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#3180 closed defect (duplicate)

Save options widgets deleted

Reported by:	ubaumann@…	Owned by:	pett
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-19.4.0-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 3rvz

Summary of feedback from opening 3rvz fetched from pdb  
---  
notes | Fetching compressed mmCIF 3rvz from
http://files.rcsb.org/download/3rvz.cif  
Fetching CCD PX4 from http://ligand-expo.rcsb.org/reports/P/PX4/PX4.cif  
  
3rvz title:  
Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.8 A)
[more info...]  
  
Chain information for 3rvz #1  
---  
Chain | Description  
A B | Ion transport protein  
  
Non-standard residues in 3rvz #1  
---  
PX4 — 1,2-dimyristoyl-Sn-glycero-3-phosphocholine  
  
3rvz mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #1 assembly 1

> view

> color #2 bychain

> hide atoms

> cartoon style modeHelix tube r2.

Expected a keyword  

> cartoon style modeHelix tube radius 2.

> rainbow #2

> show :arg atoms

> color #2 byhetero

> style #2 ball

Changed 3728 atom styles  

> cartoon style modeHelix tube radius 1.5

> save /Users/ubaumann/Desktop/image1.png supersample 3

> save /Users/ubaumann/Documents/Vorlesungen/MN-BC-
> BC1.2/SS2020/PIccies/sodium-channel-3rvz.cxs

> close session

> open 3lut

Summary of feedback from opening 3lut fetched from pdb  
---  
note | Fetching compressed mmCIF 3lut from
http://files.rcsb.org/download/3lut.cif  
  
3lut title:  
A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 [more
info...]  
  
Chain information for 3lut #1  
---  
Chain | Description  
A | Voltage-gated potassium channel subunit beta-2  
B | Potassium voltage-gated channel subfamily A member 2  
  
Non-standard residues in 3lut #1  
---  
K — potassium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
3lut mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close session

> open 1k4c

1k4c title:  
Potassium Channel KcsA-Fab complex in high concentration of K+ [more info...]  
  
Chain information for 1k4c #1  
---  
Chain | Description  
A | antibody Fab fragment heavy chain  
B | antibody Fab fragment light chain  
C | potassium channel KcsA  
  
Non-standard residues in 1k4c #1  
---  
DGA — diacyl glycerol  
F09 — nonan-1-ol  
K — potassium ion  
  
1k4c mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> close session

> open 31ut

Fetching url http://files.rcsb.org/download/31ut.cif failed: HTTP Error 404:
Not Found  

> open 3lut format mmcif fromDatabase pdb

3lut title:  
A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 [more
info...]  
  
Chain information for 3lut #1  
---  
Chain | Description  
A | Voltage-gated potassium channel subunit beta-2  
B | Potassium voltage-gated channel subfamily A member 2  
  
Non-standard residues in 3lut #1  
---  
K — potassium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
3lut mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close session

> open 31utopen 2a79

'31utopen' has no suffix  

> open 2a79

Summary of feedback from opening 2a79 fetched from pdb  
---  
note | Fetching compressed mmCIF 2a79 from
http://files.rcsb.org/download/2a79.cif  
  
2a79 title:  
Mammalian Shaker Kv1.2 potassium channel- β subunit complex [more info...]  
  
Chain information for 2a79 #1  
---  
Chain | Description  
A | Voltage-gated potassium channel beta-2 subunit  
B | Potassium voltage-gated channel subfamily A member 2  
C | poly-unknown chain  
D | poly-unknown chain  
  
Non-standard residues in 2a79 #1  
---  
K — potassium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
2a79 mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> delete /B

> close session

> open 2a79 format mmcif fromDatabase pdb

2a79 title:  
Mammalian Shaker Kv1.2 potassium channel- β subunit complex [more info...]  
  
Chain information for 2a79 #1  
---  
Chain | Description  
A | Voltage-gated potassium channel beta-2 subunit  
B | Potassium voltage-gated channel subfamily A member 2  
C | poly-unknown chain  
D | poly-unknown chain  
  
Non-standard residues in 2a79 #1  
---  
K — potassium ion  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
2a79 mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> delete /A

> cartoon style modeHelix tube radius 1.5

> rainbow #!2

> hide atoms

> show :K atoms

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 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GTX 775M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 142.0.0.0.0
      SMC Version (system): 2.15f7

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 10:56

Graphics/Displays:

    NVIDIA GeForce GTX 775M:

      Chipset Model: NVIDIA GeForce GTX 775M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x119d
      Revision ID: 0x00a2
      ROM Revision: 3782
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Change History (4)

comment:1 by pett, 5 years ago

Component:	Unassigned → Input/Output
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Save options widgets deleted

comment:2 by pett, 5 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Ulrich,

Very sorry for this problem. It was fixed on Friday and is therefore available in builds as of Saturday morning. In the version you have you can still of course use the 'save' command directly, though it would undoubtedly be more convenient if you got the fixed version.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to: 3 ; follow-up: 3 comment:3 by ubaumann@…, 5 years ago

Hi Eric No worries I just thought I let you know.
Thanks for the fix!
I love ChimeraX!!


Best wishes,
Ulrich 




  ———————Prof. Dr. Ulrich Baumann
Institute of Biochemistry, University of Cologne
Zülpicherstrasse 47
D-50674 Cologne, Germany

comment:4 by pett, 5 years ago

Thanks! Glad you like it!

--Eric

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