ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3AFA format mmcif fromDatabase pdb

3afa title:  
The human nucleosome structure [more info...]  
  
Chain information for 3afa #1  
---  
Chain | Description | UniProt  
A E | Histone H3.1 | H31_HUMAN 0-135  
B F | Histone H4 | H4_HUMAN 0-102  
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129  
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125  
I J | 146-MER DNA |   
  
Non-standard residues in 3afa #1  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> set bgColor white

> show atoms

> rainbow

> color byhetero

[Repeated 1 time(s)]

> style ball

Changed 12198 atom styles  

> style stick

Changed 12198 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> rainbow

[Repeated 1 time(s)]

> show cartoons

> show atoms

[Repeated 1 time(s)]

> show cartoons

> show atoms

> hide atoms

> show atoms

> hide atoms

> nucleotides ladder

[Repeated 4 time(s)]

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> nucleotides ladder

> show cartoons

[Repeated 1 time(s)]

> color bychain

> color bynucleotide

[Repeated 1 time(s)]

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> nucleotides fill

> style nucleic stick

Changed 5980 atom styles  

> show cartoons

> hide atoms

> show atoms

> hide atoms

> show cartoons

> hide surfaces

> style stick

Changed 12198 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> color bynucleotide

> select /I

3008 atoms, 3354 bonds, 1 pseudobond, 164 residues, 2 models selected  

> color (#!1 & sel) blue

> show target m

> log metadata #1

Metadata for 3afa #1  
---  
Title | The human nucleosome structure  
Citation | Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H. (2010). Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc.Natl.Acad.Sci.USA, 107, 10454-10459. PMID: 20498094. DOI: 10.1073/pnas.1003064107  
Non-standard residues | CL — chloride ion  
MN — manganese (II) ion  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 2.5Å  
  
> select /J

3005 atoms, 3354 bonds, 3 pseudobonds, 161 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel bychain

> color sel sienna

> color sel bychain

> select /I

3008 atoms, 3354 bonds, 1 pseudobond, 164 residues, 2 models selected  

> color (#!1 & sel) #2131a3ff

> select /J

3005 atoms, 3354 bonds, 3 pseudobonds, 161 residues, 2 models selected  

> color (#!1 & sel) #0000ffff

> color sel bynucleotide

> undo

> save C:/Users/Medine/Desktop/Nucelosome_intoduction_Fig1.cxs

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #c8b7b7ff

> select /D/H

1505 atoms, 1496 bonds, 2 pseudobonds, 219 residues, 2 models selected  

> color (#!1 & sel) #ffd5d5ff

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> color sel #de8787ff

> select /B/F

1333 atoms, 1306 bonds, 203 residues, 1 model selected  

> color sel #ac939dff

> select

12198 atoms, 12811 bonds, 362 pseudobonds, 1245 residues, 3 models selected  

> select clear

> 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

  

> nucleotides ladder

[Repeated 1 time(s)]

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 5980 atom styles  

> show atoms

> hide atoms

> select /I/J

6013 atoms, 6708 bonds, 360 pseudobonds, 325 residues, 3 models selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5980 atom styles  

> nucleotides sel ladder

> select clear

> select /J

3005 atoms, 3354 bonds, 3 pseudobonds, 161 residues, 2 models selected  

> ui tool show "Color Actions"

> color (#!1 & sel) #0000ffff

> color (#!1 & sel) #5555ffff

> select clear

> select /J

3005 atoms, 3354 bonds, 3 pseudobonds, 161 residues, 2 models selected  

> color (#!1 & sel) #3771c8ff

> select clear

> select /J

3005 atoms, 3354 bonds, 3 pseudobonds, 161 residues, 2 models selected  

> color (#!1 & sel) #87aadeff

> select clear

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #c8b7b7ff

> color sel #ffdd55ff

> color sel #d4aa00ff

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> color sel #de8787ff

> color sel #d35f5fff

> select /D/H

1505 atoms, 1496 bonds, 2 pseudobonds, 219 residues, 2 models selected  

> color (#!1 & sel) #ffd5d5ff

> color (#!1 & sel) #999999ff

> select /B/F

1333 atoms, 1306 bonds, 203 residues, 1 model selected  

> color sel #ac939dff

> color sel #5aa02cff

> select clear

> select ::name="CL"

4 atoms, 4 residues, 1 model selected  

> hide sel atoms

> select ::name="MN"

8 atoms, 8 residues, 1 model selected  

> select ::name="MN"

8 atoms, 8 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select ::name="MN"

8 atoms, 8 residues, 1 model selected  

> view sel

> select ::name="CL"

4 atoms, 4 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> save C:/Users/Medine/Desktop/Nucelosome_intoduction_Fig1.cxs

> select ::name="CL"::name="HOH"::name="MN"

195 atoms, 1 pseudobond, 195 residues, 2 models selected  

> hide sel atoms

> save C:/Users/Medine/Desktop/Nucelosome_intoduction_Fig1.cxs

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel #d35f5fff target acspfl

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #d4aa00ff target acspfl

> color sel #892ca0ff target acspfl

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #999999ff target acspfl

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> color sel #d35f5fff target acspfl

> select /B/F

1333 atoms, 1306 bonds, 203 residues, 1 model selected  

> color sel #5aa02cff target acspfl

> color sel #217867ff target acspfl

> select clear

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #892ca0ff target acspfl

> select clear

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> select /C/G

1676 atoms, 1660 bonds, 248 residues, 1 model selected  

> color sel #deaa87ff target acspfl

> select /D/H

1505 atoms, 1496 bonds, 2 pseudobonds, 219 residues, 2 models selected  

> color (#!1 & sel) #999999ff target acspfl

> color (#!1 & sel) #892ca0ff target acspfl

> color (#!1 & sel) #d35f5fff target acspfl

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> select /A/E

1671 atoms, 1641 bonds, 250 residues, 1 model selected  

> color sel #217867ff target acspfl

> color sel #d35f5fff target acspfl

> select /B/F

1333 atoms, 1306 bonds, 203 residues, 1 model selected  

> color sel #892ca0ff target acspfl

> color sel #6aaaa5ff target acspfl

> select clear

> select /D/H

1505 atoms, 1496 bonds, 2 pseudobonds, 219 residues, 2 models selected  

> color (#!1 & sel) #999999ff target acspfl

> select clear

> ui tool show "Model Loops"

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version
> None name bp1

Webservices job id: EVSOVIXK2JECQ22A  
Webservices job finished: EVSOVIXK2JECQ22A  
Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type  

> select /C

855 atoms, 845 bonds, 128 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /G

Alignment identifier is 1/G  

> select /G:56

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

> select /G:56

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

> color sel red

> color sel blue

> select /G:61

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

> select /G:61

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

> color sel blue

> select /G:16-22,26-37,45-72,79-97,112-116

546 atoms, 548 bonds, 71 residues, 1 model selected  

> select /G:64

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

> select /G:64

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

> color sel blue

> select /G:16-22,26-37,45-72,79-97,112-116

546 atoms, 548 bonds, 71 residues, 1 model selected  

> select /G:90

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

> select /G:90

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

> color sel blue

> select /G:16-22,26-37,45-72,79-97,112-116

546 atoms, 548 bonds, 71 residues, 1 model selected  

> select /G:91

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

> select /G:91-92

18 atoms, 17 bonds, 2 residues, 1 model selected  

> color sel blue

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> select /C:16-22,26-36,45-73,79-97,112-116

550 atoms, 552 bonds, 71 residues, 1 model selected  

> select /C:56

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

> select /C:56-57

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select /C:16-22,26-36,45-73,79-97,112-116

550 atoms, 552 bonds, 71 residues, 1 model selected  

> select /C:55-56

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C:55-56

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C:56

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

> select /C:56

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

> color sel blue

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> ui tool show "Show Sequence Viewer"

> sequence chain /G

Alignment identifier is 1/G  

> ui tool show "Show Sequence Viewer"

> sequence chain /C /G

Alignment identifier is 1  

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:56

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:56-57

42 atoms, 42 bonds, 4 residues, 1 model selected  

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:56

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:56

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel blue

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:61

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:61-62

34 atoms, 32 bonds, 4 residues, 1 model selected  

> select /C,G:60

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select /C,G:60-61

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select /C,G:61

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:61

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel blue

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:64

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:64-65

34 atoms, 32 bonds, 4 residues, 1 model selected  

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:64

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:64

18 atoms, 16 bonds, 2 residues, 1 model selected  

> color sel blue

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:90

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

> select /C,G:90

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

> color sel blue

> select /C,G:16-22,26-37,45-73,79-97,112-116

1108 atoms, 1112 bonds, 144 residues, 1 model selected  

> select /C,G:91

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:91-92

36 atoms, 34 bonds, 4 residues, 1 model selected  

> color sel blue

> ui tool show "Show Sequence Viewer"

> sequence chain /D /H

Alignment identifier is 2  

> select /D,H:37-49,55-84,90-124

1218 atoms, 1234 bonds, 156 residues, 1 model selected  

> save C:/Users/Medine/Desktop/Nucelosome_intoduction_Fig1.cxs

Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot  
"table_session": self.table.session_info(),  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 687, in session_info  
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'selectedRows'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
ValueError: error processing: 'tools' -> [, , , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , , ] ->  
  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot  
"table_session": self.table.session_info(),  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 687, in session_info  
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'selectedRows'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display  
run(session, cmd)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\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:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D35C621810>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.seq_view.tool.SequenceViewer object at
0x000001D357DAAF90>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
ValueError: error processing: 'tools' -> [, , , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , , ] ->  
  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> save C:/Users/Medine/Desktop/Nucelosome_intoduction_Fig1.cxs

Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot  
"table_session": self.table.session_info(),  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 687, in session_info  
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'selectedRows'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
ValueError: error processing: 'tools' -> [, , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , ] ->  
  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\blastprotein\ui\results.py", line 184, in take_snapshot  
"table_session": self.table.session_info(),  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\ui\widgets\item_table.py", line 687, in session_info  
selected = set([self.model().mapToSource(i).row() for i in
self.selectionModel().selectedRows()])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'selectedRows'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display  
run(session, cmd)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\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:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>: Error while saving session data for 'tools' ->
[<chimerax.modeller.tool.ModellerLauncher object at 0x000001D352CF7610>,
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D32564C690>, <chimerax.color_actions.tool.ColorActions object at
0x000001D336BD5F10>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D336BBD910>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D336BE4B50>, <chimerax.log.tool.Log object at 0x000001D33517AF90>] ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x000001D357D02210>  
  
ValueError: error processing: 'tools' -> [, , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , ] ->  
  
File "C:\Users\Medine\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) HD Graphics 530
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_AT.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: HP
Model: HP ProDesk 600 G3 SFF
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,463,282,176
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
OSLanguage: en-US

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    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-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    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: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0