id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15674 Restore new session in old ChimeraX chkaiser@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Opened a ChimeraX-session from collaborator Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/christoph/ownCloud/BiochSoc/FromFloAndBettina/Segmentation_Fig3/L1G1W_ts003_chimeraX.cxs Opened L1G1W_ts003_AD.mrc as #2, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 0.34, step 1, values float32 Log from Mon Jul 15 13:21:12 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /mnt/beegfs/schurgrp/bzens/ECMpaper_deposition/segmentation/DONE_crosssection_L1g1w_TS003/session.cxs Opened dust_final.mrc as #2, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 0.0272, step 2, values float32 Opened L1g1w_TS003_bin8_correct_trimmed.mrc as #3, grid size 510,720,121, pixel 17.1, shown at level 0.347, step 2, values float32 Log from Mon Jul 10 09:55:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Volumes/jhansen/group/schurgrp/jhansen/Betty_segmentation/June2023/DONE_crosssection_L1g1w_TS003/session.cxs Opened dust_final.mrc as #2, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 0.0272, step 2, values float32 Opened L1g1w_TS003_bin8_correct_trimmed_inverted_resampled.mrc as #3, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 1.51, step 2, values float32 Log from Thu Jul 6 16:49:37 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Volumes/jhansen/group/schurgrp/jhansen/Betty_segmentation/June2023/DONE_crosssection_L1g1w_TS003/session.cxs Opened dust_final.mrc as #2, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 0.0272, step 2, values float32 Opened L1g1w_TS003_bin8_correct_trimmed_inverted_resampled.mrc as #3, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 1.51, step 2, values float32 Log from Fri Jun 16 12:24:18 2023UCSF ChimeraX version: 1.7.dev202306022041 (2023-06-02) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/jessehansen/Desktop/Betty_temp/L1G1W_ts003_COLLAGEN.stl Opened STL file L1G1W_ts003_COLLAGEN.stl containing 493765 triangles > open > /Users/jessehansen/Desktop/Betty_temp/uncropped/L1g1w_TS003_collagen_smoothened_rescaled.stl Opened STL file L1g1w_TS003_collagen_smoothened_rescaled.stl containing 618868 triangles > select add #2 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-34.624,0,1,0,28.301,0,0,1,-1156.9 > view matrix models #2,1,0,0,-43.845,0,1,0,12.388,0,0,1,-1124.3 > view matrix models #2,1,0,0,-38.143,0,1,0,22.733,0,0,1,-1123.6 > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > save #2 /Users/jessehansen/Desktop/Betty_temp/collagen2.stl format stl Expected a models specifier or a keyword > save /Users/jessehansen/Desktop/Betty_temp/collagen2.stl format stl models > #2 > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > close session > open > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_ACTIN.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/dust_final.mrc > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1g1w_TS003_bin8_correct_trimmed_inverted_resampled.mrc > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_IM.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_MT.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_PM.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_smallECM.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/L1G1W_ts003_vesicles.stl > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/collagen2.stl Opened dust_final.mrc as #2, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 0.0272, step 2, values float32 Opened L1g1w_TS003_bin8_correct_trimmed_inverted_resampled.mrc as #3, grid size 510,720,122, pixel 17.1,17.1,17.1, shown at level 1.51, step 2, values float32 Opened STL file L1G1W_ts003_ACTIN.stl containing 708725 triangles Opened STL file L1G1W_ts003_IM.stl containing 1984827 triangles Opened STL file L1G1W_ts003_MT.stl containing 100944 triangles Opened STL file L1G1W_ts003_PM.stl containing 1106736 triangles Opened STL file L1G1W_ts003_smallECM.stl containing 268223 triangles Opened STL file L1G1W_ts003_vesicles.stl containing 647742 triangles Opened STL file collagen2.stl containing 618868 triangles > set bgColor white > lighting soft > select add #9 1 model selected > color #9 yellow > view matrix models #9,1,0,0,2.5086,0,1,0,-15.416,0,0,1,3.0223 > close #9 > open > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/collagen2.stl Opened STL file collagen2.stl containing 509011 triangles > hide #!2 models > show #!2 models > lighting depthCueStart 1 depthCueEnd 1 > volume #2 showOutlineBox true outlineBoxRgb grey > lighting soft > select clear > select add #6 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select clear > select add #8 1 model selected > color sel sky blue > select clear > select add #9 1 model selected > color sel medium sea green > select clear > select add #4 1 model selected > color sel #DC5A9B > select clear > select add #1 1 model selected > color sel #00F0F0 > select clear > select add #5 1 model selected > color sel dark orange > select clear > color sel peach puff > transparency #2 80 > select clear > transparency #2 70 > select add #7 1 model selected > color sel yellow > select clear > hide #!3 models > graphics silhouettes true > movie record > turn y 2 180 > wait 180 > movie encode /Users/jessehansen/Desktop/movie1.mp4 Movie saved to /Users/jessehansen/Desktop/movie1.mp4 > save > /Users/jessehansen/Desktop/Betty_temp/crosssection_L1g1w_TS003/session.cxs ——— End of log from Fri Jun 16 12:24:18 2023 ——— opened ChimeraX session > open > /Volumes/jhansen/group/schurgrp/jhansen/Betty_segmentation/June2023/DONE_crosssection_L1g1w_TS003/L1g1w_TS003_granules_smoothened.stl Opened STL file L1g1w_TS003_granules_smoothened.stl containing 604428 triangles > select #10 1 model selected > color sel #8fb38d > select clear > save /Users/jhansen/Desktop/session.cxs ——— End of log from Thu Jul 6 16:49:37 2023 ——— opened ChimeraX session > view orient > close #3 > open > /Volumes/jhansen/group/schurgrp/jhansen/Betty_segmentation/June2023/DONE_crosssection_L1g1w_TS003/old/L1g1w_TS003_bin8_correct_trimmed.mrc Opened L1g1w_TS003_bin8_correct_trimmed.mrc as #3, grid size 510,720,121, pixel 17.1, shown at level 0.347, step 2, values float32 > save /Users/jhansen/Desktop/session.cxs ——— End of log from Mon Jul 10 09:55:33 2023 ——— opened ChimeraX session > volume #2 level 0.197 > close #3 > volume #2 level 0.4037 > rename #2 L1G1W_ts003_AD.mrc > rename #9 L1G1W_ts003_collagen.stl > volume #2 level 0.3395 > volume #2 step 1 > save > /mnt/beegfs/schurgrp/bzens/ECMpaper_deposition/segmentation/DONE_crosssection_L1g1w_TS003/L1G1W_ts003_chimeraX.cxs > includeMaps true ——— End of log from Mon Jul 15 13:21:12 2024 ——— opened ChimeraX session Unable to restore session, resetting. Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 725, in restore obj = sm.restore_snapshot(self, data) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 154, in restore_snapshot mgr._ses_restore(data) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 167, in _ses_restore self.clear() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 725, in restore obj = sm.restore_snapshot(self, data) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 154, in restore_snapshot mgr._ses_restore(data) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 167, in _ses_restore self.clear() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 267, in event _open_dropped_file(self.session, event.file()) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1919, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 181, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 433, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 995, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 733, in restore self.reset() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 535, in reset sm.reset_state(container, self) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 149, in reset_state self.clear() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/bond_rot/manager.py"", line 45, in delete_all_rotations for rotater in self.bond_rotaters.values(): See log for complete Python traceback. > open > /Users/christoph/ownCloud/BiochSoc/FromFloAndBettina/Segmentation_Fig3/L1g1w_TS003_bin8_correct_trimmed.mrc Opened L1g1w_TS003_bin8_correct_trimmed.mrc as #1, grid size 510,720,121, pixel 17.1, shown at level 0.347, step 2, values float32 OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11F0001XD/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4 (23E214) Kernel Version: Darwin 23.4.0 Time since boot: 7 days, 23 hours, 48 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Sessions limitation all ChimeraX