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\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"
Alignment identifier is 1
Alignment identifier is 7/A
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\alphafold\predict.py", line 244, in _unzip_results
z.extractall(dir)
File "C:\Program Files\ChimeraX\bin\Lib\zipfile.py", line 1677, in extractall
self._extract_member(zipinfo, path, pwd)
File "C:\Program Files\ChimeraX\bin\Lib\zipfile.py", line 1731, in
_extract_member
open(targetpath, "wb") as target:
^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\Mika
Jekabsons\\\Downloads\\\ChimeraX\\\AlphaFold\\\prediction_4\\\af233.csv'
PermissionError: [Errno 13] Permission denied: 'C:\\\Users\\\Mika
Jekabsons\\\Downloads\\\ChimeraX\\\AlphaFold\\\prediction_4\\\af233.csv'
File "C:\Program Files\ChimeraX\bin\Lib\zipfile.py", line 1731, in
_extract_member
open(targetpath, "wb") as target:
^^^^^^^^^^^^^^^^^^^^^^
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
Unclear what happened. The logs shows they started 3 alphafold predictions and somehow two returned results to the same prediction_4 directory and the second one didn't want to overwrite the files of the unzipped first one. Doesn't seem too plausible.