id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9457 vseries unreliable coloring Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC) Description I haven't been able to figure out exactly what triggers it (seems more common with `movie record` and `perframe`, but there's some weirdness that happens when a vseries is coloured with `color zone`, where some frames will randomly drop their vertex colouring and revert to the original flat colour. Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc > 01_cryosparc_P3_J103_006_volume_map_A_state.mrc > 02_cryosparc_P3_J104_007_volume_map_A_state.mrc > 03_cryosparc_P3_J105_006_volume_map_A_state.mrc > 04_cryosparc_P3_J107_007_volume_map_A_state.mrc > 05_cryosparc_P3_J108_006_volume_map_A_state.mrc > 06_cryosparc_P3_J111_006_volume_map_A_state.mrc > 07_cryosparc_P3_J112_006_volume_map_A_state.mrc vseries true No such file/path: 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc > cd ""C:/Users/Tristan Croll/Documents/Structures/anti- > isrib/2023_07_21_cryosparc_pooled_classification"" Current working directory is: C:\Users\Tristan Croll\Documents\Structures\anti- isrib\2023_07_21_cryosparc_pooled_classification > open 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc > 01_cryosparc_P3_J103_006_volume_map_A_state.mrc > 02_cryosparc_P3_J104_007_volume_map_A_state.mrc > 03_cryosparc_P3_J105_006_volume_map_A_state.mrc > 04_cryosparc_P3_J107_007_volume_map_A_state.mrc > 05_cryosparc_P3_J108_006_volume_map_A_state.mrc > 06_cryosparc_P3_J111_006_volume_map_A_state.mrc > 07_cryosparc_P3_J112_006_volume_map_A_state.mrc vseries true Opened map series 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc as #1, 8 images, grid size 400,400,400, pixel 1.14, shown at level 0.0481, step 2, values float32 > volume #1.1 level 0.1348 > volume #1.1 step 1 > volume #1.1 level 0.2162 > close #1.2-8#1#1.1 > open 01_cryosparc_P3_J103_006_volume_map_A_state.mrc > 02_cryosparc_P3_J104_007_volume_map_A_state.mrc > 03_cryosparc_P3_J105_006_volume_map_A_state.mrc > 04_cryosparc_P3_J107_007_volume_map_A_state.mrc > 05_cryosparc_P3_J108_006_volume_map_A_state.mrc > 06_cryosparc_P3_J111_006_volume_map_A_state.mrc > 07_cryosparc_P3_J112_006_volume_map_A_state.mrc > 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc vseries true Opened map series 01_cryosparc_P3_J103_006_volume_map_A_state.mrc as #1, 8 images, grid size 400,400,400, pixel 1.14, shown at level 0.06, step 2, values float32 > volume #1.1 step 1 > volume #1.1 level 0.1727 > volume #1.1 level 0.2496 > open ""C:/Users/Tristan Croll/Documents/Structures/anti- > isrib/pooled_datasets/cryosparc_P3_J50_009_model.cif"" Summary of feedback from opening C:/Users/Tristan Croll/Documents/Structures/anti- isrib/pooled_datasets/cryosparc_P3_J50_009_model.cif --- warnings | Atom H is not in the residue template for GLY /C:8 Atom H is not in the residue template for VAL /E:167 Atom H is not in the residue template for GLY /D:8 Atom H is not in the residue template for VAL /F:167 Chain information for cryosparc_P3_J50_009_model.cif #2 --- Chain | Description A B | No description available C D | No description available E F | No description available G H | No description available I J | No description available > select #2 60871 atoms, 60644 bonds, 2 pseudobonds, 4489 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.43214,0.88781,-0.15825,-44.307,-0.90163,0.42185,-0.095436,364.03,-0.017971,0.18393,0.98278,-34.149 > view matrix models > #2,0.23012,0.95571,-0.18348,-7.5021,-0.95835,0.25532,0.12798,364.58,0.16916,0.14639,0.97466,-67.01 > fitmap #2 inMap #1.1 Fit molecule cryosparc_P3_J50_009_model.cif (#2) to map 01_cryosparc_P3_J103_006_volume_map_A_state.mrc (#1.1) using 60871 atoms average map value = 0.2433, steps = 140 shifted from previous position = 7.5 rotated from previous position = 13 degrees atoms outside contour = 35652, contour level = 0.24957 Position of cryosparc_P3_J50_009_model.cif (#2) relative to 01_cryosparc_P3_J103_006_volume_map_A_state.mrc (#1.1) coordinates: Matrix rotation and translation 0.21805953 0.97593385 0.00177771 -44.97743871 -0.97593187 0.21805342 0.00311197 401.54659465 0.00264944 -0.00241352 0.99999358 0.38708014 Axis -0.00283086 -0.00044661 -0.99999589 Axis point 228.09400564 228.84196039 0.00000000 Rotation angle (degrees) 77.40528249 Shift along axis -0.43908879 > hide #2&~:UNL > select clear > open ""C:/Users/Tristan > Croll/Documents/Structures/isrib_workup/6o85_rebuild.pdb"" Chain information for 6o85_rebuild.pdb #3 --- Chain | Description A | No description available B | No description available C D | No description available E F | No description available G | No description available H | No description available I J | No description available L | No description available S | No description available d | No description available > matchmaker #3/E to #2/E 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 cryosparc_P3_J50_009_model.cif, chain E (#2) with 6o85_rebuild.pdb, chain E (#3), sequence alignment score = 1776.3 RMSD between 354 pruned atom pairs is 0.431 angstroms; (across all 356 pairs: 0.468) > hide #!2 models > hide #3&~:C7B > hide HC > color :C7B orange > color byhetero > setattr :C7B bonds radius 0.4 Assigning radius attribute to 56 items > select #1.1 2 models selected > lighting soft > select clear > cofr centerOfView showPivot true > lighting soft > cofr showPivot false > volume #1.1 level 0.3059 > hide #!1 models > movie record size 1920,1080 > show #!1 models > usage vseries Subcommands are: * vseries align * vseries measure * vseries play * vseries save * vseries slider * vseries stop > perframe ""movie duplicate 15"" > vseries play #1 > wait 8 > perframe stop > movie stop > pwd Current working directory is: C:\Users\Tristan Croll\Documents\Structures\anti- isrib\2023_07_21_cryosparc_pooled_classification > movie encode pooled_maps_playthrough_isrib_site.mp4 Movie saved to pooled_maps_playthrough_isrib_site.mp4 > show #1.1 models > hide #!1 models > movie record > show #!1 models > movie stop > movie reset > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie encode pooled_maps_playthrough_isrib_site.mp4 Movie saved to pooled_maps_playthrough_isrib_site.mp4 > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie reset > movie record size 1920,1080 > movie stop > movie reset > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie encode overview.mp4 Movie saved to overview.mp4 > color zone #1 near #2 > color #2 bychain > color zone #1 near #2 > volume #1.1 level 0.2726 > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie encode fulcrum_and_t_helix.mp4 Movie saved to fulcrum_and_t_helix.mp4 > color zone #1 near #2 > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie reset > color zone #1.1-1.8 near #2 color zone: No surfaces specified. > color zone #1 near #2 > movie reset No movie being recorded. > movie record size 1920,1080 > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_b4pn --0001.ppm' > perframe stop > movie reset > color zone #1 near #2 > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie reset > color zone #1 near #2 > hide #!1 models > movie record size 1920,1080 > show #!1 models > perframe ""color zone #1 near #2; movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie reset > color zone #1 near #2 > hide #!1 models > movie record > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie encode isrib_site.mp4 Movie saved to isrib_site.mp4 > color zone #1 near #2 > movie record > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_QpdU --0001.ppm' > perframe stop > movie stop > movie reset > color zone #1 near #2 > movie record > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_FoR2 --0001.ppm' > perframe stop > movie reset > movie record > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_M9Dz --0001.ppm' > perframe stop > movie stop > movie reset > color zone #1 near #2 > hide #!1 models > movie record > show #!1 models > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 > perframe stop > movie stop > movie encode overview.mp4 Movie saved to overview.mp4 > color zone #1 near #2 > hide #!1 models > show #!1 models > movie record > movie stop > movie reset > movie record > perframe ""movie duplicate 15"" > vseries play #1 > wait 9 Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_GKYs --0001.ppm' > perframe stop > movie stop > movie reset > hide #!1 models > show #!1 models > color zone #1 near #2 > show #2 > style #!3 stick Changed 70792 atom styles > show #!2 models > hide #!3 models > color byhetero > select #2 60871 atoms, 60644 bonds, 2 pseudobonds, 4489 residues, 2 models selected > style sel stick Changed 60871 atom styles > select #1.1 2 models selected > hide HC > cartoon > hide #!1 models > show #!1 models > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > volume #1.4 level 0.2625 > show #!2 models > hide #!2 models OpenGL version: 3.3.0 NVIDIA 518.01 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46 ChimeraX-AtomicLibrary: 10.0.7 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.3 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202307112022 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.2 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.30.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.40.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2023.3.16 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.7 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.8.1 prompt-toolkit: 3.0.39 psutil: 5.9.4 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.6 PyOpenGL-accelerate: 3.1.6 pyparsing: 3.1.0 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.3 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 WMI: 1.5.1 }}} " defect closed normal Volume Data not a bug all ChimeraX