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#3479 closed defect (fixed)

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

Reported by:	chimerax-bug-report@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
I get this error run time error when I try to save a session.

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

> open /Users/vkasaragod/Desktop/complex-session-1.cxs

Log from Fri Jul 3 14:21:17 2020UCSF ChimeraX version: 1.0rc202005080235
(2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/vkasaragod/Downloads/vikram_state1NU_2point59_map_sharp_local.mrc

Opened vikram_state1NU_2point59_map_sharp_local.mrc, grid size 536,536,536,
pixel 0.652, shown at level 0.0354, step 4, values float32  

> volume #1 step 1

> volume #1 level 0.0898

> surface dust #1 size 15

> surface dust #1 size 10

> surface dust #1 size 5

> ui mousemode right zoom

> graphics silhouettes true

> lighting soft

> volume #1 level 0.08102

> surface dust #1 size 9

> open /Users/vkasaragod/Desktop/gaba-
> lh4-tmd/RealSpaceRefine_39/test.updated_real_space_refined-coot-8.pdb

Summary of feedback from opening /Users/vkasaragod/Desktop/gaba-
lh4-tmd/RealSpaceRefine_39/test.updated_real_space_refined-coot-8.pdb  
---  
warnings | Cannot find LINK/SSBOND atom C312 in residue POV /B:3301  
Cannot find LINK/SSBOND atom C312 in residue POV /B:3301  
  
Chain information for test.updated_real_space_refined-coot-8.pdb #2  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C | No description available  
F | No description available  
G P | No description available  
N | No description available  
  

> show cartoons

> hide atoms

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select /A:12-416

5500 atoms, 5572 bonds, 2 pseudobonds, 2 models selected  

> select /D:12-416

5499 atoms, 5571 bonds, 2 pseudobonds, 2 models selected  

> select /A:12-416

5500 atoms, 5572 bonds, 2 pseudobonds, 2 models selected  

> toolshed show "Color Actions"

> color sel orange red

> select /D:12-416

5499 atoms, 5571 bonds, 2 pseudobonds, 2 models selected  

> color sel orange red

> select /B:9-447

5440 atoms, 5514 bonds, 2 pseudobonds, 2 models selected  

> color sel royal blue

> select /E:9-447

5440 atoms, 5514 bonds, 2 pseudobonds, 2 models selected  

> color sel royal blue

> color sel royal blue

> color sel cornflower blue

> color sel royal blue

> color sel cornflower blue

> color sel royal blue

> select /B:9-447

5440 atoms, 5514 bonds, 2 pseudobonds, 2 models selected  

> color sel royal blue

> select /F:17-197

2803 atoms, 2843 bonds, 1 model selected  

> select /C:27-436

5392 atoms, 5467 bonds, 2 pseudobonds, 2 models selected  

> toolshed show "Color Actions"

> color sel yellow

> select /A:12-416

5500 atoms, 5572 bonds, 2 pseudobonds, 2 models selected  

> color sel tomato

> color sel tomato

> select /A:12-416

5500 atoms, 5572 bonds, 2 pseudobonds, 2 models selected  

> select /D:12-416

5499 atoms, 5571 bonds, 2 pseudobonds, 2 models selected  

> color sel tomato

> color sel indian red

> color sel orange red

> color sel red

> color sel crimson

> color sel orange red

> color sel indian red

> color sel sienna

> color sel coral

> color sel saddle brown

> color sel chocolate

> set bgColor white

> color sel crimson

> select /A:12-416

5500 atoms, 5572 bonds, 2 pseudobonds, 2 models selected  

> color sel crimson

> select clear

> select /F:17-197

2803 atoms, 2843 bonds, 1 model selected  

> color sel dark turquoise

> color sel medium sea green

> color sel light sea green

> select /G:1-123

1850 atoms, 1872 bonds, 1 model selected  

> color sel medium spring green

> color sel chartreuse

> color sel lime

> color sel yellow green

> select /P:1-123

1850 atoms, 1872 bonds, 1 model selected  

> color sel yellow green

Drag select of  
Drag select of 5 residues  
Drag select of  
Drag select of  

> show #!1 models

> color zone #1 near #5 distance 5

> color zone #1 near #2 distance 5

> color zone #1 near #2 distance 3

> hide #!2 models

> volume #1 level 0.07049

> volume #1 level 0.07576

> volume #1 level 0.08804

> volume #1 level 0.09507

> volume #1 level 0.08629

> volume #1 level 0.08102

> toolshed show "Side View"

> select ::name="MAN"

238 atoms, 243 bonds, 1 model selected  

> toolshed show "Color Actions"

> color sel orange

> color sel orange

> select ::name="NAG"

335 atoms, 341 bonds, 1 model selected  

> color sel orange

> select ::name="BMA"

75 atoms, 75 bonds, 1 model selected  

> color sel orange

> color sel orange

> color zone #1 near #2 distance 3

> select ::name="R16"

350 atoms, 343 bonds, 1 model selected  

> toolshed show "Color Actions"

> color sel cornflower blue

> color sel light salmon

> select ::name="R16"

350 atoms, 343 bonds, 1 model selected  

> color sel light salmon

> color zone #1 near #2 distance 3

> color zone #1 near #2 distance 5

> color zone #1 near #2 distance 2

> color zone #1 near #2 distance 3

> select ::name="D10"

307 atoms, 296 bonds, 1 model selected  

> color sel light salmon

> color zone #1 near #2 distance 3

> select ::name="PIO"

182 atoms, 182 bonds, 1 model selected  

> color sel light salmon

> color zone #1 near #2 distance 3

> select ::name="PTY"

65 atoms, 64 bonds, 1 model selected  

> color sel salmon

> color zone #1 near #2 distance 3

> select ::name="CLR"

74 atoms, 77 bonds, 1 model selected  

> color sel dim gray

> color sel dim gray

> color sel magenta

> color zone #1 near #2 distance 3

> color zone #1 near #2 distance 4

> color zone #1 near #2 distance 5

> save /Users/vkasaragod/Desktop/complex-session-1.cxs

opened ChimeraX session  

> hide #!1 models

> show #!2 models

> select ::name="D10"

307 atoms, 296 bonds, 1 model selected  

> show sel atoms

> style sel ball

Changed 307 atom styles  

> select H

17997 atoms, 1 model selected  

> hide sel atoms

Drag select of  

> select ::name="R16"

350 atoms, 343 bonds, 1 model selected  

> show sel atoms

> select ::name="PTY"

65 atoms, 64 bonds, 1 model selected  

> style sel ball

Changed 65 atom styles  

> show sel atoms

> select ::name="PTY"

65 atoms, 64 bonds, 1 model selected  

> select ::name="PTY" ::name="PIO"

247 atoms, 246 bonds, 1 model selected  

> select ::name="PTY" ::name="PIO" ::name="D10" ::name="R16"

904 atoms, 885 bonds, 1 model selected  

> show sel atoms

> select :H

Nothing selected  

> select H

17997 atoms, 1 model selected  

> hide sel atoms

> select ::name="PTY" ::name="PIO" ::name="D10" ::name="R16"

904 atoms, 885 bonds, 1 model selected  

> style sel ball

Changed 904 atom styles  

> style sel sphere

Changed 904 atom styles  

> style sel ball

Changed 904 atom styles  

> color sel byhetero

> select ::name="NAG" ::name="MAN" ::name="BMA"

648 atoms, 670 bonds, 1 model selected  

> show sel atoms

> style sel ball

Changed 648 atom styles  

> color sel byhetero

> select H

17997 atoms, 1 model selected  

> hide sel atoms

Drag select of  

> select ::name="PTY" ::name="CLR"

139 atoms, 141 bonds, 1 model selected  

> show sel atoms

> select ::name="PTY" ::name="CLR" ::name="POV"

175 atoms, 176 bonds, 1 model selected  

> show sel atoms

> color sel byhetero

> select H

17997 atoms, 1 model selected  

> hide sel atoms

> select clear

> select ::name="PTY" ::name="CLR" ::name="POV"

175 atoms, 176 bonds, 1 model selected  

> style sel ball

Changed 175 atom styles  

> select clear

> cartoon style #2 xsection oval modeHelix default

> cartoon style #2 modeHelix tube sides 20

> cartoon style #2 xsection oval modeHelix default

> cartoon style #2 xsection rectangle modeHelix default

> cartoon style (#2 & coil) xsection oval

> cartoon style #2 xsection barbell modeHelix default

> toolshed show "Side View"

> lighting soft

> lighting flat

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes true

> lighting soft

> lighting flat

> lighting flat

> lighting soft

> lighting full

> lighting soft

> lighting soft

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> save /Users/vkasaragod/Desktop/image1.png supersample 3

> save /Users/vkasaragod/Desktop/gaba-lh4-tmd/RealSpaceRefine_39/1.png width
> 1104 height 773 supersample 3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1543, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 111, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1660, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 453, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1660, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/__init__.py", line 38, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1543, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 111, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Applications/ChimeraX-1.0-rc-2020.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.40.124.0.0 (iBridge: 17.16.11081.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G1012)
      Kernel Version: Darwin 18.7.0
      Time since boot: 9 days 7:35

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.01.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Change History (2)

comment:1 by pett, 5 years ago

Component:	Unassigned → Input/Output
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Save dialog: wrapped C/C++ object of type SaveOptionsWidget has been deleted

comment:2 by pett, 5 years ago

Resolution:	→ fixed
Status:	accepted → closed

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