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#4916 closed defect (duplicate)

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

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	UI	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
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 "/Users/michaelsoniat/Desktop/Logan's TRF2-Nuc.cxs"

Log from Mon Jul 19 10:41:23 2021UCSF 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/michaelsoniat/Desktop/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 200,200,200, pixel 1.5, shown at
level 0.00993, step 1, values float32  

> volume #1 level -0.002151

> volume #1 level 0.001046

> volume #1 level 0.002112

> volume #1 level 0.01135

> volume #1 level 0.006731

> transparency 60

> open /Users/michaelsoniat/Downloads/1aoi.pdb

1aoi.pdb title:  
Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 BP long DNA
fragment [more info...]  
  
Chain information for 1aoi.pdb #2  
---  
Chain | Description  
A E | histone H3  
B F | histone H4  
C G | histone H2A  
D H | histone H2B  
I J | palindromic 146 BP DNA repeat 8/9 from human X- chromosome α satellite
DNA  
  
Non-standard residues in 1aoi.pdb #2  
---  
MN — manganese (II) ion  
  

> hide #!1 models

> show #!1 models

> ui mousemode right "translate selected models"

> select #2

12385 atoms, 13176 bonds, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> select #1

2 models selected  

> ui mousemode right select

> ~select #1

Nothing selected  

> volume #1 level 0.004244

> set bgColor white

> save "/Users/michaelsoniat/Desktop/Logan's TRF2-Nuc.cxs"

opened ChimeraX session  

> volume #1 level 0.002467

> open /Users/michaelsoniat/Desktop/TRF2.cif

Summary of feedback from opening /Users/michaelsoniat/Desktop/TRF2.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Fetching CCD GOL from http://ligand-
expo.rcsb.org/reports/G/GOL/GOL.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
Chain information for TRF2.cif #3  
---  
Chain | Description  
D | No description available  
  

> select #3

3299 atoms, 3099 bonds, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> show sel atoms

> show sel atoms

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> show sel cartoons

> ~select #3

Nothing selected  

> open /Users/michaelsoniat/Desktop/TRF2.pdb

Chain information for TRF2.pdb #4  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> select #4

3299 atoms, 3300 bonds, 1 model selected  

> ui mousemode right "translate selected models"

> hide #3 models

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> toolshed show "Fit in Map"

Fit molecule TRF2.pdb (#4) to map postprocess_masked.mrc (#1) using 3299 atoms  
average map value = 0.002644, steps = 176  
shifted from previous position = 12  
rotated from previous position = 27.7 degrees  
atoms outside contour = 2098, contour level = 0.0024675  
  
Position of TRF2.pdb (#4) relative to postprocess_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70335688 -0.70500820 0.09084344 175.75257559  
0.68329434 0.63533067 -0.35981075 195.40850338  
0.19595390 0.31514818 0.92859232 131.29079908  
Axis 0.43622958 -0.06793346 0.89726740  
Axis point -188.46410499 216.47381462 0.00000000  
Rotation angle (degrees) 50.68081621  
Shift along axis 181.19665223  
  

> ~select #4

Nothing selected  

> save "/Users/michaelsoniat/Desktop/Logan's TRF2-Nuc.cxs"

> color #1-2,4 black

> undo

> volume #1 level 0.006556

Fit molecule TRF2.pdb (#4) to map postprocess_masked.mrc (#1) using 3299 atoms  
average map value = 0.002645, steps = 60  
shifted from previous position = 0.0289  
rotated from previous position = 0.0139 degrees  
atoms outside contour = 2717, contour level = 0.0065561  
  
Position of TRF2.pdb (#4) relative to postprocess_masked.mrc (#1) coordinates:  
Matrix rotation and translation  
0.70347236 -0.70488968 0.09086905 175.78008055  
0.68315783 0.63537734 -0.35998750 195.42013351  
0.19601534 0.31531916 0.92852130 131.28616281  
Axis 0.43647539 -0.06795989 0.89714586  
Axis point -188.54491951 216.47113229 0.00000000  
Rotation angle (degrees) 50.67744126  
Shift along axis 181.22578443  
  

> volume #1 level 0.004512

> open /Users/michaelsoniat/Desktop/Myb.pdb

Chain information for Myb.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui mousemode right select

> select #5

483 atoms, 472 bonds, 1 model selected  

> ui mousemode right "translate selected models"

> volume #1 level 0.002059

> volume #1 level 0.006965

> volume #1 level 0.000832

> volume #1 level 0.00165

> volume #1 level 0.007374

> volume #1 level 0.00165

> volume #1 level 0.00533

> ui mousemode right "translate selected models"

> ui mousemode right select

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/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/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 INTEL-14.7.17
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 429.120.4.0.0
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1217)
      Kernel Version: Darwin 19.6.0
      Time since boot: 4:26

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → UI
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → File→Save: wrapped C/C++ object of type SaveOptionsWidget has been deleted

comment:2 by Eric Pettersen, 4 years ago

Resolution:	→ duplicate
Status:	accepted → closed

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