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#20259 closed defect (fixed)

Save MD analysis GUI info in sessions

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

Description

The following bug report has been submitted:
Platform:        macOS-26.4.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202605011815 (2026-05-01 18:15:32 UTC)
Description
Trying to save a session with one of the md_crds guis open.

Log:
UCSF ChimeraX version: 1.12.dev202605011815 (2026-05-01)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help

> open 48725 fromDatabase emdb

Summary of feedback from opening 48725 fetched from emdb  
---  
notes | Fetching compressed map 48725 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-48725/map/emd_48725.map.gz  
Fetching map header 48725 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-48725/header/emd-48725.xml  
  
Opened emdb 48725 as #1, grid size 336,336,336, pixel 0.96, shown at level
0.093, step 2, values float32, fit PDB 9my3  

> ui tool show anim

> scenes save 1

> color bfactor #1

No atoms specified  

> open 9my3

9my3 title:  
Structure of Xenopus KCNQ1-CaM in GDN [more info...]  
  
Chain information for 9my3 #2  
---  
Chain | Description | UniProt  
A C E G | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA 66-610  
B D F H | Calmodulin-1 | CALM1_HUMAN 1-149  
  

> color bfactor #1

No atoms specified  

> close #1

> close #2

> open 9my3

9my3 title:  
Structure of Xenopus KCNQ1-CaM in GDN [more info...]  
  
Chain information for 9my3 #1  
---  
Chain | Description | UniProt  
A C E G | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA 66-610  
B D F H | Calmodulin-1 | CALM1_HUMAN 1-149  
  

> open 48725 fromDatabase emdb

Opened emdb 48725 as #2, grid size 336,336,336, pixel 0.96, shown at level
0.093, step 2, values float32, fit PDB 9my3  

> color bfactor #1

15004 atoms, 1904 residues, atom bfactor range 63 to 228  

> color zone #4 near #1 distance 10

color zone: No surfaces specified.  

> color zone #2 near #1 distance 10

> rock angle 90 center #4 cycle 600 frames 600

Invalid "center" argument: Center argument no objects specified  

> scenes save 2

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> scenes restore 1

[Repeated 1 time(s)]

> scenes restore 2

> scenes restore 1

> close

> open 9my3 9my4

9my3 title:  
Structure of Xenopus KCNQ1-CaM in GDN [more info...]  
  
Chain information for 9my3 #1  
---  
Chain | Description | UniProt  
A C E G | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA 66-610  
B D F H | Calmodulin-1 | CALM1_HUMAN 1-149  
  
9my4 title:  
Structure of Xenopus KCNQ1(E150R/R221E)-CaM with the VSD in the intermediate
state [more info...]  
  
Chain information for 9my4 #2  
---  
Chain | Description | UniProt  
A C E G | Potassium voltage-gated channel subfamily KQT member 1 | KCNQ1_XENLA 66-610  
B D F H | Calmodulin-1 | CALM1_HUMAN 1-149  
  

> scenes save 3

> hide atoms

> show cartoons

> scenes save 4

> matchmaker #2 to #1

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 9my3, chain A (#1) with 9my4, chain A (#2), sequence alignment
score = 2524.3  
RMSD between 284 pruned atom pairs is 0.639 angstroms; (across all 339 pairs:
2.216)  
  

> scenes save 5

> morph #1, 2

Computed 51 frame morph #3  

> coordset #3 1,51

> scenes save 6

> scenes save 7

> changechains #1 C,G,D,H G,C,H,D

Chain IDs of 952 residues changed  

> morph #1, 2

Computed 51 frame morph #4  

> coordset #4 1,51

> close #3

> close #4

> morph #1, 2

Computed 51 frame morph #3  

> coordset #3 1,51

> scenes save 8

> scenes save 9

> show #!3 models

> hide #!2 models

> hide #!1 models

> scenes save 10

> scenes save 11

> scenes save 12

> scenes restore 11

> color #3/B,D,F,H yellow

> color #3/A,C,E,G skyblue

> lighting soft

> scenes save 13

> coordset #3 1,51 bounce true loop 3

> open 48725 fromDatabase emdb

Opened emdb 48725 as #4, grid size 336,336,336, pixel 0.96, shown at level
0.093, step 2, values float32, fit PDB 9my3  

> color bfactor #1

15004 atoms, 1904 residues, atom bfactor range 63 to 228  

> scenes save 14

> color zone #4 near #1 distance 10

> scenes save 15

> hide #3 models

> show #1 models

> hide #1 cartoons

> select #1/A:217-232

132 atoms, 133 bonds, 16 residues, 1 model selected  

> show sel

> style #1 stick

Changed 15004 atom styles  

> color #1 tan

> color #1 byhetero

> volume zone #4 nearAtoms sel range 3

> scenes save 16

> volume #4 style mesh

> scenes save 17

> transparency #4 50

> scenes save 18

> label sel bgColor black

> scenes save 19

> hbonds sel reveal true restrict cross interModel false select true

9 hydrogen bonds found  

> scenes save 20

> label sel

> scenes save 21

> hide #1,4 models

> show #3 models

> scenes save 22

> hide #3 atoms, ribbons

> select #3/A:217-232

128 atoms, 129 bonds, 16 residues, 1 model selected  

> show sel atoms,ribbons

> scenes save 23

> style #3 stick

Changed 14968 atom styles  

> scenes save 24

> color sel byhetero

> scenes save 25

> label sel bgColor yellow

> scenes save 26

> select clear

> scenes save 27

> scenes save 28

> scenes save 29

> save movie2025.cxs

Traceback (most recent call last):  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot  
from chimerax.md_crds.gui import get_session_info  
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/md_crds/gui.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x13156d810>,
<chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x15a297090>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 731, in save  
mgr.discovery(self._state_containers)  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x13156d810>, <chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x13156d810>,
<chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x15a297090>  
  
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->  
  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot  
from chimerax.md_crds.gui import get_session_info  
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/md_crds/gui.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x13156d810>,
<chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x15a297090>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute  
cmd.run(cmd_text)  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/commands/cli.py",
line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/commands/cli.py",
line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/zjp/git/rbvi/ChimeraX/develop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 731, in save  
mgr.discovery(self._state_containers)  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> [<chimerax.log.tool.Log object at
0x13156d810>, <chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>: Error while saving session data for 'tools' ->
[<chimerax.log.tool.Log object at 0x13156d810>,
<chimerax.animations.tool.AnimationsTool object at 0x14298f210>,
<chimerax.map.volume_viewer.VolumeViewer object at 0x148555e90>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x15a297090>, <chimerax.model_panel.tool.ModelPanel object at 0x101bc20d0>,
<chimerax.cmd_line.tool.CommandLine object at 0x13158ed50>,
<chimerax.help_viewer.tool.HelpUI object at 0x1456de150>,
<chimerax.toolbar.tool.ToolbarTool object at 0x1454201d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x15a297090>  
  
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->  
  
File "/Users/zjp/git/rbvi/ChimeraX/develop/src/bundles/core/src/session.py",
line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> save movie2025.cxs




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 Performance and 2 Efficiency)
      Memory: 16 GB
      System Firmware Version: 18000.101.7
      OS Loader Version: 18000.101.7

Software:

    System Software Overview:

      System Version: macOS 26.4.1 (25E253)
      Kernel Version: Darwin 25.4.0
      Time since boot: 5 hours, 49 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.2
    ChimeraX-AtomicLibrary: 14.4
    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-CamTools: 0.1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3.1
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202605011815
    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: 1.2.1
    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: 1.8.2
    ChimeraX-Label: 1.4
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    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-MatchAlign: 1.0.1
    ChimeraX-MatchMaker: 2.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.5.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-TutorialReadFormat: 0.1
    ChimeraX-UI: 1.50.5
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    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: 8.3.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    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: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 6.7.1
    narwhals: 2.18.1
    narwhals: 2.20.0
    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: 2.4.3
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.6
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.5.2
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    py-spy: 0.4.2
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.3
    pydantic-settings: 2.14.0
    pydantic_core: 2.46.3
    pydata-sphinx-theme: 0.17.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.5.0
    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: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.26
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 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: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.3.4
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.14.0
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.6.3
    uvicorn: 0.44.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.23.0

Change History (2)

comment:1 by Eric Pettersen, 8 days ago

Component:	Unassigned → Sessions
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Save MD analysis GUI info in sessions

comment:2 by Eric Pettersen, 22 hours ago

Resolution:	→ fixed
Status:	accepted → closed

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