Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6582 closed defect (duplicate)

Settings save failure when saving non-default color

Reported by: djurenas@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core 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: 0.92 (2020-01-15)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.92 (2020-01-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales lab/++
> Photorhabdus Xenorhabdus collab/NTer
> domain_alphafold/prediction/selected_prediction.pdb"

Chain information for selected_prediction.pdb #1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> set bgColor white

> select /C:1-139

2158 atoms, 2186 bonds, 1 model selected  

> color sel dodger blue

> select /C:1-139

2158 atoms, 2186 bonds, 1 model selected  

> color sel steel blue

> select /C:1-139

2158 atoms, 2186 bonds, 1 model selected  

> select /C:1-139

2158 atoms, 2186 bonds, 1 model selected  

> select /B:1-139

2158 atoms, 2186 bonds, 1 model selected  

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

> color sel dodger blue

> select /A:1-308

4449 atoms, 4485 bonds, 1 model selected  

> select /A:1-308

4449 atoms, 4485 bonds, 1 model selected  
Alignment identifier is 1.A  
Drag select of 9 residues  

> hide sel cartoons

> color sel sienna

> color sel sienna

> color sel pink

> color sel rosy brown

> color sel tan

> color sel hot pink

Drag select of 10 residues  

> select clear

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting simple

> hide sel cartoons

> save session "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales lab/++
> Photorhabdus Xenorhabdus collab/NTer domain_alphafold/prediction/session NTD
> of Rhs AF.cxs"

> save image "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales lab/++
> Photorhabdus Xenorhabdus collab/NTer domain_alphafold/prediction/NTD of Rhs
> AF_side.tif" width 816 height 634

> save image "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales lab/++
> Photorhabdus Xenorhabdus collab/NTer domain_alphafold/prediction/NTD of Rhs
> AF_top.tif" width 816 height 634

> close

> open "/Users/dukasjurenas/Documents/Dukas/+Postdoc Fronzes
> lab/Rhs3/cryosparc_P6_J240_008_volume_map_sharp.mrc"

Opened cryosparc_P6_J240_008_volume_map_sharp.mrc, grid size 256,256,256,
pixel 0.93, shown at level 0.0928, step 1, values float32  

> volume #1 level 0.2406

> movie record

> turn y 2 180

> wait 180

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

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

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie2.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie3.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie3.mp4  
  

> close #1

> open "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales
> lab/crystallo/Tri23/Tre23_alpha/tre23_WT_f06c4.result/tre23-color-
> activesite-chimerasession.cxs" format session

opened ChimeraX session  

> select clear

> hide atoms

> save image /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tre23.tif width 817 height 634

> show sel atoms

> hide sel atoms

> show sel atoms

> show sel atoms

> select clear

> save image /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tre23-active-site.tif width 817 height 634

> close

> open
> /Users/dukasjurenas/Documents/Phenix_data/Tri23/tri23_native/Refine_15/tri23_nat_refine_15.pdb

Chain information for tri23_nat_refine_15.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> select /A:1-106

883 atoms, 904 bonds, 1 model selected  

> color sel green

> color sel spring green

> select /B:1-106

883 atoms, 904 bonds, 1 model selected  

> color sel sea green

> select /A:1-106

883 atoms, 904 bonds, 1 model selected  

> color sel gold

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie4.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie4.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie5.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie5.mp4  
  

> save session /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-session.cxs

> close

> open "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales
> lab/crystallo/Tri23/HDOCK_tretri/all_results/610d081a4d2fc/model_1.pdb"

Summary of feedback from opening /Users/dukasjurenas/Documents/Dukas/+Postdoc
Cascales
lab/crystallo/Tri23/HDOCK_tretri/all_results/610d081a4d2fc/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: lig_610d081a4d2fc.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -210.33  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 27.80  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /A:997-106

Nothing selected  

> select /A:997-106

Nothing selected  

> select /A:997-106

Nothing selected  

> select /A:997-106

Nothing selected  

> select /A:997-106

Nothing selected  

> select /B:1-106

883 atoms, 904 bonds, 1 model selected  

> color sel gold

> select /B:1-106

883 atoms, 904 bonds, 1 model selected  

> close

> open "/Users/dukasjurenas/Documents/Dukas/+Postdoc Cascales lab/++
> Photorhabdus Xenorhabdus collab/ART toxin/TRE-TRI complex
> prediction/prediction/selected_prediction.pdb"

Chain information for selected_prediction.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> select /A:1-106

1767 atoms, 1788 bonds, 1 model selected  

> color sel gold

> select /B:1-106

1767 atoms, 1788 bonds, 1 model selected  

> color sel sea green

> select /C:1-129

2061 atoms, 2081 bonds, 1 model selected  

> color sel firebrick

> select /D:1-129

2061 atoms, 2081 bonds, 1 model selected  

> color sel firebrick

> select clear

> lighting shadows true

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> save session "/Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-Tre23 session.cxs"

> save image "/Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-Tre23 side.tif" width 864 height 634

> save image "/Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-Tre23 bottom.tif" width 864 height 634

> save image "/Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-Tre23 side-imm-centered.tif" width 864 height 634

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie6.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie6.mp4  
  

> close

> open /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-session.cxs format session

opened ChimeraX session  

> graphics silhouettes true

> lighting simple

> save image /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-bottom.tif width 864 height 634

> save image /Users/dukasjurenas/Documents/Dukas/Lecture/TA-
> Collectif/Tri23-side.tif width 864 height 634

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/dukasjurenas/Desktop/movie7.mp4

Movie saved to /Users/dukasjurenas/Desktop/movie7.mp4  
  

> close

> open "/Users/dukasjurenas/Documents/Dukas/ongoing articles/CheA
> article/comparison acetyltransferases/pdbs/Dpa-codecolor.cxs" format session

opened ChimeraX session  

> select /A:1-106

1693 atoms, 1717 bonds, 1 model selected  

> select /B:1-106

1636 atoms, 1655 bonds, 1 model selected  

> select /C:1-129

160 atoms, 164 bonds, 1 model selected  

> select /D:1-129

18 atoms, 1 model selected  

> select /A:1-106

1693 atoms, 1717 bonds, 1 model selected  

> select /A:1-106

1693 atoms, 1717 bonds, 1 model selected  
Alignment identifier is 1.A  

> hide sel cartoons

> graphics silhouettes false

> lighting soft

> select /A:1-106

1693 atoms, 1717 bonds, 1 model selected  

> color sel goldenrod

> color sel goldenrod

> select clear

> lighting full

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> lighting full

> graphics silhouettes false

> lighting shadows false

> select /B:1-106

1636 atoms, 1655 bonds, 1 model selected  

> close

> open "/Users/dukasjurenas/Documents/Dukas/ongoing articles/CheA
> article/comparison acetyltransferases/pdbs/monomers for alignments/polimaine
> version/Dpa-polyamine.cxs" format session

opened ChimeraX session  

Expected an integer >= 1 or a keyword  

Expected a number or a keyword  

Expected an integer >= 1 or a keyword  

> turn y 180 models #1

> select /A:1-106

845 atoms, 866 bonds, 1 model selected  

> color sel cornflower blue

> color sel gold

> color sel goldenrod

> graphics silhouettes false

> lighting full

> lighting shadows false

> lighting soft

> lighting soft

> lighting simple

> select clear

> turn y 180 models #1

> turn y 180 models #1

> turn x 180 models #1

> hide sel cartoons

> color sel steel blue

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> close

> open "/Users/dukasjurenas/Documents/Phenix_data/BapT project/BapT-I-Trx-
> eco/menage a trois-ref12.cxs"

opened ChimeraX session  
Alignment identifier is 1.A  
Alignment identifier is 1.B  
Alignment identifier is 1.C  

> hbonds sel

7 hydrogen bonds found  

> hbonds sel

2 hydrogen bonds found  

> hbonds sel

2 hydrogen bonds found  

> ~hbonds

> hbonds sel

0 hydrogen bonds found  

> ~hbonds

> hbonds sel

17 hydrogen bonds found  

> ~hbonds

> select clear

> hbonds

528 hydrogen bonds found  

> ~hbonds

> hbonds sel

3 hydrogen bonds found  

> ~hbonds

> show sel atoms

> show sel atoms

> hbonds sel

7 hydrogen bonds found  

> select clear

> ~hbonds

> hide sel atoms

> select clear

> hide atoms

> show sel atoms

> show sel atoms

> select clear

> select clear

> hbonds sel

5 hydrogen bonds found  

> show sel atoms

> hide sel atoms

> show sel atoms

> hbonds sel

7 hydrogen bonds found  

> color sel steel blue

> color sel orange

> select clear

Drag select of  

> save image "/Users/dukasjurenas/Documents/Dukas/ongoing
> articles/BapT/figures_structures/M-a-3-hydrogen-bonds.tif" width 913 height
> 1013

> save session "/Users/dukasjurenas/Documents/Dukas/ongoing
> articles/BapT/figures_structures/M-a-3-hydrogen-bonds.cxs"

> close #1

> open "/Users/dukasjurenas/Documents/Phenix_data/BapT project/BapT-
> BapI/Refine_3/sesssion_color.cxs"

opened ChimeraX session  

> color sel orange

> select clear

Alignment identifier is 1.A  
Destroying pre-existing alignment with identifier 1.B  
Alignment identifier is 1.B  

> show sel atoms

> hbonds sel

16 hydrogen bonds found  

> ~hbonds

> show sel atoms

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> ~hbonds

> select H

1044 atoms, 1 model selected  

> hide sel target a

> select

3200 atoms, 3247 bonds, 1 model selected  

> hide sel atoms

> show sel atoms

> select H

1044 atoms, 1 model selected  

> hide sel target a

> toolshed show Contacts

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/gui.py", line 570, in get_command  
self.settings.save(settings=saveables)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 205, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__  
self._session, value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string  
return self.from_str(str_value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 46, in literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
[0.3764706 0.91764706 0.9764706 1. ]  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
[0.3764706 0.91764706 0.9764706 1. ]  
^  
SyntaxError: invalid syntax  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  

> select clear

> toolshed show Contacts

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/tool.py", line 55, in run_command  
run(self.session, " ".join(self.gui.get_command()))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/clashes/gui.py", line 570, in get_command  
self.settings.save(settings=saveables)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/settings.py", line 205, in save  
ConfigFile.__setattr__(self, name, self._cur_settings[name], call_save=False)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 359, in __setattr__  
self._session, value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 488, in convert_to_string  
new_value = self.convert_from_string(session, str_value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/configfile.py", line 482, in convert_from_string  
return self.from_str(str_value)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 46, in literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 1  
[0.5647059 1. 0.96862745 1. ]  
^  
SyntaxError: invalid syntax  
  
File "", line 1  
[0.5647059 1. 0.96862745 1. ]  
^  
SyntaxError: invalid syntax  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ast.py",
line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Settings save failure when saving non-default color

comment:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Dukas,

Thanks for reporting this error. It has been fixed in more recent releases of ChimeraX, so if you upgrade your ChimeraX you won't run into it again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by djurenas@…, 4 years ago 

Hi Eric,
thanks! great, I actually realised it crashed because of the color change only after a few runs. I will upgrade asap

thank you again

Dukas
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