Save dialog failure

[raoulmartin@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-08)
Description
I can't save sessions anymore?

Log:
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/sessionX_v3.cxs
> format session

Log from Mon May 25 12:05:04 2020UCSF 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/raoulmartin/Box/Paper/Figures/Fig_1_Whole/map_wholecomplex_v2.mrc

Opened map_wholecomplex_v2.mrc, grid size 497,496,484, pixel
0.939,0.939,0.939, shown at level 0.00777, step 2, values float32  

> volume #1 level 0.01516

> volume #1 level 0.01669

> volume #1 step 1

> volume #1 level 0.1 step 1

> volume #1 level 0.02181

> volume #1 level 0.01822

> volume #1 level 0.018 step 1

> lighting full

> lighting soft

> lighting simple

> lighting soft

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> graphics silhouettes true

> lighting shadows true

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> open
> /Users/raoulmartin/Box/Paper/Figures/Figure3_NBDs/assembled_chain_ksdssp_addedsheets-
> coot-1.pdb

Chain information for assembled_chain_ksdssp_addedsheets-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> volume #1 color #b2b2b200

> volume #1 color #b2b2b207

> volume #1 color #b2b2b24c

> volume #1 color #b2b2b24d

> volume #1 color #b2b2b266

> volume #1 color #b2b2b2a6

> volume #1 color #b2b2b2c5

> volume #1 color #b2b2b2e8

> volume #1 color #b2b2b2f9

> volume #1 color #b2b2b2

> hide #!2 models

> volume #1 level 0.018 step 1

> volume #1 level 0.01704

> surface dust #1 size 5

> open /Users/raoulmartin/Box/Paper/Figures/Figure3_NBDs/4_Roq1s_newchains.pdb

Summary of feedback from opening
/Users/raoulmartin/Box/Paper/Figures/Figure3_NBDs/4_Roq1s_newchains.pdb  
---  
warnings | Ignored bad PDB record found on line 99  
  
  
Ignored bad PDB record found on line 100  
  
  
Ignored bad PDB record found on line 101  
  
  
Ignored bad PDB record found on line 102  
  
  
Ignored bad PDB record found on line 103  
  
  
4 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 GLN B 196 SER B 202
1 7  
Start residue of secondary structure not found: HELIX 2 2 LYS B 224 TYR B 235
1 12  
Start residue of secondary structure not found: HELIX 3 3 LYS B 249 GLN B 253
1 5  
Start residue of secondary structure not found: HELIX 4 4 LEU B 257 LEU B 268
1 12  
Start residue of secondary structure not found: HELIX 5 5 THR B 279 LEU B 290
1 12  
410 messages similar to the above omitted  
  
Chain information for 4_Roq1s_newchains.pdb  
---  
Chain | Description  
3.2/A 3.2/B 3.5/C 3.5/D | No description available  
3.3/A 3.1/B 3.6/C 3.4/D | No description available  
3.1/X 3.3/X 3.4/X 3.6/X | No description available  
  

> close #2

> close #3

> open /Users/raoulmartin/Box/Paper/Figures/Figure3_NBDs/4_Roq1s_newchains.pdb

Summary of feedback from opening
/Users/raoulmartin/Box/Paper/Figures/Figure3_NBDs/4_Roq1s_newchains.pdb  
---  
warnings | Ignored bad PDB record found on line 99  
  
  
Ignored bad PDB record found on line 100  
  
  
Ignored bad PDB record found on line 101  
  
  
Ignored bad PDB record found on line 102  
  
  
Ignored bad PDB record found on line 103  
  
  
4 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 GLN B 196 SER B 202
1 7  
Start residue of secondary structure not found: HELIX 2 2 LYS B 224 TYR B 235
1 12  
Start residue of secondary structure not found: HELIX 3 3 LYS B 249 GLN B 253
1 5  
Start residue of secondary structure not found: HELIX 4 4 LEU B 257 LEU B 268
1 12  
Start residue of secondary structure not found: HELIX 5 5 THR B 279 LEU B 290
1 12  
410 messages similar to the above omitted  
  
Chain information for 4_Roq1s_newchains.pdb  
---  
Chain | Description  
2.2/A 2.2/B 2.5/C 2.5/D | No description available  
2.3/A 2.1/B 2.6/C 2.4/D | No description available  
2.1/X 2.3/X 2.4/X 2.6/X | No description available  
  

> color #eef4c2e95fcf #1:1-185.A,1-185.B,1-185.C,1-185.D

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #9999ffff9999 #1:185-505.A,185-505.B,185-505.C,185-505.D

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #9999a3d6ffff #1:505-1310.A,505-1310.B,505-1310.C,505-1310.D

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #13b1c977ffff #1:1128-1310.A,1128-1310.B,1128-1310.C,1128-1310.D

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #ffff99999999 #1:.X

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red element.O;color blue element.N;color yellow element.S;

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #eef4c2e95fcf,r #1:1-185.A,1-185.B,1-185.C,1-185.D

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #9999ffff9999,r #1:185-505.A,185-505.B,185-505.C,185-505.D

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #9999a3d6ffff,r #1:505-1310.A,505-1310.B,505-1310.C,505-1310.D

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #13b1c977ffff,r #1:1128-1310.A,1128-1310.B,1128-1310.C,1128-1310.D

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #ffff99999999,r #1:.X

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #eef4c2e95fcf #1:1-185/A,1-185/B,1-185/C,1-185/D

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> hide #!1 models

> color #eef4c2e95fcf #1:1-185

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #eef4c2e95fcf,r #1:1-185

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> ksdssp

Unknown command: ksdssp  

> ksdssp

Unknown command: ksdssp  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> color #1:1-185/A,1-185/B,1-185/C,1-185/D #eef4c2e95fcf

> color #1:1-185 #eef4c2e95fcf

> select #1

2 models selected  

> color #2 red

> select #1/B

Nothing selected  

> color #2 blue

> select #1/B

Nothing selected  

> select #2/B

9796 atoms, 10001 bonds, 8 pseudobonds, 3 models selected  

> select #2:1-200

9056 atoms, 9214 bonds, 6 models selected  

> select #2/A-D:1-200

5564 atoms, 5662 bonds, 6 models selected  

> color #2/A-D:1-200 #eef4c2e95fcf

> select clear

> color #2/A-D:1-185 #eef4c2e95fcf

> color #2/A-D:185-505 #9999ffff9999

> color #2/A-D:505-1128 #9999a3d6ffff

> color #2/A-D:128-1310 #13b1c977ffff

> color #2/X #ffff99999999

> color #2/A-D:1-185 #eef4c2e95fcf

> color #2/A-D:185-505 #9999ffff9999

> color #2/A-D:505-1128 #9999a3d6ffff

> color #2/A-D:1128-1310 #13b1c977ffff

> color #2/X #ffff99999999

> hide #2 target a

> color #1 zone #2 distance 5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> show #!1 models

> color #1 zone #2 distance 5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> scolor #1 zone #2 distance 5

Unknown command: scolor #1 zone #2 distance 5  

> color #1 zone #2 distance 5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color zone #1 near #2 distance 5

> hide #!2 models

> color zone #1 near #2 distance 20

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> save
> /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/sessionX_v1.cxs

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

> save /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/image1.png
> supersample 3

> turn y 90

> turn y 90

> turn y 90

> turn y 90

> turn y 90

> turn y 90

> save /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/image1.png
> supersample 3

> turn y 90

> save /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/image2.png
> supersample 3

> turn y 90

> save /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/image3.png
> supersample 3

> movie record

> turn y 2 180

> wait 180

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

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

> save
> /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/sessionX_v2.cxs

> open "/Users/raoulmartin/Box/Paper/Figures/models for
> figure/finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb"

Summary of feedback from opening /Users/raoulmartin/Box/Paper/Figures/models
for figure/finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb  
---  
warnings | Ignored bad PDB record found on line 36  
  
  
Ignored bad PDB record found on line 42  
  
  
Ignored bad PDB record found on line 97  
  
  
Ignored bad PDB record found on line 103  
  
  
Ignored bad PDB record found on line 159  
  
  
20 messages similar to the above omitted  
  
Chain information for finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb #3  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> show #!3 cartoons

> style #!3 stick

Changed 50828 atom styles  

> style #!3 ball

Changed 50828 atom styles  

> hide #!3 atoms

> color #2/A-D:1-185 #eef4c2e95fcf

> color #2/A-D:185-505 #9999ffff9999

> color #2/A-D:505-1128 #9999a3d6ffff

> color #2/A-D:1128-1310 #13b1c977ffff

> color #2/E,F,G,H #ffff99999999

> close #2

> close #3

> open "/Users/raoulmartin/Box/Paper/Figures/models for
> figure/finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb"

Summary of feedback from opening /Users/raoulmartin/Box/Paper/Figures/models
for figure/finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb  
---  
warnings | Ignored bad PDB record found on line 36  
  
  
Ignored bad PDB record found on line 42  
  
  
Ignored bad PDB record found on line 97  
  
  
Ignored bad PDB record found on line 103  
  
  
Ignored bad PDB record found on line 159  
  
  
20 messages similar to the above omitted  
  
Chain information for finally_4units_ksdssp_nomdl_ksd_chiansallfix.pdb #2  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> hide atoms

> show cartoons

> color #2/A-D:1-185 #eef4c2e95fcf

> color #2/A-D:185-505 #9999ffff9999

> color #2/A-D:505-1128 #9999a3d6ffff

> color #2/A-D:1128-1310 #13b1c977ffff

> color #2/E,F,G,H #ffff99999999

> show #!1 models

> hide #!1 models

> show #!1 models

> save
> /Users/raoulmartin/Box/Paper/Figures/Fig_1_Whole/ChimeraX/sessionX_v3.cxs

opened ChimeraX session  
Traceback (most recent call last):  
File
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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
"/private/var/folders/05/2zgl_48s6dgfw9v_j79sqy1w0000gn/T/AppTranslocation/B81B278A-86C0-4CB6-84AA-2F083A383E91/d/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 450 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 265.0.0.0.0
      SMC Version (system): 2.38f10

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 21 days 33 minutes

Graphics/Displays:

    Intel HD Graphics 530:

      Chipset Model: Intel HD Graphics 530
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x191b
      Revision ID: 0x0006
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 450:

      Chipset Model: AMD Radeon Pro 450
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00ef
      ROM Revision: 113-C980AF-908
      VBIOS Version: 113-C9801AL-028
      EFI Driver Version: 01.A0.908
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2718Q:
          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: 4K8X777B113L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No
          Adapter Firmware Version: ff.c1

[pett]

Hi Raoul,

This problem was fixed in the build immediately after the one you have, so if you upgrade then things should work. In the build you currently have, due to the quirky nature of this bug you should be able to use the save dialog once, but after that only directly typing the proper "save" command will work. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab