Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been deleted

[uma.muthurajan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.0 (2020-05-08)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\Users\Uma\Desktop\050621hydrogenbonds.cxs format session

Log from Thu May 6 10:12:12 2021UCSF ChimeraX version: 1.0rc202005080235
(2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  

> open C:/Users/Uma/Downloads/class792_redo_coot_isolde.pdb

Summary of feedback from opening
C:/Users/Uma/Downloads/class792_redo_coot_isolde.pdb  
---  
warning | Ignored bad PDB record found on line 23468  
END  
  
Chain information for class792_redo_coot_isolde.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
  

> toolshed show "Color Actions"

> set bgColor white

> hide atoms

> show cartoons

> lighting simple

> cartoon style nucleic xsection oval width 1 thickness 1

> select /I

4682 atoms, 5054 bonds, 1 model selected  

> color sel dark gray

> select /J

4646 atoms, 5007 bonds, 1 model selected  

> color sel dark gray

> nucleotides sel atoms

> style nucleic & sel stick

Changed 4646 atom styles  

> show sel atoms

> select /J

4646 atoms, 5007 bonds, 1 model selected  

> select /I

4682 atoms, 5054 bonds, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 4682 atom styles  

> show sel atoms

> cartoon style nucleic xsection oval width 0.5 thickness 0.5

> select clear

> select /A

1618 atoms, 1630 bonds, 1 model selected  

> toolshed show "Color Actions"

> set bgColor light steel blue

> set bgColor white

No target buttons for the coloring action are checked  

> select clear

> select /A

1618 atoms, 1630 bonds, 1 model selected  

> toolshed show "Color Actions"

No target buttons for the coloring action are checked  

> color sel light steel blue target c

> select clear

> select /E

1686 atoms, 1698 bonds, 1 model selected  

> color sel light steel blue target c

> select /B

1273 atoms, 1280 bonds, 1 model selected  

> color sel #aa99ffff

> color sel #a9f7bcff

> select /F

1461 atoms, 1469 bonds, 1 model selected  

> color sel #aaf7bcff

> color sel #aaaaffff

> color sel #aa99ffff

> color sel #a9f7bcff

> select /C

1735 atoms, 1745 bonds, 1 model selected  

> color sel #aa99ffff

> color sel #eeddffff

> color sel #edf7b6ff

> select /G

1669 atoms, 1679 bonds, 1 model selected  

> color sel #edf7b7ff

> color sel #edf7b6ff

> select /D

1463 atoms, 1474 bonds, 1 model selected  

> color sel #eeddffff

> color sel #ff7799ff

> color sel #f79f97ff

> select /H

1452 atoms, 1463 bonds, 1 model selected  

> color sel #f7a098ff

> color sel #ff77aaff

> color sel #ff7799ff

> color sel #f79f97ff

> select /K

1538 atoms, 1544 bonds, 1 model selected  

> color sel orchid target c

> select clear

> lighting soft

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting full

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting full

> lighting full

> lighting simple

> lighting soft

> lighting simple

> select /K:421

7 atoms, 6 bonds, 1 model selected  

> select /K:420

14 atoms, 13 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> hide sel atoms

> show sel atoms

> hide sel atoms

> style sel stick

Changed 35 atom styles  

> show sel atoms

> color sel byelement

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> undo

> undo

> show (sel-residues & sidechain) target ab

> select clear

> select /K:420@HG1

1 atom, 1 model selected  

> select clear

> hide target a

> undo

> select /K:422@HB

1 atom, 1 model selected  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /J:66

30 atoms, 31 bonds, 1 model selected  

> view

> view sel

> clip off

> ui mousemode right clip

> select clear

> ui mousemode right clip

> select /J:67

32 atoms, 34 bonds, 1 model selected  

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> select clear

> select /J:67

32 atoms, 34 bonds, 1 model selected  

> hide #* target a

> show sel target ab

> undo

> undo

> show sel atoms

> select clear

> select /K:421

7 atoms, 6 bonds, 1 model selected  

> style sel stick

Changed 7 atom styles  

> show sel atoms

> show sel target ab

> show sel atoms

> style sel stick

Changed 7 atom styles  

> hide sel cartoons

> show sel atoms

> hide sel cartoons

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /J:67

32 atoms, 34 bonds, 1 model selected  

> select /J:66

30 atoms, 31 bonds, 1 model selected  

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> undo

> select clear

> select /K:421@CA

1 atom, 1 model selected  

> view sel

> clip off

> select clear

> clip on

Expected a keyword  

> undo

> undo

> select clear

> select /J:67

32 atoms, 34 bonds, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select H

10453 atoms, 1 model selected  

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> color sel byelement

> select clear

> select /K:422@OG1

1 atom, 1 model selected  

> show Dist

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

> save C:/Users/Uma/Desktop/050621hydrogenbonds.cxs

opened ChimeraX session  

> select clear

> hide sel atoms

> show sel cartoons

> select clear

> select /K:422@CG2

1 atom, 1 model selected  

> select /K:422@OG1

1 atom, 1 model selected  

> hide sel atoms

> select clear

> select /K:422@CG2

1 atom, 1 model selected  

> hide sel atoms

> hide sel atoms

> show sel cartoons

> hide sel atoms

> hide sel atoms

> hide sel atoms

> hide sel target ab

> select /K:420@CG2

1 atom, 1 model selected  

> select /K:420@CB

1 atom, 1 model selected  

> hide sel target a

> select /K:420@CA

1 atom, 1 model selected  

> hide sel target a

> show sel cartoons

> select /K:422

14 atoms, 13 bonds, 1 model selected  

> show sel cartoons

> select clear

> select /K

1538 atoms, 1544 bonds, 1 model selected  

> show sel cartoons

> select clear

> clip off

> select /K:404

14 atoms, 13 bonds, 1 model selected  

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> hide sel atoms

> style sel stick

Changed 22 atom styles  

> show sel atoms

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select up

2 atoms, 1 bond, 1 model selected  

> select down

1 bond, 1 model selected  

> color sel byelement

> select clear

> color sel byelement

> color sel blue

> select clear

> color sel blue

> select clear

> select clear

> select /K:405@CG

1 atom, 1 model selected  

> select clear

> color sel byhetero

> color sel byelement

> select clear

> select /K:405@NZ

1 atom, 1 model selected  

> color sel blue

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> toolshed show "Color Actions"

> color sel yellow

> undo

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> color sel byelement

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> view sel

> clip off

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> color sel byelement

> select clear

> select clear

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> toolshed show "Color Actions"

> color sel orchid

> select clear

> select /K:409

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /K:418

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /K:394

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /K:425

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /K:441

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /K:442

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> ui mousemode right clip

> select /K:405

22 atoms, 21 bonds, 1 model selected  

> view sel

> select clear

> clip off

> save "C:/Users/Uma/Desktop/chimeraX pics and
> movies/04222021/050621hbonds.cxs"

> select /J:68

32 atoms, 33 bonds, 1 model selected  

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> show sel target ab

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> show sel atoms

> select clear

> select clear

> select /J:66@P

1 atom, 1 model selected  

> select clear

> select clear

> select /J

4646 atoms, 5007 bonds, 1 model selected  

> show sel cartoons

> show (sel-residues & sidechain) target ab

> color sel byelement

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select /I

4682 atoms, 5054 bonds, 1 model selected  

> select /J

4646 atoms, 5007 bonds, 1 model selected  

> show sel target ab

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select P

294 atoms, 1 model selected  

> show sel atoms

> select O

2959 atoms, 1 model selected  

> select clear

> select /I

4682 atoms, 5054 bonds, 1 model selected  

> style sel stick

Changed 4682 atom styles  

> select phosphate

1460 atoms, 1168 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 1460 atom styles  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> ui mousemode right clip

> select clear

> ui mousemode right clip

> clip off

> select /K:438

22 atoms, 21 bonds, 1 model selected  

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 22 atom styles  

> select H

10453 atoms, 1 model selected  

> hide sel atoms

> select clear

> select clear

> toolshed show "Color Actions"

> color sel orchid

> color sel byelement

> color sel byelement

> color sel orchid

> select clear

> color sel orchid

> select clear

> select /K:405@CB

1 atom, 1 model selected  

> select clear

> select /K

1538 atoms, 1544 bonds, 1 model selected  

> toolshed show "Color Actions"

> color sel orchid

> select clear

> select /K:438@NZ

1 atom, 1 model selected  

> color sel blue

> undo

> select clear

> select N1

Nothing selected  

> select N1+

Nothing selected  

> color sel byelement

> select clear

> color sel byelement

> select clear

> select /K:442@CD

1 atom, 1 model selected  

> toolshed show "Color Actions"

> color sel orchid

> select clear

> color sel orchid

> select clear

> select /K:441@NZ

1 atom, 1 model selected  

> color sel blue

> undo

> undo

> color sel byelement

> color sel byelement

> select clear

> color sel byelement

> select clear

> color sel byelement

> select clear

> color sel byelement

> select /K:394@CA

1 atom, 1 model selected  

> color sel byelement

> select /K:418@CA

1 atom, 1 model selected  

> color sel byelement

> select clear

> toolshed show "Color Actions"

> color sel orchid

> color sel orchid

> select clear

> select /K:418@CA

1 atom, 1 model selected  

> show (sel-residues & sidechain) target ab

> select /K:394@CA

1 atom, 1 model selected  

> color sel orchid

> color sel orchid

> select clear

> select /K:405@NZ

1 atom, 1 model selected  

> ui mousemode right distance

> toolshed show Distances

> distance /J:68@OP2 /K:405@NZ

Distance between /J DT 68 OP2 and /K LYS 405 NZ: 2.744Å  

> select /K:425@NZ

1 atom, 1 model selected  

> distance /J:66@OP1 /K:425@NZ

Distance between /J DC 66 OP1 and /K LYS 425 NZ: 3.098Å  

> select /K:438@NZ

1 atom, 1 model selected  

> distance /I:-72@OP1 /K:438@NZ

Distance between /I DT -72 OP1 and /K LYS 438 NZ: 3.093Å  

> select /I:-71@OP2

1 atom, 1 model selected  

> distance /I:-71@OP2 /K:441@NZ

Distance between /I DC -71 OP2 and /K LYS 441 NZ: 2.804Å  

> hide #2.1 models

> select clear

> save C:\Users\Uma\Desktop\image1.png supersample 3

> distance save "C:/Users/Uma/Desktop/chimeraX pics and
> movies/04222021/lysineswithdistances"

> ui mousemode right distance

> ui mousemode right distance

> ui mousemode right distance

> select clear

> ui mousemode right distance

> select clear

> ui mousemode right clip

> save C:\Users\Uma\Desktop\image1.png supersample 3

> ui mousemode right clip

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1660, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
  
See log for complete Python traceback.  
  

> save C:\Users\Uma\Desktop\image1.png supersample 3

> save C:\Users\Uma\Desktop\image1.png supersample 3

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1660, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
File "C:\Program Files\ChimeraX 1.0rc202005080235\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 461.09
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 7590
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 8,304,021,504
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"

[pett]

Hi Uma,

Thanks for reporting this problem. It has been fixed for awhile now, so if you upgrade to a newer version of ChimeraX you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab