Unable to restore session, blastprotein missing argument, ChimeraX 1.3

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/charlottebryson/Library/Mobile
> Documents/com~apple~CloudDocs/PhD/Thesis/Chapter 2 Pifithrin-Valine/crystal
> structures/PET-16 NRLLLTG DnaK xtal structure.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 245, in restore_snapshot  
return BlastProteinTool.from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 221, in from_snapshot  
tmp = cls(  
TypeError: __init__() missing 1 required positional argument: 'str'  
  
Log from Thu Jul 10 18:36:08 2025UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:4R5G format mmcif fromDatabase pdb

4r5g title:  
Crystal structure of the DnaK C-terminus with the inhibitor PET-16 [more
info...]  
  
Chain information for 4r5g #1  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
  
Non-standard residues in 4r5g #1  
---  
3JE — triphenyl(phenylethynyl)phosphonium  
  
4r5g mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> select /A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select /B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> surface (#!1 & sel)

> color (#!1 & sel) #8ca0adff

> transparency (#!1 & sel) 20

> select ligand

27 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel #d0a415ff

> color sel #f3df95ff

> color sel #fff3ceff

> color sel #f3df95ff

> color sel #ecc492ff

> color sel byhetero

> select clear

> ui tool show "Blast Protein"

> blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

ChimeraX REST job id: V3QBQTPJZ6VQA0UL  
BlastProtein finished.  
Parsing BLAST results.  

> open pdb:4EZX

Summary of feedback from opening 4EZX fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezx from
http://files.rcsb.org/download/4ezx.cif  
  
4ezx title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLMLTG [more info...]  
  
Chain information for 4ezx #2  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
C D | synthetic peptide NRLMLTG |  
  
Non-standard residues in 4ezx #2  
---  
SO4 — sulfate ion  
  
4ezx mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #2/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezx, chain A (#2), sequence alignment
score = 1015  
RMSD between 172 pruned atom pairs is 1.139 angstroms; (across all 198 pairs:
1.760)  
  

> hide #2 models

> open pdb:4EZW

Summary of feedback from opening 4EZW fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezw from
http://files.rcsb.org/download/4ezw.cif  
  
4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #3  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #3  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #3/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain A (#3), sequence alignment
score = 1006  
RMSD between 179 pruned atom pairs is 1.015 angstroms; (across all 198 pairs:
1.672)  
  

> hide #3#!1 cartoons

> hide #3#!1 atoms

> show #3#!1 atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> hide sel atoms

> hide sel target a

> cartoon hide sel

> surface sel

> style sel stick

Changed 239 atom styles  

> select #2/C#2/D

128 atoms, 112 bonds, 28 residues, 1 model selected  

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> cartoon hide (#!3 & sel)

> hide sel atoms

> show sel atoms

> hide #3.2 models

> hide #3.3 models

> hide #3.4 models

> hide #3.1 models

> hide #!3 models

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> select #2/A

1809 atoms, 1640 bonds, 395 residues, 1 model selected  

> show #1 target ab

> select #2/C

67 atoms, 58 bonds, 15 residues, 1 model selected  

> show #!1 atoms

> select #3/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> hide sel atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

[Repeated 1 time(s)]

> hide #!1 atoms

> select #3/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> open pdb:4EZW

4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #4  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #4  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #4/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain B (#4), sequence alignment
score = 1006  
RMSD between 172 pruned atom pairs is 1.108 angstroms; (across all 198 pairs:
1.748)  
  

> select #4/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> hide sel atoms

> select #4/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> hide sel atoms

> select ligand

692 atoms, 662 bonds, 94 residues, 4 models selected  

> show sel & #4#!1 atoms

> select clear

> select ::name="HOH"

1570 atoms, 1570 residues, 4 models selected  

> hide sel & #4#!1 atoms

> select ::name="3JE"

27 atoms, 30 bonds, 1 residue, 1 model selected  

> select ::name="SO4"

115 atoms, 92 bonds, 23 residues, 3 models selected  

> hide sel & #4 atoms

> select #4/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #a2b6a3ff

> color sel #9dc38eff

> color sel #b7cdb8ff

> color sel #cae2cfff

> color sel #d4dbd5ff

> color sel #c8deceff

> color sel byhetero

> color sel #a2b6a3ff

> color sel byhetero

> select #4/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select #4/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #9c97cbff

> color sel #b7cdb8ff

> select clear

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel byhetero

> select clear

> transparency #1,4 20

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> show sel cartoons

> select clear

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.png" width
> 1294 height 770 supersample 3 transparentBackground true

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.cxs"

> save "/Users/charlottebryson/Desktop/PET-16 NRLLLTG DnaK xtal structure.cxs"

——— End of log from Thu Jul 10 18:36:08 2025 ———

opened ChimeraX session  

> open "/Users/charlottebryson/Library/Mobile
> Documents/com~apple~CloudDocs/PhD/Thesis/Chapter 2 Pifithrin-Valine/crystal
> structures/PET-16 NRLLLTG DnaK xtal structure.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 245, in restore_snapshot  
return BlastProteinTool.from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 221, in from_snapshot  
tmp = cls(  
TypeError: __init__() missing 1 required positional argument: 'str'  
  
Log from Thu Jul 10 18:36:08 2025UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:4R5G format mmcif fromDatabase pdb

4r5g title:  
Crystal structure of the DnaK C-terminus with the inhibitor PET-16 [more
info...]  
  
Chain information for 4r5g #1  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
  
Non-standard residues in 4r5g #1  
---  
3JE — triphenyl(phenylethynyl)phosphonium  
  
4r5g mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> select /A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select /B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> surface (#!1 & sel)

> color (#!1 & sel) #8ca0adff

> transparency (#!1 & sel) 20

> select ligand

27 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel #d0a415ff

> color sel #f3df95ff

> color sel #fff3ceff

> color sel #f3df95ff

> color sel #ecc492ff

> color sel byhetero

> select clear

> ui tool show "Blast Protein"

> blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

ChimeraX REST job id: V3QBQTPJZ6VQA0UL  
BlastProtein finished.  
Parsing BLAST results.  

> open pdb:4EZX

Summary of feedback from opening 4EZX fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezx from
http://files.rcsb.org/download/4ezx.cif  
  
4ezx title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLMLTG [more info...]  
  
Chain information for 4ezx #2  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
C D | synthetic peptide NRLMLTG |  
  
Non-standard residues in 4ezx #2  
---  
SO4 — sulfate ion  
  
4ezx mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #2/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezx, chain A (#2), sequence alignment
score = 1015  
RMSD between 172 pruned atom pairs is 1.139 angstroms; (across all 198 pairs:
1.760)  
  

> hide #2 models

> open pdb:4EZW

Summary of feedback from opening 4EZW fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezw from
http://files.rcsb.org/download/4ezw.cif  
  
4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #3  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #3  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #3/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain A (#3), sequence alignment
score = 1006  
RMSD between 179 pruned atom pairs is 1.015 angstroms; (across all 198 pairs:
1.672)  
  

> hide #3#!1 cartoons

> hide #3#!1 atoms

> show #3#!1 atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> hide sel atoms

> hide sel target a

> cartoon hide sel

> surface sel

> style sel stick

Changed 239 atom styles  

> select #2/C#2/D

128 atoms, 112 bonds, 28 residues, 1 model selected  

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> cartoon hide (#!3 & sel)

> hide sel atoms

> show sel atoms

> hide #3.2 models

> hide #3.3 models

> hide #3.4 models

> hide #3.1 models

> hide #!3 models

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> select #2/A

1809 atoms, 1640 bonds, 395 residues, 1 model selected  

> show #1 target ab

> select #2/C

67 atoms, 58 bonds, 15 residues, 1 model selected  

> show #!1 atoms

> select #3/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> hide sel atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

[Repeated 1 time(s)]

> hide #!1 atoms

> select #3/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> open pdb:4EZW

4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #4  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #4  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #4/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain B (#4), sequence alignment
score = 1006  
RMSD between 172 pruned atom pairs is 1.108 angstroms; (across all 198 pairs:
1.748)  
  

> select #4/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> hide sel atoms

> select #4/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> hide sel atoms

> select ligand

692 atoms, 662 bonds, 94 residues, 4 models selected  

> show sel & #4#!1 atoms

> select clear

> select ::name="HOH"

1570 atoms, 1570 residues, 4 models selected  

> hide sel & #4#!1 atoms

> select ::name="3JE"

27 atoms, 30 bonds, 1 residue, 1 model selected  

> select ::name="SO4"

115 atoms, 92 bonds, 23 residues, 3 models selected  

> hide sel & #4 atoms

> select #4/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #a2b6a3ff

> color sel #9dc38eff

> color sel #b7cdb8ff

> color sel #cae2cfff

> color sel #d4dbd5ff

> color sel #c8deceff

> color sel byhetero

> color sel #a2b6a3ff

> color sel byhetero

> select #4/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select #4/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #9c97cbff

> color sel #b7cdb8ff

> select clear

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel byhetero

> select clear

> transparency #1,4 20

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> show sel cartoons

> select clear

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.png" width
> 1294 height 770 supersample 3 transparentBackground true

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.cxs"

> save "/Users/charlottebryson/Desktop/PET-16 NRLLLTG DnaK xtal structure.cxs"

——— End of log from Thu Jul 10 18:36:08 2025 ———

opened ChimeraX session  

> open "/Users/charlottebryson/Library/Mobile
> Documents/com~apple~CloudDocs/PhD/Thesis/Chapter 2 Pifithrin-Valine/crystal
> structures/PET-16 NRLLLTG DnaK xtal structure.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 245, in restore_snapshot  
return BlastProteinTool.from_snapshot(session, data)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/tool.py", line 221, in from_snapshot  
tmp = cls(  
TypeError: __init__() missing 1 required positional argument: 'str'  
  
Log from Thu Jul 10 18:36:08 2025UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:4R5G format mmcif fromDatabase pdb

4r5g title:  
Crystal structure of the DnaK C-terminus with the inhibitor PET-16 [more
info...]  
  
Chain information for 4r5g #1  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
  
Non-standard residues in 4r5g #1  
---  
3JE — triphenyl(phenylethynyl)phosphonium  
  
4r5g mmCIF Assemblies  
---  
1| author_defined_assembly  
2| software_defined_assembly  
  

> select /A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select /B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> surface (#!1 & sel)

> color (#!1 & sel) #8ca0adff

> transparency (#!1 & sel) 20

> select ligand

27 atoms, 30 bonds, 1 residue, 1 model selected  

> color sel #d0a415ff

> color sel #f3df95ff

> color sel #fff3ceff

> color sel #f3df95ff

> color sel #ecc492ff

> color sel byhetero

> select clear

> ui tool show "Blast Protein"

> blastprotein /B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

ChimeraX REST job id: V3QBQTPJZ6VQA0UL  
BlastProtein finished.  
Parsing BLAST results.  

> open pdb:4EZX

Summary of feedback from opening 4EZX fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezx from
http://files.rcsb.org/download/4ezx.cif  
  
4ezx title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLMLTG [more info...]  
  
Chain information for 4ezx #2  
---  
Chain | Description | UniProt  
A B | Chaperone protein DnaK | DNAK_ECOLI  
C D | synthetic peptide NRLMLTG |  
  
Non-standard residues in 4ezx #2  
---  
SO4 — sulfate ion  
  
4ezx mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #2/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezx, chain A (#2), sequence alignment
score = 1015  
RMSD between 172 pruned atom pairs is 1.139 angstroms; (across all 198 pairs:
1.760)  
  

> hide #2 models

> open pdb:4EZW

Summary of feedback from opening 4EZW fetched from pdb  
---  
note | Fetching compressed mmCIF 4ezw from
http://files.rcsb.org/download/4ezw.cif  
  
4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #3  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #3  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #3/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain A (#3), sequence alignment
score = 1006  
RMSD between 179 pruned atom pairs is 1.015 angstroms; (across all 198 pairs:
1.672)  
  

> hide #3#!1 cartoons

> hide #3#!1 atoms

> show #3#!1 atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> hide sel atoms

> hide sel target a

> cartoon hide sel

> surface sel

> style sel stick

Changed 239 atom styles  

> select #2/C#2/D

128 atoms, 112 bonds, 28 residues, 1 model selected  

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> cartoon hide (#!3 & sel)

> hide sel atoms

> show sel atoms

> hide #3.2 models

> hide #3.3 models

> hide #3.4 models

> hide #3.1 models

> hide #!3 models

> select #3/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> select #2/A

1809 atoms, 1640 bonds, 395 residues, 1 model selected  

> show #1 target ab

> select #2/C

67 atoms, 58 bonds, 15 residues, 1 model selected  

> show #!1 atoms

> select #3/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> show #!1 atoms

> select #3/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> hide sel atoms

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

> select #1/A

1414 atoms, 1426 bonds, 1 pseudobond, 219 residues, 2 models selected  

> select #3/E#3/F#3/G#3/H

239 atoms, 216 bonds, 47 residues, 1 model selected  

> show #!1 atoms

[Repeated 1 time(s)]

> hide #!1 atoms

> select #3/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> select #3/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

> open pdb:4EZW

4ezw title:  
Crystal structure of the substrate binding domain of E.coli DnaK in complex
with the designer peptide NRLLLTG [more info...]  
  
Chain information for 4ezw #4  
---  
Chain | Description | UniProt  
A B C D | Chaperone protein DnaK | DNAK_ECOLI  
E F G H | synthetic peptide NRLLLTG |  
  
Non-standard residues in 4ezw #4  
---  
SO4 — sulfate ion  
  
4ezw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> matchmaker #4/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4r5g, chain B (#1) with 4ezw, chain B (#4), sequence alignment
score = 1006  
RMSD between 172 pruned atom pairs is 1.108 angstroms; (across all 198 pairs:
1.748)  
  

> select #4/A

1808 atoms, 1653 bonds, 383 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/C

1777 atoms, 1650 bonds, 356 residues, 1 model selected  

> hide sel atoms

> select #4/D

1768 atoms, 1663 bonds, 335 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> hide sel atoms

> select ligand

692 atoms, 662 bonds, 94 residues, 4 models selected  

> show sel & #4#!1 atoms

> select clear

> select ::name="HOH"

1570 atoms, 1570 residues, 4 models selected  

> hide sel & #4#!1 atoms

> select ::name="3JE"

27 atoms, 30 bonds, 1 residue, 1 model selected  

> select ::name="SO4"

115 atoms, 92 bonds, 23 residues, 3 models selected  

> hide sel & #4 atoms

> select #4/E

59 atoms, 54 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select #4/B

1817 atoms, 1654 bonds, 392 residues, 1 model selected  

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #a2b6a3ff

> color sel #9dc38eff

> color sel #b7cdb8ff

> color sel #cae2cfff

> color sel #d4dbd5ff

> color sel #c8deceff

> color sel byhetero

> color sel #a2b6a3ff

> color sel byhetero

> select #4/G

61 atoms, 54 bonds, 13 residues, 1 model selected  

> hide sel atoms

> select #4/H

58 atoms, 54 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel #9c97cbff

> color sel #b7cdb8ff

> select clear

> select #4/F

61 atoms, 54 bonds, 13 residues, 1 model selected  

> color sel byhetero

> select clear

> transparency #1,4 20

> select #1/B

1420 atoms, 1436 bonds, 2 pseudobonds, 210 residues, 2 models selected  

> show sel cartoons

> select clear

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.png" width
> 1294 height 770 supersample 3 transparentBackground true

> save "/Users/charlottebryson/PET-16 NRLLLTG DnaK xtal structure.cxs"

> save "/Users/charlottebryson/Desktop/PET-16 NRLLLTG DnaK xtal structure.cxs"

——— End of log from Thu Jul 10 18:36:08 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-23.0.26
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine (1x6x8 (fused) LP
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir9,1
      Processor Name: Dual-Core Intel Core i3
      Processor Speed: 1.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 512 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
      OS Loader Version: 583~1350

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 11 days, 16 hours, 20 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a5c
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0