Opened 2 years ago

Closed 2 years ago

#10230 closed defect (duplicate)

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

Reported by: Dbarrero@… Owned by: Eric Pettersen
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-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 8OW1 format mmcif fromDatabase pdb

8ow1 title:  
Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome.
[more info...]  
  
Chain information for 8ow1 #1  
---  
Chain | Description  
A B | Centromere-binding protein 1  
CE ce | Centromere DNA-binding protein complex CBF3 subunit B  
CT | Centromere DNA-binding protein complex CBF3 subunit C  
D | C0N3  
E | C0N3  
H HH | Inner kinetochore subunit MCM16  
I II | Inner kinetochore subunit CTF3  
K KK | Inner kinetochore subunit MCM22  
L LL | Inner kinetochore subunit IML3  
N NN | Inner kinetochore subunit CHL4  
O OO | Inner kinetochore subunit MCM21  
P PP | Inner kinetochore subunit CTF19  
Q QQ | Inner kinetochore subunit OKP1  
SK | Suppressor of kinetochore protein 1  
T TT | Inner kinetochore subunit CNN1  
U UU | Inner kinetochore subunit AME1  
W WW | Inner kinetochore subunit WIP1  
Y YY | Inner kinetochore subunit NKP1  
Z ZZ | Inner kinetochore subunit NKP2  
a e | Histone H3-like centromeric protein CSE4  
b f | Histone H4  
c g | Histone H2A.1  
d h | Histone H2B.1  
  

> mmap #1 4

Unknown command: mmap #1 4  

> molmap #1 4

> molmap #1 4

> hide #!1 models

> molmap #1 40

> molmap #1 30

> molmap #1 10

> show #!1 models

> hide #!2 models

> select #1

78671 atoms, 80705 bonds, 385 pseudobonds, 3 models selected  

> style sel stick

Changed 78671 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 6273 atom styles  

> hide sel atoms

> show sel cartoons

> select clear

> select clear

> select /PP:290

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select /B:292

5 atoms, 4 bonds, 1 model selected  

> show sel atoms

> select clear

> toolshed show Distances

Exactly two atoms must be selected!  

> select /PP:290@NH2

1 atom, 1 model selected  

> select /PP:290@NH2

1 atom, 1 model selected  

> select /PP:290@NH2

1 atom, 1 model selected  

> distance /B:292@CB /PP:290@NH2

Distance between /B ALA 292 CB and /PP ARG 290 NH2: 276.376Å  

> select /K:172

8 atoms, 7 bonds, 1 model selected  

> show sel atoms

> select /ce:480

5 atoms, 4 bonds, 1 model selected  

> show sel atoms

> select /ce:480@CB

1 atom, 1 model selected  
Exactly two atoms must be selected!  
Exactly two atoms must be selected!  

> select clear

> select /K:172@OD2

1 atom, 1 model selected  

> distance /K:172@OD2 /ce:480@CB

Distance between /K ASP 172 OD2 and /ce ALA 480 CB: 227.562Å  

> hide #!3 models

> hide #3.1 models

> set bgColor white

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> lighting flat

> toolshed show "Side View"

> save /Users/dbarrero/Desktop/image2.png supersample 3

> set bgTransperancy 100

Expected a keyword  
Cannot determine format for 'CCAN_graphic'  

> save CCAN_graphic.png [format png] [transparentBackground true]

Expected a keyword  
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.  
  
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.  
  

> save /Users/dbarrero/Desktop/image3.png supersample 3

Must select one or more distances in the table  

> ~distance /K:172@OD2 /ce:480@CB

> ~distance /B:292@CB /PP:290@NH2

> select #2

2 models selected  
No distances to delete!  

> ~select #2

Nothing selected  

> select #1

78671 atoms, 80705 bonds, 385 pseudobonds, 3 models selected  

> ~select #1

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.  
  




OpenGL version: 4.1 ATI-3.10.23
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: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 55 days 23:14

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.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        DELL U2720Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: FQYMT83     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
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 Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Daniel,

You reported this problem 2 years ago and at that time I suggested you update your version of ChimeraX because the problem had been fixed. You are still running the same version as two years ago. The solution remains the same: update your version of ChimeraX.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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