Save options widgets deleted

[chimerax-bug-report@…]

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)

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/ms/Library/Mobile Documents/com~apple~CloudDocs/FORSCHUNGS-
> DATA-UKE/EMBL-DESY/3.BEAMTIME_13-15DEC19/Models IgG and
> Prp/6D11-PrPc_complex/C_series_for_the_supporting_info/mAb6D11/mAb6D11only-1.pdb"

Summary of feedback from opening /Users/ms/Library/Mobile
Documents/com~apple~CloudDocs/FORSCHUNGS-DATA-UKE/EMBL-
DESY/3.BEAMTIME_13-15DEC19/Models IgG and
Prp/6D11-PrPc_complex/C_series_for_the_supporting_info/mAb6D11/mAb6D11only-1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Project description: Fab1, Fc, Fab2 and 2x20 AA linkers at hinge  
  
Ignored bad PDB record found on line 2  
REMARK j: 66 T: 0.106E-01 Suc: 72 Eva: 1122059 CPU: 0.241E+05 F: 0.8735 Pen:
0.0202  
  
Ignored bad PDB record found on line 3  
REMARK The best Chi^2 values: .85325  
  
Ignored bad PDB record found on line 4  
REMARK Cross: 0.00006 Center: 0.00142  
  
Ignored bad PDB record found on line 5  
REMARK Cont Penalt.: 0.00000  
  
14 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2048 messages similar to the above omitted  
Ignored bad PDB record found on line 4119  
REMARK *******************************  
  
Ignored bad PDB record found on line 4120  
REMARK Evaluated from PDB file rc01-Bc.pdb  
  
Ignored bad PDB record found on line 4121  
REMARK Old center positioned at 7.851 -33.020 -12.912  
  
Ignored bad PDB record found on line 4122  
REMARK Rotated by Euler angles 243.957 17.021 277.600  
  
Ignored bad PDB record found on line 4123  
REMARK New center positioned at -3.131 29.233 -12.886  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2037 messages similar to the above omitted  
Ignored bad PDB record found on line 6169  
REMARK *******************************  
  
Ignored bad PDB record found on line 6170  
REMARK Evaluated from PDB file rc01-Dn.pdb  
  
Ignored bad PDB record found on line 6171  
REMARK Old center positioned at -21.888 29.136 -0.043  
  
Ignored bad PDB record found on line 6172  
REMARK Rotated by Euler angles 18.277 126.007 104.912  
  
Ignored bad PDB record found on line 6173  
REMARK New center positioned at -10.054 3.603 56.156  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2057 messages similar to the above omitted  
Ignored bad PDB record found on line 8238  
REMARK *******************************  
  
Ignored bad PDB record found on line 8239  
REMARK Evaluated from PDB file rc01-Dc.pdb  
  
Ignored bad PDB record found on line 8240  
REMARK Old center positioned at 28.982 -16.714 -11.378  
  
Ignored bad PDB record found on line 8241  
REMARK Rotated by Euler angles 243.957 17.021 277.600  
  
Ignored bad PDB record found on line 8242  
REMARK New center positioned at -18.077 7.201 -15.332  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2038 messages similar to the above omitted  
Ignored bad PDB record found on line 10714  
REMARK *******************************  
  
Ignored bad PDB record found on line 10715  
REMARK Evaluated from PDB file rc01-C.pdb  
  
Ignored bad PDB record found on line 10716  
REMARK Old center positioned at -32.756 28.134 14.772  
  
Ignored bad PDB record found on line 10717  
REMARK Rotated by Euler angles 18.277 126.007 104.912  
  
Ignored bad PDB record found on line 10718  
REMARK New center positioned at -19.080 17.916 48.926  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2028 messages similar to the above omitted  
  
Chain information for mAb6D11only-1.pdb #1  
---  
Chain | Description  
A H | No description available  
B E | No description available  
C F | No description available  
D G | No description available  
  

> lighting full

> lighting soft

> style stick

Changed 12702 atom styles  

> show cartoons

> style stick

Changed 12702 atom styles  

> hide atoms

> volume planes z style image imageMode "full region"

No volumes specified  

> color bychain

> rainbow

> mlp

Map values for surface "mAb6D11only-1.pdb_A SES surface": minimum -27.22, mean
-6.393, maximum 22.25  
Map values for surface "mAb6D11only-1.pdb_B SES surface": minimum -26.67, mean
-5.458, maximum 22.32  
Map values for surface "mAb6D11only-1.pdb_C SES surface": minimum -5.216, mean
-3.955, maximum -2.667  
Map values for surface "mAb6D11only-1.pdb_D SES surface": minimum -28.8, mean
-5.249, maximum 22.86  
Map values for surface "mAb6D11only-1.pdb_E SES surface": minimum -27.87, mean
-5.654, maximum 22.83  
Map values for surface "mAb6D11only-1.pdb_F SES surface": minimum -5.08, mean
-3.933, maximum -2.823  
Map values for surface "mAb6D11only-1.pdb_G SES surface": minimum -26.29, mean
-5.092, maximum 22.99  
Map values for surface "mAb6D11only-1.pdb_H SES surface": minimum -24.85, mean
-6.143, maximum 22.24  

> color bfactor

12702 atoms, 1338 residues, 8 surfaces, atom bfactor range 20 to 20  

> rainbow

> mlp

Map values for surface "mAb6D11only-1.pdb_A SES surface": minimum -27.22, mean
-6.393, maximum 22.25  
Map values for surface "mAb6D11only-1.pdb_B SES surface": minimum -26.67, mean
-5.458, maximum 22.32  
Map values for surface "mAb6D11only-1.pdb_C SES surface": minimum -5.216, mean
-3.955, maximum -2.667  
Map values for surface "mAb6D11only-1.pdb_D SES surface": minimum -28.8, mean
-5.249, maximum 22.86  
Map values for surface "mAb6D11only-1.pdb_E SES surface": minimum -27.87, mean
-5.654, maximum 22.83  
Map values for surface "mAb6D11only-1.pdb_F SES surface": minimum -5.08, mean
-3.933, maximum -2.823  
Map values for surface "mAb6D11only-1.pdb_G SES surface": minimum -26.29, mean
-5.092, maximum 22.99  
Map values for surface "mAb6D11only-1.pdb_H SES surface": minimum -24.85, mean
-6.143, maximum 22.24  

> mlp

Map values for surface "mAb6D11only-1.pdb_A SES surface": minimum -27.22, mean
-6.393, maximum 22.25  
Map values for surface "mAb6D11only-1.pdb_B SES surface": minimum -26.67, mean
-5.458, maximum 22.32  
Map values for surface "mAb6D11only-1.pdb_C SES surface": minimum -5.216, mean
-3.955, maximum -2.667  
Map values for surface "mAb6D11only-1.pdb_D SES surface": minimum -28.8, mean
-5.249, maximum 22.86  
Map values for surface "mAb6D11only-1.pdb_E SES surface": minimum -27.87, mean
-5.654, maximum 22.83  
Map values for surface "mAb6D11only-1.pdb_F SES surface": minimum -5.08, mean
-3.933, maximum -2.823  
Map values for surface "mAb6D11only-1.pdb_G SES surface": minimum -26.29, mean
-5.092, maximum 22.99  
Map values for surface "mAb6D11only-1.pdb_H SES surface": minimum -24.85, mean
-6.143, maximum 22.24  

> color bfactor

12702 atoms, 1338 residues, 8 surfaces, atom bfactor range 20 to 20  

> rainbow

> style stick

Changed 12702 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> show cartoons

> hide atoms

> style ball

Changed 12702 atom styles  

> color byhetero

> color byhetero

> hide atoms

> hide surfaces

> show surfaces

> show surfaces

> hide surfaces

> select

12702 atoms, 12922 bonds, 38 pseudobonds, 2 models selected  

> color (#!1 & sel) hot pink

> select /A

2033 atoms, 2071 bonds, 1 model selected  

> select clear

> toolshed show "Color Actions"

> set bgColor white

> set bgColor salmon

> set bgColor salmon

> set bgColor white

> color salmon target c

> color dark salmon target c

> color salmon target c

> color coral target c

> color tomato target c

> show atoms

> show atoms

> hide atoms

> style stick

Changed 12702 atom styles  

> style sphere

Changed 12702 atom styles  

> style stick

Changed 12702 atom styles  

> save /Users/ms/Desktop/6D11.png width 905 height 601 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/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.  
  




OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2,7 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 190.0.0.0.0
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 26 days 15:03

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      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]

Can't cache format-specific options because the dialog is destroyed after each use.