id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20259 Save MD analysis GUI info in sessions Zach Pearson Eric Pettersen "{{{ 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' -> [, , , , , , , ] -> 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' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> 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' -> [, , , , , , , ] -> 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' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> 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 }}} " defect closed normal Sessions fixed all ChimeraX