Opened 21 months ago

Closed 18 months ago

#14404 closed defect (fixed)

Session restore, tasks: KeyError

Reported by: jekabson@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "C:\\\Protein structures\\\BclxLVDAC1 human chimera.cxs"

Log from Thu Dec 21 11:58:35 2023UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "C:\Protein structures\BclxL human WT.cxs" format session

Log from Wed Dec 20 17:00:37 2023 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> ui tool show AlphaFold

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold search
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequence" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help help:user

> alphafold predict
> "msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> ui tool show "Side View"

[Repeated 1 time(s)]

> alphafold predict
> openmsqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"openmsqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> openmsqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"openmsqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> open"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"

Missing or invalid "sequences" argument: Sequences argument
"open"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk""
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> help help:user/tools/alphafold.html

> alphafold search openAF-Q07817-F1

Missing or invalid "sequence" argument: Sequences argument "openAF-Q07817-F1"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold search AF-Q07817-F1

Missing or invalid "sequence" argument: Sequences argument "AF-Q07817-F1" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> ui tool show "Side View"

> alphafold search AF-Q07817-F-

Missing or invalid "sequence" argument: Sequences argument "AF-Q07817-F-" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold search AF-Q07817-F1

Missing or invalid "sequence" argument: Sequences argument "AF-Q07817-F1" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold match AF-Q07817-F1 trim false

Missing or invalid "sequences" argument: Sequences argument "AF-Q07817-F1" is
not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold match 1BXL trim false

Missing or invalid "sequences" argument: Sequences argument "1BXL" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold search 1BXL

Missing or invalid "sequence" argument: Sequences argument "1BXL" is not a
chain specifier, alignment id, UniProt id, or sequence characters  
Fetching compressed Q07817 UniProt info from
https://www.uniprot.org/uniprot/Q07817.xml  

> alphafold search Q07817

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  

> alphafold predict Q07817

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 3 time(s)]AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_1  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_1\best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> alphafold predict
> msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk

Missing or invalid "sequences" argument: Sequences argument
"msqsnrelvvdflsyklsqkgyswsqfsdveenrteapegtesemetpsaingnpswhladspavngatahsssldarevavpptyadlgksardvftkgygfgfsdltsqlhitpgtayqsfeqvvnelfrdgvnwgrivaffsfggalcvesvdkemqvlvsriaawmatylndhlepwiqenggwdtfvelygnnaaaesrkgqerfnrwfltgmtvagvvllgslfsrk"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> save "C:/Program Files/ChimeraX/bin/human BclxL wild type.cxs"

[Errno 13] Permission denied: 'C:/Program Files/ChimeraX/bin/human BclxL wild
type.cxs.17456.tmp'  

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> save "C:/Protein structures/BclxL human WT.cxs"

——— End of log from Wed Dec 20 17:00:37 2023 ———

opened ChimeraX session  

> ui tool show AlphaFold

> alphafold predict #1

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
[Repeated 2 time(s)]AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

AlphaFold prediction matching best_model.pdb #1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 0.00 | 233 | 233 | 100  
  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

AlphaFold prediction matching best_model.pdb #1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 0.00 | 233 | 233 | 100  
  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

AlphaFold prediction matching best_model.pdb #1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 0.00 | 233 | 233 | 100  
  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb

AlphaFold prediction matching best_model.pdb #1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 0.00 | 233 | 233 | 100  
  

> hide #1 models

> hide #2 models

> log metadata #1

The model has no metadata

> log chains #1

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

> log metadata #2

The model has no metadata

> log chains #2

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> log metadata #3

The model has no metadata

> log chains #3

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> log metadata #4

The model has no metadata

> log chains #4

Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
  

> log metadata #5

The model has no metadata

> log chains #5

Chain information for best_model.pdb #5  
---  
Chain | Description  
A | No description available  
  

> log metadata #6

The model has no metadata

> log chains #6

Chain information for best_model.pdb #6  
---  
Chain | Description  
A | No description available  
  

> show #3-6 atoms

[Repeated 1 time(s)]

> hide #3-6 atoms

> show #3-6 cartoons

> hide #3-6 cartoons

> show #3-6 cartoons

> show #3-6 surfaces

> hide #!3-6 surfaces

> show #!3-6 surfaces

> hide #!3-6 surfaces

> hide #!3 models

> hide #!4 models

> hide #!5 models

> select add #6

1837 atoms, 1880 bonds, 233 residues, 1 model selected  

> select subtract #6

1 model selected  

> hide #!6 models

> show #!5 models

> show #!6 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> select add #5

1837 atoms, 1880 bonds, 233 residues, 1 model selected  

> select subtract #5

1 model selected  

> show #!6 target m

> hide #!6 models

> view

[Repeated 1 time(s)]

> coulombic #!5

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #5.1: minimum, -18.59, mean
-2.44, maximum 12.62  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!5

Map values for surface "best_model.pdb_A SES surface": minimum -26.78, mean
-5.57, maximum 26.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!5

Coulombic values for best_model.pdb_A SES surface #5.1: minimum, -18.59, mean
-2.44, maximum 12.62  
To also show corresponding color key, enter the above coulombic command and
add key true  

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  

> show #!5 cartoons

[Repeated 2 time(s)]

> mlp #!5

Map values for surface "best_model.pdb_A SES surface": minimum -26.78, mean
-5.57, maximum 26.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!5

Coulombic values for best_model.pdb_A SES surface #5.1: minimum, -18.59, mean
-2.44, maximum 12.62  
To also show corresponding color key, enter the above coulombic command and
add key true  

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  

> show #!5 cartoons

> show #!5 atoms

> hide #!5 atoms

> color #!5 bychain

> rainbow #!5

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  

> hide #!5 surfaces

> show #!5 cartoons

Alignment identifier is 1  
Alignment identifier is 2  

> show #!5 cartoons

> hide #!5 cartoons

> show #!5 cartoons

> hide #5.1 models

> show #5.1 models

> select
> #1/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231
> #2/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231
> #3/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231
> #4/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231
> #5/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231
> #6/A:3-20,24-26,28-33,83-100,102-111,119-130,137-156,160-184,187-195,202-231

7380 atoms, 7494 bonds, 906 residues, 6 models selected  

> select add #4

7987 atoms, 8125 bonds, 988 residues, 10 models selected  

> select add #3

8594 atoms, 8756 bonds, 1070 residues, 10 models selected  

> select subtract #3

6757 atoms, 6876 bonds, 837 residues, 9 models selected  

> select subtract #4

4920 atoms, 4996 bonds, 604 residues, 7 models selected  

> select subtract #5.1

3690 atoms, 3747 bonds, 453 residues, 5 models selected  

> view #5 clip false

> log metadata #5

No models had metadata

> log chains #5

Chain information for best_model.pdb #5  
---  
Chain | Description  
A | No description available  
  

> log metadata #5

No models had metadata

> log chains #5

Chain information for best_model.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hbonds #!5 reveal true

2000 hydrogen bonds found  

> ~hbonds

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  
Alignment identifier is 3  

> show #!5 target m

> volume style surface

No volumes specified  

> hide #!5 surfaces

> hide #!5 cartoons

> show #!5 cartoons

> hbonds #!5 reveal true

2000 hydrogen bonds found  

> hbonds #!5 reveal true

2000 hydrogen bonds found  

> show #!5 atoms

> hide #!5 atoms

> ~hbonds

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!6 models

> select add #6

4297 atoms, 4378 bonds, 535 residues, 4 models selected  

> select subtract #6

2460 atoms, 2498 bonds, 302 residues, 3 models selected  

> hide #!6 atoms

Alignment identifier is 4  

> log metadata #6

No models had metadata

> log chains #6

Chain information for best_model.pdb #6  
---  
Chain | Description  
A | No description available  
  

> log metadata #6

No models had metadata

> log chains #6

Chain information for best_model.pdb #6  
---  
Chain | Description  
A | No description available  
  

> view #6 clip false

> open "C:\Users\Mika
> Jekabsons\Downloads\ChimeraX\AlphaFold\prediction_1\best_model.pdb" format
> pdb

Chain information for best_model.pdb #7  
---  
Chain | Description  
A | No description available  
  

> hide #7 models

> close #7

> show #!6 target m

Alignment identifier is 5  

> select add #6

4297 atoms, 4378 bonds, 535 residues, 3 models selected  

> select subtract #6

2460 atoms, 2498 bonds, 302 residues, 3 models selected  

> select #1/A:83 #2/A:83

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:83 #2/A:83

16 atoms, 14 bonds, 2 residues, 2 models selected  
5 [ID: 5] region 2 chains [83] RMSD: 0.000  
  

> select #1/A:83-84 #2/A:83-84

26 atoms, 24 bonds, 4 residues, 2 models selected  

> select #1/A:83-86 #2/A:83-86

50 atoms, 48 bonds, 8 residues, 2 models selected  
5 [ID: 5] region 2 chains [83-86] RMSD: 0.000  
  

> select add #2

1862 atoms, 1904 bonds, 237 residues, 2 models selected  

> select add #1

3674 atoms, 3760 bonds, 466 residues, 2 models selected  

> hide #!6 target m

> select subtract #2

1837 atoms, 1880 bonds, 233 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #5.1 models

> show #5.1 models

> show #!5 cartoons

> hide #!5 cartoons

> show #!5 cartoons

> nucleotides #!5 tube/slab shape box

> nucleotides #!5 atoms

> style nucleic & #!5 stick

Changed 0 atom styles  

> hide #!5 models

> hide #5.1 models

> show #5.1 models

> hide #!5 models

Alignment identifier is 1  

> show #!5 target m

[Repeated 1 time(s)]

> hide #!5 target m

Alignment identifier is 2  

> show #!5 target m

> show #!6 models

> hide #!5 models

> alphafold predict #6

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_3  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_3\best_model.pdb

AlphaFold prediction matching best_model.pdb #6/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 0.00 | 233 | 233 | 100  
  

> hide #7 models

> hide #!6 models

> show #7 models

Alignment identifier is 1  

> log metadata #7

The model has no metadata

> log chains #7

Chain information for best_model.pdb #7  
---  
Chain | Description  
A | No description available  
  

> log metadata #7

The model has no metadata

> log chains #7

Chain information for best_model.pdb #7  
---  
Chain | Description  
A | No description available  
  

> log metadata #7

The model has no metadata

> log chains #7

Chain information for best_model.pdb #7  
---  
Chain | Description  
A | No description available  
  

> close #7

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 atoms

> hide #!4 models

> show #!3 models

> hide #!3 atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A #3/A #4/A #5/A #6/A

Alignment identifier is 1  

> ui tool show "Modeller Comparative"

> alphafold search #6

[Repeated 1 time(s)]

> alphafold predict #6

Running AlphaFold prediction  

> alphafold search #6

> alphafold predict #5

Running AlphaFold prediction  

> alphafold predict #5

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\Mika Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_4  

> open C:\Users\Mika
> Jekabsons/Downloads/ChimeraX/AlphaFold/prediction_4\best_model.pdb

AlphaFold prediction matching best_model.pdb #5/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 10.13 | 233 | 233 | 91  
  

> hide #!3 models

> show #2 models

> hide #2,7 atoms

> hide #2 models

> save "C:/Protein structures/BclxLVDAC1 human chimera.cxs"

——— End of log from Thu Dec 21 11:58:35 2023 ———

opened ChimeraX session  

> open "C:/Protein structures/BclxLVDAC1 human chimera.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 713, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 713, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 514, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 37, in open  
return cxs_open(session, data, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 1017, in open  
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 755, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
KeyError: 4  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  

> open "C:/Protein structures/BclxLVDAC1 human chimera.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 713, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 713, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\dialog.py", line 334, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 514, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 37, in open  
return cxs_open(session, data, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 1017, in open  
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 755, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 641, in reset_state  
task.terminate()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 208, in terminate  
self.session.tasks.remove(self)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 556, in remove  
self.__delitem__(task.id)  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
KeyError: 4  
  
KeyError: 4  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\tasks.py",
line 545, in __delitem__  
task = self._tasks[key]  
~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.1338
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7400
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,981,233,664
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Component: Unassigned → Sessions
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session restore, tasks: KeyError

comment:2 by Zach Pearson, 18 months ago

Resolution: → fixed
Status: assigned → closed

It is ​no longer possible for that function to fail.

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