id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17430 Restore session: invalid MRC header value andysen@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3-arm64-arm-64bit ChimeraX Version: 1.8rc202406102315 (2024-06-10 23:15:52 UTC) Description cannot open the session Log: UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/Extreme Pro/P1/tail/sheath_normal/new/session_fit_whole.cxs"" Error opening map ""/Volumes/Extreme Pro/P1/tail/sheath_normal/new/session_fit_whole.cxs"": File session_fit_whole.cxs, format mrc MRC header value nsymbt (15866409) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 757, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8-rc2024.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Wed May 10 14:32:25 2023UCSF ChimeraX version: 1.5.dev202210110346 (2022-10-11) © 2016-2022 Regents of the University of California. All rights reserved. > open /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_1.cxs format > session Unable to parse symmetry operators of P1_tail.mrc b'{\n\t""compression"": 0, \n\t""filename"": ""P1_tail.mrc"", \n\t""image"": [{\n\t\t""average"": 0.00149451, \n\t\t""background"": 0, \n\t\t""fom"": 1, \n\t\t""maximum"": 0.501089, \n\t\t""minimum"": -0.293842, \n\t\t""number"": 1, \n\t\t""origin"": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t""sampling"": [\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t""select"": 1, \n\t\t""standard_deviation"": 0.031601, \n\t\t""view"": [\n\t\t\t0, 0, 1, 0\n\t\t]\n\t}], \n\t""label"": ""bimg -verb 7 -size 512,512,512 -origin 256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc P1_tail.mrc "", \n\t""pointgroup"": ""C1"", \n\t""spacegroup"": 0, \n\t""time"": 1658610729, \n\t""user"": ""andy"", \n\t""version"": ""2.1.3-20210901""\n}\n' Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694, shown at level 0.1, step 1, values float32 Log from Wed May 10 12:57:24 2023UCSF ChimeraX version: 1.5.dev202210110346 (2022-10-11) © 2016-2022 Regents of the University of California. All rights reserved. > open /Volumes/Anindito/P1/tail/sheath_normal/all_previous/ses1.cxs format > session Unable to parse symmetry operators of P1_tail.mrc b'{\n\t""compression"": 0, \n\t""filename"": ""P1_tail.mrc"", \n\t""image"": [{\n\t\t""average"": 0.00149451, \n\t\t""background"": 0, \n\t\t""fom"": 1, \n\t\t""maximum"": 0.501089, \n\t\t""minimum"": -0.293842, \n\t\t""number"": 1, \n\t\t""origin"": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t""sampling"": [\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t""select"": 1, \n\t\t""standard_deviation"": 0.031601, \n\t\t""view"": [\n\t\t\t0, 0, 1, 0\n\t\t]\n\t}], \n\t""label"": ""bimg -verb 7 -size 512,512,512 -origin 256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc P1_tail.mrc "", \n\t""pointgroup"": ""C1"", \n\t""spacegroup"": 0, \n\t""time"": 1658610729, \n\t""user"": ""andy"", \n\t""version"": ""2.1.3-20210901""\n}\n' Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694, shown at level 0.1, step 1, values float32 Log from Sat Jul 23 16:26:39 2022UCSF ChimeraX version: 1.3.dev202104230049 (2021-04-23) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/andy/Documents/p1/sheath_normal/P1_tail.mrc Summary of feedback from opening /Users/andy/Documents/p1/sheath_normal/P1_tail.mrc --- notes | Unable to parse symmetry operators of P1_tail.mrc b'{\n\t""compression"": 0, \n\t""filename"": ""P1_tail.mrc"", \n\t""image"": [{\n\t\t""average"": 0.00149451, \n\t\t""background"": 0, \n\t\t""fom"": 1, \n\t\t""maximum"": 0.501089, \n\t\t""minimum"": -0.293842, \n\t\t""number"": 1, \n\t\t""origin"": [\n\t\t\t256, 256, 256\n\t\t], \n\t\t""sampling"": [\n\t\t\t0.69445, 0.69445, 0.69445\n\t\t], \n\t\t""select"": 1, \n\t\t""standard_deviation"": 0.031601, \n\t\t""view"": [\n\t\t\t0, 0, 1, 0\n\t\t]\n\t}], \n\t""label"": ""bimg -verb 7 -size 512,512,512 -origin 256,256,256 -samp 0.69445 cryosparc_P4_J176_006_volume_map_sharp.mrc P1_tail.mrc "", \n\t""pointgroup"": ""C1"", \n\t""spacegroup"": 0, \n\t""time"": 1658610729, \n\t""user"": ""andy"", \n\t""version"": ""2.1.3-20210901""\n}\n' Opened P1_tail.mrc as #1, grid size 512,512,512, pixel 0.694,0.694,0.694, shown at level 0.152, step 2, values float32 > volume #1 step 1 > lighting soft > volume #1 level 0.1 > lighting shadows true intensity 0.5 > lighting full > ui tool show ""Side View"" > ui tool show ""Surface Color"" > color cylindrical #1.1 palette #ff0000:#ffffff:#0000ff center > -7.6294e-06,0,1.043 > ac wb Unknown command: ac wb > set bgColor white > color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:100.4,#0000ff center > -7.6294e-06,0,1.043 > color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:90,#0000ff center > -7.6294e-06,0,1.043 > color cylindrical #1.1 palette 0,#ff0000:80,#ffffff:100,#0000ff center > -7.6294e-06,0,1.043 > color cylindrical #1.1 palette 0,#ff0000:70,#ffffff:100,#0000ff center > -7.6294e-06,0,1.043 > lighting soft [Repeated 1 time(s)] > lighting full > lighting soft > lighting full > graphics silhouettes true > save /Users/andy/Documents/p1/sheath_normal/image2.tif width 740 height 597 > supersample 3 > color cylindrical #1.1 palette 0,#0000ff:70,#ffffff:100,#ff0000 center > -7.6294e-06,0,1.043 > color cylindrical #1.1 palette 0,#ff0000:70,#ffffff:100,#0000ff center > -7.6294e-06,0,1.043 > save /Users/andy/Documents/p1/sheath_normal/ses1.cxs ——— End of log from Sat Jul 23 16:26:39 2022 ——— opened ChimeraX session > open /Volumes/Anindito/P1/tail/sheath_normal/new/new_sheath_ring.pdb Chain information for new_sheath_ring.pdb #2 --- Chain | Description B V W X Y Z | No description available > ui tool show ""Side View"" > hide #!1 models > select add #2 24018 atoms, 24504 bonds, 3174 residues, 1 model selected > show #!1 models > select subtract #2 Nothing selected > select add #2 24018 atoms, 24504 bonds, 3174 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 24018 atoms, 24504 bonds, 3174 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 24018 atoms, 24504 bonds, 3174 residues, 1 model selected > ui mousemode right translate > select clear > show cartoons > hide atoms > volume #1 style mesh > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule new_sheath_ring.pdb (#2) to map P1_tail.mrc (#1) using 24018 atoms average map value = 0.03914, steps = 88 shifted from previous position = 2.71 rotated from previous position = 0.788 degrees atoms outside contour = 18944, contour level = 0.1 Position of new_sheath_ring.pdb (#2) relative to P1_tail.mrc (#1) coordinates: Matrix rotation and translation 0.99998631 -0.00406135 0.00329806 -0.61103413 0.00410299 0.99991072 -0.01271664 2.36806838 -0.00324612 0.01273000 0.99991370 -0.35889780 Axis 0.92486505 0.23785035 0.29673533 Axis point 0.00000000 26.94170884 188.05601229 Rotation angle (degrees) 0.78823974 Shift along axis -0.10837587 > select add #2 24018 atoms, 24504 bonds, 3174 residues, 1 model selected > ui mousemode right ""translate selected atoms"" > select subtract #2 Nothing selected > fitmap #2 inMap #1 Fit molecule new_sheath_ring.pdb (#2) to map P1_tail.mrc (#1) using 24018 atoms average map value = 0.1406, steps = 60 shifted from previous position = 1.57 rotated from previous position = 1.64 degrees atoms outside contour = 8243, contour level = 0.1 Position of new_sheath_ring.pdb (#2) relative to P1_tail.mrc (#1) coordinates: Matrix rotation and translation 0.99979130 0.02040689 -0.00096007 -1.93526745 -0.02040535 0.99979052 0.00159357 3.50327467 0.00099238 -0.00157365 0.99999827 -0.74075150 Axis -0.07728427 -0.04764227 -0.99587015 Axis point 172.40236343 93.86907961 0.00000000 Rotation angle (degrees) 1.17411536 Shift along axis 0.72035408 > cd /Volumes/Anindito/P1/tail/sheath_normal/new Current working directory is: /Volumes/Anindito/P1/tail/sheath_normal/new > save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_1.cxs ——— End of log from Wed May 10 12:57:24 2023 ——— opened ChimeraX session > hide #!1 models > show #!1 models > select /B 4003 atoms, 4084 bonds, 529 residues, 1 model selected > select ~sel 20015 atoms, 20420 bonds, 2645 residues, 3 models selected > delete atoms (#2 & sel) > delete bonds (#2 & sel) > select clear > sym #2 c6*h,39.15,19.32,6,-2 > save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_whole.cxs > lighting full > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting flat > lighting full > lighting soft > lighting simple > select : 401-529 992 atoms, 1012 bonds, 129 residues, 1 model selected > ui tool show ""Color Actions"" > hide #!1 models > show #!1 models > select : 401-529 992 atoms, 1012 bonds, 129 residues, 1 model selected > ui tool show ""Color Actions"" > color sel fire brick > select : 222-400 1347 atoms, 1375 bonds, 179 residues, 1 model selected > color sel cornflower blue > select : 102-221 918 atoms, 933 bonds, 120 residues, 1 model selected > color sel salmon > select : 1-101 746 atoms, 761 bonds, 101 residues, 1 model selected > color sel dark turquoise > select clear > hide #!1 models > show #!1 models > save /Volumes/Anindito/P1/tail/sheath_normal/new/session_fit_whole.cxs ——— End of log from Wed May 10 14:32:25 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MXCU3LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3 (23D2057) Kernel Version: Darwin 23.3.0 Time since boot: 57 days, 8 hours, 58 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202406102315 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Sessions duplicate all ChimeraX