTP_Dissociation/Figures/Figure_2/Frame_20_Zoom.png" width
> 798 height 793 supersample 3 transparentBackground true

> select /A:364-369

75 atoms, 73 bonds, 12 residues, 2 models selected  

> color sel lilac

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

> color sel purple

> show #!2 models

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel plum

> select /A:53-64

163 atoms, 160 bonds, 23 residues, 3 models selected  

> color sel yellow

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> hide #!2 models

> show #!3 models

> select /A:53-68

184 atoms, 181 bonds, 27 residues, 3 models selected  

> color sel yellow

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> select /A:370-394

414 atoms, 416 bonds, 50 residues, 2 models selected  

> color sel lightskyblue

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> hide #!3 models

> select /A:370-394

414 atoms, 416 bonds, 50 residues, 2 models selected  

> show #!2 models

> select up

459 atoms, 461 bonds, 57 residues, 2 models selected  

> select /A:53-68

184 atoms, 181 bonds, 27 residues, 3 models selected  

> select /A:370-394

414 atoms, 416 bonds, 50 residues, 2 models selected  

> select /A:364-369

75 atoms, 73 bonds, 12 residues, 2 models selected  

> color sel fuscia

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

> color sel fuscia

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

> color sel fucsia

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

> color sel fuchsia

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> hide #!2 models

> show #!2 models

> hide #!2 models

> select /A:370-394

414 atoms, 416 bonds, 50 residues, 2 models selected  

> color sel medium spring green

> select #2-4

14256 atoms, 14536 bonds, 17 pseudobonds, 1962 residues, 5 models selected  

> color zone #1 near sel distance 20

> show #!2 models


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

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX
1.4.dev202203170703\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\mpapa\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\mpapa\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\pkg_resources\\__init__.py", line 891, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\pkg_resources\\__init__.py", line 782, in resolve  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 6.1.1
(c:\program files\chimerax 1.4.dev202203170703\bin\lib\site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX-ISOLDE'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 359, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 503, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX 1.4.dev202203170703\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 6.1.1 (c:\program files\chimerax
1.4.dev202203170703\bin\lib\site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=4.2'), {'ChimeraX-ISOLDE'})  
  

> lighting soft

> set bgColor white

> graphics silhouettes true

UCSF ChimeraX version: 1.4.dev202203170703 (2022-03-17)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.14 30.0.13014.8
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Locale: en_US.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 7415 2-in-1
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 16,483,872,768
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203170703
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.9
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.30.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.4.0
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

pre-Python upgrade