Opened 2 hours ago

#19418 new defect

ChimeraX bug report submission

Reported by: 2410928@… Owned by:
Priority: normal Milestone:
Component: Unassigned Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform:
Project:

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
I have been looking at and annotating protein and peptide models but do not seem to be able to save a session. I can save a pdb file but this does not include colors or labels. I have been able to save sessions when I used chimerax on a different computer some years ago.....

Log:
Log from Mon Nov 17 16:20:00 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\ChimeraX\PSR1 initial.cxs" format
> session

Log from Mon Nov 17 13:27:10 2025 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: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/2410928/Downloads/AF-Q9S807-F1-model_v6.pdb

AF-Q9S807-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for phosphate starvation regulator protein
(Q9S807) [more info...]  
  
Chain information for AF-Q9S807-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | phosphate starvation regulator protein | Q9S807_CHLRE 1-752  
  
Computing secondary structure  

> select /A:1-752

5318 atoms, 5429 bonds, 752 residues, 1 model selected  

> style sel sphere

Changed 5318 atom styles  

> style sel sphere

Changed 5318 atom styles  

> rainbow sel

> style sel ball

Changed 5318 atom styles  

> show sel atoms

> style sel sphere

Changed 5318 atom styles  

> color sel bychain

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.1: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow sel

[Repeated 1 time(s)]

> mlp sel

Map values for surface "AF-Q9S807-F1-model_v6.pdb_A SES surface": minimum
-27.96, mean -6.166, maximum 22.46  
To also show corresponding color key, enter the above mlp command and add key
true  

> style sel sphere

Changed 5318 atom styles  

> style sel ball

Changed 5318 atom styles  

> style sel stick

Changed 5318 atom styles  

> style sel sphere

Changed 5318 atom styles  

> style sel ball

Changed 5318 atom styles  

> show sel atoms

> show sel cartoons

> lighting simple

> lighting soft

> graphics silhouettes true

> view

> view orient

> lighting full

> close

> open C:\Users\2410928\Downloads\AF-Q9S807-F1-model_v6.pdb format pdb

AF-Q9S807-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for phosphate starvation regulator protein
(Q9S807) [more info...]  
  
Chain information for AF-Q9S807-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | phosphate starvation regulator protein | Q9S807_CHLRE 1-752  
  
Computing secondary structure  

> open C:\Users\2410928\Downloads\AF-Q9S807-F1-model_v6.pdb format pdb

AF-Q9S807-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for phosphate starvation regulator protein
(Q9S807) [more info...]  
  
Chain information for AF-Q9S807-F1-model_v6.pdb #2  
---  
Chain | Description | UniProt  
A | phosphate starvation regulator protein | Q9S807_CHLRE 1-752  
  
Computing secondary structure  

> view clip false

> log metadata #1

Metadata for AF-Q9S807-F1-model_v6.pdb #1  
---  
Title | Alphafold monomer V2.0 prediction for phosphate starvation regulator protein (Q9S807)  
Source (natural) | Chlamydomonas reinhardtii  
  
> log chains #1

Chain information for AF-Q9S807-F1-model_v6.pdb #1  
---  
Chain | Description | UniProt  
A | phosphate starvation regulator protein | Q9S807_CHLRE 1-752  
  

> log metadata #2

Metadata for AF-Q9S807-F1-model_v6.pdb #2  
---  
Title | Alphafold monomer V2.0 prediction for phosphate starvation regulator protein (Q9S807)  
Source (natural) | Chlamydomonas reinhardtii  
  
> log chains #2

Chain information for AF-Q9S807-F1-model_v6.pdb #2  
---  
Chain | Description | UniProt  
A | phosphate starvation regulator protein | Q9S807_CHLRE 1-752  
  

> select add #1

5318 atoms, 5429 bonds, 752 residues, 1 model selected  

> select ::name="CYS"

24 atoms, 20 bonds, 4 residues, 2 models selected  

> label sel attribute name

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  
'pip install pyKVFinder' failed. Error from pip:  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder  
import pyKVFinder  
ModuleNotFoundError: No module named 'pyKVFinder'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool  
check_pyKVFinder(session.logger)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder  
run(logger.session, pip_cmd, log=False)  
File "C:\Program Files\ChimeraX 1.10.1\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 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip  
raise RuntimeError(s)  
RuntimeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\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 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #!2 models

> select add #1

5330 atoms, 5439 bonds, 754 residues, 3 models selected  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> coulombic sel & #!1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel & #!1

Map values for surface "AF-Q9S807-F1-model_v6.pdb_A SES surface": minimum
-27.96, mean -6.166, maximum 22.46  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

[Repeated 1 time(s)]

> coulombic sel & #!1

Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

> help help:user

> ui mousemode right "mark point"

> cd "C:/Users/2410928/OneDrive - Swansea
> University/Documents/Research/Area_Ch1/ChimeraX"

Current working directory is: C:\Users\2410928\OneDrive - Swansea
University\Documents\Research\Area_Ch1\ChimeraX  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1/A:153 #2/A:153

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:153-167 #2/A:153-167

170 atoms, 172 bonds, 30 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [153-167] RMSD:
0.000  
  

> toolshed show

Downloading bundle chimerax_isolde-1.10.1-cp311-cp311-win_amd64.whl  
[Repeated 1 time(s)]

> ui tool show "Selection Inspector"

> style sel & #!1 sphere

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> color (#!1 & sel) red

> marker #3 position 0.6345,13.37,25.63 color yellow radius 1

> marker #3 position -17.22,-51.6,-38.82 color yellow radius 1

> label sel attribute name

> save "C:/Users/2410928/OneDrive - Swansea
> University/Documents/Research/Area_Ch1/ChimeraX/PSR1 initial.cxs"

[Repeated 1 time(s)]

——— End of log from Mon Nov 17 13:27:10 2025 ———

> view name session-start

opened ChimeraX session  

> cartoon hide sel

> select #1/A:153 #2/A:153

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:153-167 #2/A:153-167

170 atoms, 172 bonds, 30 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [153-167] RMSD:
0.000  
  

> name frozen revertant sel

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

[Repeated 1 time(s)]

> show sel & #!1 cartoons

> style sel & #!1 stick

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> show sel & #!1 atoms

> surface style #1 mesh

> undo

[Repeated 2 time(s)]

> show sel & #!1 atoms

> style sel & #!1 ball

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> color (#!1 & sel) lime

> surface style #1 solid

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 85 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "initial styles" "space-filling (chain colors)"

Using preset: Initial Styles / Space-Filling (Chain Colors)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> undo

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> show sel & #!1 atoms

[Repeated 1 time(s)]

> style sel & #!1 sphere

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> color (#!1 & sel) cyan

> color (#!1 & sel) cornflower blue

> color (#!1 & sel) light sea green

> select clear

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 85 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "initial styles" "space-filling (chain colors)"

Using preset: Initial Styles / Space-Filling (Chain Colors)  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "chain id coloring (opaque)"

Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)  
Changed 10636 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> select #1/A:153-167 #2/A:153-167

170 atoms, 172 bonds, 30 residues, 2 models selected  

> color (#!1 & sel) cornflower blue

> style sel & #!1 sphere

Changed 85 atom styles  

> show sel & #!1 atoms

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> undo

[Repeated 1 time(s)]

> redo

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 85 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> style sel & #!1 sphere

Changed 85 atom styles  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> show sel & #!1 atoms

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 85 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> cofr sel

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

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

> select #1/A:1-512 #2/A:1-512

7232 atoms, 7386 bonds, 1024 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [1-512] RMSD:
0.000  
  

> select #1/A:717-752 #2/A:717-752

572 atoms, 578 bonds, 72 residues, 2 models selected  

> select #1/A:282-752 #2/A:282-752

6552 atoms, 6674 bonds, 942 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [282-752] RMSD:
0.000  
  

> select #1/A:282 #2/A:282

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

> select #1/A:141-282 #2/A:141-282

2084 atoms, 2126 bonds, 284 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [141-282] RMSD:
0.000  
  

> select

10638 atoms, 10858 bonds, 1506 residues, 6 models selected  

> color (#!1 & sel) yellow

> color (#!1 & sel) black

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> style sel & #!1 sphere

Changed 5318 atom styles  

> style sel & #!1 sphere

Changed 5318 atom styles  

> style sel & #!1 ball

Changed 5318 atom styles  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> select down

10638 atoms, 10858 bonds, 1506 residues, 8 models selected  

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> color (#!1 & sel) dim gray

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> lighting soft

> lighting full

> lighting simple

> ui tool show "Selection Inspector"

> view sel

> select #1/A:44-85 #2/A:44-85

612 atoms, 626 bonds, 84 residues, 2 models selected  

> select #1/A:44-92 #2/A:44-92

696 atoms, 710 bonds, 98 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [44-92] RMSD:
0.000  
  

> select #1/A:153 #2/A:153

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:153-163 #2/A:153-163

124 atoms, 124 bonds, 22 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [153-163] RMSD:
0.000  
  

> show sel & #!1 atoms

[Repeated 1 time(s)]

> style sel & #!1 sphere

Changed 62 atom styles  

> select #1/A:194-207,215-222,229-244,376-427,429-431,492-528,539-551,654-678
> #2/A:194-207,215-222,229-244,376-427,429-431,492-528,539-551,654-678

2736 atoms, 2760 bonds, 336 residues, 2 models selected  

> select #1/A:153-163 #2/A:153-163

124 atoms, 124 bonds, 22 residues, 2 models selected  

> select #1/A:153 #2/A:153

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:153-167 #2/A:153-167

170 atoms, 172 bonds, 30 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [153-167] RMSD:
0.000  
  

> style sel & #!1 sphere

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> style sel & #!1 sphere

Changed 85 atom styles  

> show sel & #!1 atoms

> color (#!1 & sel) light sea green

> save C:\ProgramData\ChimeraX\image1.png supersample 3

> save "C:/Users/2410928/OneDrive - Swansea
> University/Documents/Research/Area_Ch1/ChimeraX/PSR1 model showing affected
> region.cxs"

> save C:\ProgramData\ChimeraX\image2.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie1.mp4

Movie saved to C:\ProgramData\ChimeraX\movie1.mp4  
  

> save "C:/Users/2410928/OneDrive - Swansea
> University/Documents/Research/Area_Ch1/ChimeraX/PSR1 model showing affected
> region.cxs"

——— End of log from Mon Nov 17 16:20:00 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1 models

> show #!2 models

> show #!3 models

> select #1/A:147 #2/A:147

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/A:147-165 #2/A:147-165

234 atoms, 236 bonds, 38 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [147-165] RMSD:
0.000  
  

> color (#!2 & sel) orange

> label (#!2 & sel) atoms attribute name

> label size 12 height fixed

> show #!1 models

> hide #!2 models

> select add #1

5435 atoms, 5547 bonds, 771 residues, 5 models selected  

> ui mousemode right select

> show sel & #!1 atoms

> color sel & #!1 byhetero

> hide sel & #!1 surfaces

> style sel & #!1 stick

Changed 5318 atom styles  

> color (#!1 & sel) forest green

> ~label (#!1 & sel) atoms

> ui mousemode right label

> label #1/A:530

> label #1/A:529

> label (#!1 & sel) atoms attribute name

> transparency (#!1 & sel) 70

> select ::name="CYS"

24 atoms, 20 bonds, 4 residues, 2 models selected  

> ~label (#!1 & sel) residues

> select

10638 atoms, 10858 bonds, 1506 residues, 6 models selected  

> show sel & #!1,3 surfaces

> coulombic sel & #!1,3

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue mark (net charge +0) with am1-bcc method  
Could not determine GAFF type for atom markers #3/M mark 1 M  
Could not determine GAFF type for atom markers #3/M mark 2 M  
Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
Coulombic values for markers_M SES surface #3.2: minimum, 0.00, mean 0.00,
maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel & #!1,3

Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
Coulombic values for markers_M SES surface #3.2: minimum, 0.00, mean 0.00,
maximum 0.00  
To also show corresponding color key, enter the above coulombic command and
add key true  

> surface style #1,3 solid

> transparency (#!1,3 & sel) 70

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

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

> select #1/A:1-3 #2/A:1-3

50 atoms, 48 bonds, 6 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [1-3] RMSD:
0.000  
  

> hide sel & #!1 surfaces

> show sel & #!1 surfaces

> color (#!1 & sel) magenta

> select #1/A:145-146 #2/A:145-146

28 atoms, 28 bonds, 4 residues, 2 models selected  

> select #1/A:145-165 #2/A:145-165

262 atoms, 266 bonds, 42 residues, 2 models selected  
Phosphate Starvation Regulator Protein [ID: 1] region 2 chains [145-165] RMSD:
0.000  
  

> color (#!1 & sel) lime

> view clip false

> hide sel & #!1 surfaces

[Repeated 1 time(s)]

> undo

> show sel & #!1 surfaces

> label (#!1 & sel) attribute name

> undo

> ~label (#!1 & sel) residues

> hide #!3 models

> close #2

> close #3

> select /A:145

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:145-164

127 atoms, 129 bonds, 20 residues, 1 model selected  

> select /A:146

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:146-165

127 atoms, 129 bonds, 20 residues, 1 model selected  

> label (#!1 & sel) attribute name

> label size 20 height fixed

> label size 12 height fixed

> label size 10 height fixed

[Repeated 1 time(s)]

> ~label (#!1 & sel) residues

> select clear

> select

5318 atoms, 5429 bonds, 752 residues, 2 models selected  

> ~label (#!1 & sel) residues

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select clear

Alignment identifier is 1/A  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> lighting full

[Repeated 1 time(s)]

> lighting simple

> color (#!1 & sel) blue

> select /A:3

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1-3

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> 2dlabels

> 2dlabels text N terminal

Expected a keyword  

> 2dlabels text "N terminal"

> undo

> hide #!2 models

> show #!2 models

> select add #2

8 atoms, 7 bonds, 1 residue, 4 models selected  

> hide #1.1 models

> close #1.1

> close #1.2

> close #2

> select /A:146

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:146-165

127 atoms, 129 bonds, 20 residues, 1 model selected  

> color sel lime

> select /A:145

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:1-145

1038 atoms, 1066 bonds, 145 residues, 1 model selected  

> color sel cyan

> color sel light sea green

> color sel cornflower blue

> select /A:105

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:15-105

680 atoms, 701 bonds, 91 residues, 1 model selected  

> select /A:236

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:236-244

84 atoms, 84 bonds, 9 residues, 1 model selected  

> select /A:395

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:395-400

53 atoms, 53 bonds, 6 residues, 1 model selected  

> select /A:153

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:153-154

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:96-146

349 atoms, 356 bonds, 51 residues, 1 model selected  

> select /A:96-180

587 atoms, 601 bonds, 85 residues, 1 model selected  

> select /A:146

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:146-165

127 atoms, 129 bonds, 20 residues, 1 model selected  

> label sel attribute name

> label size 10 height fixed

> label size 6 height fixed

> label size 5 height fixed

[Repeated 1 time(s)]

> label sel attribute label_one_letter_code

> ~label sel residues

> label sel text "mutation region"

> undo

> ~label sel residues

> select /A:146

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:146-165

127 atoms, 129 bonds, 20 residues, 1 model selected  

> ~label sel residues

> select /A:153

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:153

6 atoms, 5 bonds, 1 residue, 1 model selected  

> label sel text "psr1-1 mutation site"

> label size 5 height fixed

> label size 10 height fixed

> label size 12 height fixed

[Repeated 1 time(s)]

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> label sel text N-terminus

> label size 12 height fixed

[Repeated 1 time(s)]

> select /A:337-387

328 atoms, 330 bonds, 51 residues, 1 model selected  

> select /A:337-386

319 atoms, 321 bonds, 50 residues, 1 model selected  

> select /A:184

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:184-244

485 atoms, 496 bonds, 61 residues, 1 model selected  

> color sel orange

> color sel purple

> select /A:190

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:190

8 atoms, 7 bonds, 1 residue, 1 model selected  

> label sel text "HTH myb-type"

> label size 12 height fixed

[Repeated 1 time(s)]

> label size 10 height fixed

> label size 11 height fixed

[Repeated 2 time(s)]

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image1.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image2.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image3.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image4.png" supersample 3

> show sel surfaces

[Repeated 1 time(s)]

> coulombic sel

Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select

5318 atoms, 5429 bonds, 752 residues, 2 models selected  

> coulombic sel

Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency (#!1 & sel) 70

> style sel sphere

Changed 5318 atom styles  

> style sel stick

Changed 5318 atom styles  

> show sel atoms

> style sel stick

Changed 5318 atom styles  

> show sel atoms

> hide sel atoms

> hide sel cartoons

[Repeated 2 time(s)]

> show sel cartoons

> select clear

> mlp

Map values for surface "AF-Q9S807-F1-model_v6.pdb_A SES surface": minimum
-27.96, mean -6.166, maximum 22.46  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Coulombic values for AF-Q9S807-F1-model_v6.pdb_A SES surface #1.2: minimum,
-18.34, mean -1.56, maximum 10.63  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select

5318 atoms, 5429 bonds, 752 residues, 2 models selected  

> transparency (#!1 & sel) 70

> select clear

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image5.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image6.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image7.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image8.png" supersample 3

> save "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\image9.png" supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode "C:\Users\2410928\OneDrive - Swansea
> University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold
> analysis\movie1.mp4"

Movie saved to \C:Users\\...\Pepfold analysis\movie1.mp4  
  

> cd "C:/Users/2410928/OneDrive - Swansea
> University/Documents/Research/Area_Ch1/Area1Notes/Var.7.PSR1/Pepfold
> analysis"

Current working directory is: C:\Users\2410928\OneDrive - Swansea
University\Documents\Research\Area_Ch1\Area1Notes\Var.7.PSR1\Pepfold analysis  

> label delete residues

[Repeated 1 time(s)]

> 2dlabels text "N terminal"

> hide #!3 target m

> select add #3

2 models selected  

> ui favorite true "Model Panel"

> ui tool show "Model Panel"

> view #3 clip false

No displayed objects specified.  

> show #!3 models

> show #!3 target m

> close #3

> file save session

Unknown command: file save session  

> save session

Cannot determine format for 'session'  

> label size 11 height fixed

Label command requires an atom specifier to create labels.  

> export scene

Unknown command: export scene  

> help help:user

> ui mousemode right "pick blobs"

> export

Unknown command: export  

> save

Missing or invalid "fileName" argument: Expected a file name  

> save_session

Unknown command: save_session  

> session_save

Unknown command: session_save  

> session-save

Unknown command: session-save  




OpenGL version: 3.3.0 - Build 32.0.101.7077
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 650 15.6 inch G10 Notebook PC
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 16,794,288,128
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-ChopChopMF: 1.0
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    pandas: 2.3.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt5: 5.15.11
    PyQt5-Qt5: 5.15.2
    PyQt5_sip: 12.17.1
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

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