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

[msoniat@…]

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.  
How to cite UCSF ChimeraX  

> open "/Users/michaelsoniat/Desktop/090721 A11/Tiff/startup_volume_1_1.mrc"

Opened startup_volume_1_1.mrc, grid size 216,216,216, pixel 1.63, shown at
level 10.3, step 1, values float32  

> transparency 60

> lighting simple

> set bgColor white

> open "/Users/michaelsoniat/Desktop/090721 A11/5czz.pdb"

5czz.pdb title:  
Crystal structure of staphylococcus aureus CAS9 In complex with sgRNA and
target DNA (ttgaat pam) [more info...]  
  
Chain information for 5czz.pdb #2  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9  
B | RNA (73-mer)  
C | DNA (28-mer)  
D | DNA (5'-D(*TP*TP*GP*ap*ap*TP*ap*G)-3')  
  
Non-standard residues in 5czz.pdb #2  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
NA — sodium ion  
PO4 — phosphate ion  
  

> select #2

10792 atoms, 11115 bonds, 26 pseudobonds, 3 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> toolshed show "Fit in Map"

Fit molecule 5czz.pdb (#2) to map startup_volume_1_1.mrc (#1) using 10792
atoms  
average map value = 14.84, steps = 208  
shifted from previous position = 9.07  
rotated from previous position = 45 degrees  
atoms outside contour = 2108, contour level = 10.339  
  
Position of 5czz.pdb (#2) relative to startup_volume_1_1.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87597270 0.01367763 -0.48216672 181.67235388  
0.26459557 0.82216103 0.50402423 80.54981300  
0.40331255 -0.56909065 0.71657158 139.97835128  
Axis -0.75907084 -0.62634626 0.17748751  
Axis point 0.00000000 234.20369128 126.01480406  
Rotation angle (degrees) 44.98007396  
Shift along axis -163.50985168  
  

> volume #1 level 12.57

> volume #1 level 12.08

> volume #1 level 12.57

> volume #1 level 13.06

> lighting simple

> lighting soft

> lighting simple

> save "/Users/michaelsoniat/Desktop/090721 A11/A11.cxs"

> save "/Users/michaelsoniat/Desktop/090721 A11/A11.png" width 864 height 678
> supersample 3

> ~select #2

Nothing selected  
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 days 12:21

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

[Eric Pettersen]

Hi Michael,

Thanks for reporting this problem. It is fixed in the 1.2.5 release, so if you upgrade to that then it won't bother you anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab