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#3186 closed defect (duplicate)

Save options widgets deleted

Reported by:	tomasiak@…	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-17.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-07)
Description
Tried to save a map generated from a model and said that a there was a missing C++ wrapper.

Log:
UCSF ChimeraX version: 1.0rc202005070439 (2020-05-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/tomasiak/projects/ycf1/em/phenix/run1/ResolveCryoEM_4/denmod_map.ccp4

Opened denmod_map.ccp4, grid size 136,129,176, pixel 1.05, shown at level
0.371, step 1, values float32  

> volume #1 level 0.177

> open /Users/tomasiak/projects/ycf1/em/coot/run2/ycf1_chimerax-coot-0.pdb

Chain information for ycf1_chimerax-coot-0.pdb #2  
---  
Chain | Description  
B | No description available  
  
Drag select of 17 residues  

> select up

2140 atoms, 2158 bonds, 1 model selected  

> select up

22471 atoms, 22695 bonds, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

Drag select of  

> toolshed show "Fit in Map"

Fit molecule ycf1_chimerax-coot-0.pdb (#2) to map denmod_map.ccp4 (#1) using
22471 atoms  
average map value = 0.1486, steps = 144  
shifted from previous position = 6.57  
rotated from previous position = 7.7 degrees  
atoms outside contour = 13923, contour level = 0.17704  
  
Position of ycf1_chimerax-coot-0.pdb (#2) relative to denmod_map.ccp4 (#1)
coordinates:  
Matrix rotation and translation  
-0.99999980 -0.00054994 -0.00031318 231.01848424  
-0.00055022 0.99999945 0.00088914 0.08374962  
0.00031269 0.00088931 -0.99999955 229.78424368  
Axis 0.00027222 -0.99999986 -0.00044311  
Axis point 115.49127652 0.00000000 114.91017685  
Rotation angle (degrees) 179.98207003  
Shift along axis -0.12268116  
  

> save /Users/tomasiak/projects/ycf1/em/coot/run2/ycf1_chimerax-
> coot-0_resolve.pdb

> show target ab

> select H

11217 atoms, 1 model selected  

> hide sel target a

Drag select of  

> toolshed show "Side View"

Drag select of 1 denmod_map.ccp4 , 4 atoms, 3 residues, 2 bonds  
Drag select of  

> ui mousemode right pivot

> ui mousemode right select

Drag select of  

> hide #!2 models

> hide #!1 models

> show #!2 models

Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> view sel

Drag select of  

> ui mousemode right clip

> show #!1 models

> ui mousemode right translate

> volume #1 level 0.3396

> volume #1 level 0.1083

> volume #1 level 0.202

> ui mousemode right clip

> open /Users/tomasiak/projects/ycf1/em/phenix/run1/flip_987_mask.mrc

Opened flip_987_mask.mrc, grid size 220,220,220, pixel 1.05, shown at level 1,
step 1, values float32  

> hide #!3 models

> show #!3 models

> volume #3 level 1

Drag select of 1 denmod_map.ccp4 , 3 flip_987_mask.mrc  

> select clear

> volume #3 level 1

> molmap #2 6 fullMap True

Expected a keyword  

> molmap #2 6 onGrid #1

> ui mousemode right translate

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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 QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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-2020.05.07.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 QLabel has been deleted  
  
RuntimeError: wrapped C/C++ object of type QLabel has been deleted  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.07.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-1.68.24
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Memory: 16 GB
      Boot ROM Version: 180.0.0.0.0
      SMC Version (system): 2.41f1

Software:

    System Software Overview:

      System Version: macOS 10.13.6 (17G11023)
      Kernel Version: Darwin 17.7.0
      Time since boot: 45 days 53 minutes

Graphics/Displays:

    Radeon Pro 575:

      Chipset Model: Radeon Pro 575
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Dynamic, Max): 4096 MB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1P-025
      EFI Driver Version: 01.00.931
      Metal: Supported, feature set macOS GPUFamily1 v3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
        DELL P2715Q:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: X24K178B841L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

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 Thomas,

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 tomasiak@…, 5 years ago

Hi Eric,

Thank you very much for the fix. The release candidate of ChimeraX is really great!

Cheers,

Thomas

On 5/12/20, 8:41 AM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    External Email
    
    #3186: Save options widgets deleted
    -----------------------------------+----------------------------
              Reporter:  tomasiak@…    |      Owner:  Eric Pettersen
                  Type:  defect        |     Status:  closed
              Priority:  normal        |  Milestone:
             Component:  Input/Output  |    Version:
            Resolution:  duplicate     |   Keywords:
            Blocked By:                |   Blocking:
    Notify when closed:                |   Platform:  all
               Project:  ChimeraX      |
    -----------------------------------+----------------------------
    Changes (by Eric Pettersen):
    
     * status:  accepted => closed
     * resolution:   => duplicate
    
    
    Comment:
    
     Hi Thomas,
             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
    
    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3186#comment:2>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker

comment:4 by pett, 5 years ago

Thanks! Glad you like it.

--Eric

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