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

[Dbarrero@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
(Describe the actions that caused this problem to occur here)
Attemped to save going through file->save 

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/dbarrero/Desktop/PDB_FILES/2ve7.pdb format pdb

2ve7.pdb title:  
Crystal structure of A bonsai version of the human NDC80 complex [more
info...]  
  
Chain information for 2ve7.pdb #1  
---  
Chain | Description  
A B | kinetochore protein HEC1, kinetochore protein SPC25  
C D | kinetochore protein NUF2, kinetochore protein SPC24  
  
Non-standard residues in 2ve7.pdb #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPH — phenol  
  

> select /D:4-1197

1983 atoms, 2037 bonds, 1 model selected  

> open /Users/dbarrero/Desktop/PDB_FILES/2ve7.pdb

2ve7.pdb title:  
Crystal structure of A bonsai version of the human NDC80 complex [more
info...]  
  
Chain information for 2ve7.pdb #2  
---  
Chain | Description  
A B | kinetochore protein HEC1, kinetochore protein SPC25  
C D | kinetochore protein NUF2, kinetochore protein SPC24  
  
Non-standard residues in 2ve7.pdb #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPH — phenol  
  

> hide #!1 models

> color #!2 byhetero

> color #!2 bychain

> show target m

> show target m

> show target m

> hide #!1 models

> select #2/A:79-1221

1980 atoms, 2020 bonds, 8 pseudobonds, 2 models selected  

> select #1/A

1991 atoms, 2025 bonds, 8 pseudobonds, 2 models selected  

> color #2 white

> select #1/A

1991 atoms, 2025 bonds, 8 pseudobonds, 2 models selected  

> color #2 orange red

> close session

> open /Users/dbarrero/Desktop/PDB_FILES/2ve7.pdb

2ve7.pdb title:  
Crystal structure of A bonsai version of the human NDC80 complex [more
info...]  
  
Chain information for 2ve7.pdb #1  
---  
Chain | Description  
A B | kinetochore protein HEC1, kinetochore protein SPC25  
C D | kinetochore protein NUF2, kinetochore protein SPC24  
  
Non-standard residues in 2ve7.pdb #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPH — phenol  
  

> select /B:79-1224

2447 atoms, 2499 bonds, 4 pseudobonds, 2 models selected  

> select /B:79-1224

2447 atoms, 2499 bonds, 4 pseudobonds, 2 models selected  

> select /B:79-1224

2447 atoms, 2499 bonds, 4 pseudobonds, 2 models selected  

> select /B:79-1224

2447 atoms, 2499 bonds, 4 pseudobonds, 2 models selected  

> sequence chain #1/C#1/D

Alignment identifier is 1  

> close session

> open /Users/dbarrero/Desktop/PDB_FILES/6qld.pdb

6qld.pdb title:  
Structure of inner kinetochore ccan-cenp-A complex [more info...]  
  
Chain information for 6qld.pdb #1  
---  
Chain | Description  
C | inner kinetochore subunit MIF2  
G | DNA (125-mer)  
H | inner kinetochore subunit MCM16  
I | inner kinetochore subunit CTF3  
J | DNA (125-mer)  
K | inner kinetochore subunit MCM22  
L | inner kinetochore subunit IML3  
N | inner kinetochore subunit CHL4  
O | inner kinetochore subunit MCM21  
P | inner kinetochore subunit CTF19  
Q | inner kinetochore subunit OKP1  
U | inner kinetochore subunit AME1  
Y | inner kinetochore subunit NKP1  
Z | inner kinetochore subunit NKP2  
a | histone H3-like centromeric protein CSE4  
b f | histone H4  
d | histone H2B.2  
e | histone H3-like centromeric protein CSE4  
g | histone H2A.1  
h | suppressor OF TY protein 12  
i | histone H2A.1  
  

> color bychain

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> set bgColor white

> hide surfaces

> hide surfaces

> select #1

29086 atoms, 30037 bonds, 66 pseudobonds, 2 models selected  

> hide sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5084 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5084 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5084 atom styles  

> hide sel surfaces

> show sel atoms

> show sel cartoons

> hide sel surfaces

> style sel stick

Changed 29086 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5084 atom styles  

> ~select #1

Nothing selected  

> style stick

Changed 29086 atom styles  

> select #1

29086 atoms, 30037 bonds, 66 pseudobonds, 2 models selected  

> style sel stick

Changed 29086 atom styles  

> style sel stick

Changed 29086 atom styles  

> style sel stick

Changed 29086 atom styles  

> style sel stick

Changed 29086 atom styles  

> style sel ball

Changed 29086 atom styles  

> style sel ball

Changed 29086 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 5084 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 5084 atom styles  

> nucleotides sel tube/slab shape box

> ~select #1

Nothing selected  

> nucleotides tube/slab shape box

> nucleotides atoms

> style nucleic stick

Changed 5084 atom styles  

> style stick

Changed 29086 atom styles  

> style stick

Changed 29086 atom styles  

> style ball

Changed 29086 atom styles  

> style ball

Changed 29086 atom styles  

> style stick

Changed 29086 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 5084 atom styles  

> show atoms

> hide atoms

> nucleotides atoms

> style nucleic stick

Changed 5084 atom styles  

> nucleotides ladder

> show cartoons

> show atoms

> hide cartoons

> hide atoms

> show cartoons

> select /G:2-125

2524 atoms, 2827 bonds, 1 model selected  

> nucleotides sel ladder

> show sel atoms

> sequence chain #1/J

Alignment identifier is 1.J  

> select /J:-125--2

2560 atoms, 2875 bonds, 1 model selected  

> show sel atoms

> select #1

29086 atoms, 30037 bonds, 66 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> lighting soft

> lighting soft

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> view orient

> view orient

> toolshed show "Side View"

> view

> view

> ui mousemode right "rotate slab"

> ui mousemode right "rotate slab"

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dbarrero/Desktop/movie1.mp4

Movie saved to /Users/dbarrero/Desktop/movie1.mp4  
  

> save /Users/dbarrero/Desktop/PDB_FILES/Ctf19_Barford_image.jpg width 1088
> height 836 supersample 3

> close session

> open /Users/dbarrero/Desktop/PDB_FILES/5t58.pdb

5t58.pdb title:  
Structure of the mind complex shows A regulatory focus of yeast kinetochore
assembly [more info...]  
  
Chain information for 5t58.pdb #1  
---  
Chain | Description  
A | KLLA0F02343P  
B | KLLA0E05809P  
D | KLLA0D15741P  
N | KLLA0C15939P  
  

> color bychain

> show surfaces

> hide surfaces

> lighting soft

> lighting flat

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

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 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 3 days 6:26

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: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.01.190
      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: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

[Eric Pettersen]

Hi Daniel,

This problem was fixed the day after the version you have, so if you get a newer version then things will work. Also, in the version you have you can use the 'save' command directly, though I realize the dialog may be more convenient. Thanks for reporting the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab