id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9887 Chimera-like control of model display olibclarke@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.6-arm64-arm-64bit ChimeraX Version: 1.7.dev202309281956 (2023-09-28 19:56:46 UTC) Description Hi, I still really miss the ""display next/previous model"" interface from Chimera. While I have migrated most of my workflow to ChimeraX now, and I love it, when I want to compare a set of 3D classes, I still turn to Chimera because this makes it really easy to quickly flick between them, and to toggle on/off display of individual volumes in the series (and compare with a reference atomic model). I can use volume series for this in ChimeraX, but they lack the same level of granularity in turning on and off individual frames in the series - there are certain advantages to having individual models remain separate. Volume/model series are great for trajectories with 100s of frames/models, but for comparing and discriminating between <20 classes/frames (which single particle folks do a lot), the approach in Chimera still has its advantages. I know a full implementation (with checkboxes etc) is unlikely to be a priority in the near term, but at some point in the future would it be possible to add a next/previous model widget of some sort? Ideally (in my mind) such a widget would work as follows: * If multiple models are displayed, display only the first; * If a single model is displayed, undisplay it and display the next (or previous) * If the displayed model is the last model, display the first model next (or vice-versa). * Ideally, allow the user to lock display status of individual models (""skip"") so they are ignored in the sequence (either remaining displayed or undisplayed depending on status). * This could be implemented as a separate widget, or perhaps as a enhancement/modification of the existing Model Panel? If such a widget could also separately discriminate between volumes and atomic models that would be even better - so one could quickly flick through multiple maps and compare them to a single atomic model fit to the consensus (we do this a lot in Chimera). I realize this is not something that is likely to be addressed soon, just putting it out there as an RFE for the future (as it is now one of the only remaining pain-points in transitioning from Chimera to ChimeraX, for my workflow at least). Thanks very much for all the work you do, ChimeraX is a truly superb piece of software! Best, Oli Log: > camera ortho > cofr centerOfView > mousemode alt rightMode ""contour level"" > mousemode rightMode clip > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > mousemode alt control leftMode ""pick blobs"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode set bgColor black; surface cap false; surface style solid; > lighting flat; graphics silhouettes false; style stick; ~rib; color > ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style > solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70; > cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues > cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size > ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far > 10 position cofr; color ##~num_residues #3d60ffff; transparency 50 > alias project_map set bgColor black; lighting depthcue false; volume $1 > style image sdlevel 0,0 color white sdlevel 100,0.15 color white > projectionmode 3d maximumIntensityProjection false dimTransparentVoxels > false btcorrection true showOutlineBox false linearinterpolation true > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136; > movie encode ~/Desktop/rock_movie.mp4; stop > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #20000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings UCSF ChimeraX version: 1.7.dev202309281956 (2023-09-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 34282 fromDatabase emdb_fits Summary of feedback from opening 34282 fetched from emdb_fits --- notes | Fetching compressed map header 34282 from https://files.wwpdb.org/pub/emdb/structures/EMD-34282/header/emd-34282.xml Fetching compressed mmCIF 8gv3 from http://files.rcsb.org/download/8gv3.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif Opened emdb 34282 as #1, grid size 180,180,180, pixel 1.1, shown at level 0.7, step 1, values float32, fit PDB 8gv3 8gv3 title: The cryo-EM structure of GSNOR with NYY001 [more info...] Chain information for 8gv3 #2 --- Chain | Description | UniProt A B | Alcohol dehydrogenase class-3 | ADHX_HUMAN 0-373 Non-standard residues in 8gv3 #2 --- NAD — nicotinamide-adenine-dinucleotide WKZ — (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide ZN — zinc ion > cootmode > surface cap false Changed 5714 atom styles Changed 4 atom styles Changed 0 atom styles Changed 1 ball scales Changed 5828 bond radii > close all > open 34282 fromDatabase emdb fits true Opened emdb 34282 as #1, grid size 180,180,180, pixel 1.1, shown at level 0.7, step 1, values float32, fit PDB 8gv3 8gv3 title: The cryo-EM structure of GSNOR with NYY001 [more info...] Chain information for 8gv3 #2 --- Chain | Description | UniProt A B | Alcohol dehydrogenase class-3 | ADHX_HUMAN 0-373 Non-standard residues in 8gv3 #2 --- NAD — nicotinamide-adenine-dinucleotide WKZ — (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide ZN — zinc ion > cootmode Changed 5714 atom styles Changed 4 atom styles Changed 0 atom styles Changed 1 ball scales Changed 5828 bond radii > close all > tool show Models > open 34282 format ccp4 fromDatabase emdb_fits Opened emdb 34282 as #1, grid size 180,180,180, pixel 1.1, shown at level 0.7, step 1, values float32, fit PDB 8gv3 8gv3 title: The cryo-EM structure of GSNOR with NYY001 [more info...] Chain information for 8gv3 #2 --- Chain | Description | UniProt A B | Alcohol dehydrogenase class-3 | ADHX_HUMAN 0-373 Non-standard residues in 8gv3 #2 --- NAD — nicotinamide-adenine-dinucleotide WKZ — (4P)-4-{2-[4-(1H-imidazol-1-yl)phenyl]-5-[3-oxo-3-(2-oxo-1,3-thiazolidin-3-yl)propyl]-1H-pyrrol-1-yl}-3-methylbenzamide ZN — zinc ion > open > /Users/oc2188/Library/CloudStorage/Dropbox/ankyrin_complex_final_maps_and_models/consensus_DONE/consensus_refinement_rh_ar15_mask_DONE/resolve_cryo_em_0_DONE/denmod_map_resample.mrc > format mrc Opened denmod_map_resample.mrc as #3, grid size 266,266,266, pixel 0.415, shown at level 1.69, step 1, values float32 > cootmode Changed 5714 atom styles Changed 4 atom styles Changed 0 atom styles Changed 1 ball scales Changed 5828 bond radii > close all > help setattr > open 8cml Summary of feedback from opening 8cml fetched from pdb --- note | Fetching compressed mmCIF 8cml from http://files.rcsb.org/download/8cml.cif 8cml title: Cryo-EM structure of complement C5 in complex with nanobodies UNbC5-1 and UNbC5-2 [more info...] Chain information for 8cml #1 --- Chain | Description | UniProt A | Nanobody UNbC5-2 | B | Complement C5 alpha chain | CO5_HUMAN 678-1676 C | Nanobody UNbC5-1 | E | Complement C5 beta chain | CO5_HUMAN 19-673 Non-standard residues in 8cml #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > tool show Log > log metadata #1 Metadata for 8cml #1 --- Title | Cryo-EM structure of complement C5 in complex with nanobodies UNbC5-1 and UNbC5-2 Citation | Struijf, E.M., De la O Becerra, K.I., Ruyken, M., de Haas, C.J.C., van Oosterom, F., Siere, D.Y., van Keulen, J.E., Heesterbeek, D.A.C., Dolk, E., Heukers, R., Bardoel, B.W., Gros, P., Rooijakkers, S.H.M. (2023). Inhibition of cleavage of human complement component C5 and the R885H C5 variant by two distinct high affinity anti-C5 nanobodies. J.Biol.Chem., 299, 104956-104956. PMID: 37356719. DOI: 10.1016/j.jbc.2023.104956 Non-standard residue | NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D- GLUCOSAMINE) Source (natural) | Homo sapiens (human) Gene source | Lama glama CryoEM Map | EMDB 16730 — open map Experimental method | Electron microscopy Resolution | 3.6Å > open 16730 fromDatabase emdb Summary of feedback from opening 16730 fetched from emdb --- notes | Fetching compressed map 16730 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16730/map/emd_16730.map.gz Fetching map header 16730 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16730/header/emd-16730.xml Opened emdb 16730 as #2, grid size 320,320,320, pixel 1.04, shown at level 0.186, step 1, values float32, fit PDB 8cml > volume #2 level 0.3245 > cootmode Changed 13594 atom styles Changed 0 atom styles [Repeated 1 time(s)]Changed 1 ball scales Changed 13897 bond radii > close all > tool show Models > open 8cml format mmcif fromDatabase pdb 8cml title: Cryo-EM structure of complement C5 in complex with nanobodies UNbC5-1 and UNbC5-2 [more info...] Chain information for 8cml #1 --- Chain | Description | UniProt A | Nanobody UNbC5-2 | B | Complement C5 alpha chain | CO5_HUMAN 678-1676 C | Nanobody UNbC5-1 | E | Complement C5 beta chain | CO5_HUMAN 19-673 Non-standard residues in 8cml #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > open > /Users/oc2188/Library/CloudStorage/Dropbox/ankyrin_complex_final_maps_and_models/consensus_DONE/consensus_refinement_rh_ar15_mask_DONE/resolve_cryo_em_0_DONE/rh_ar15_start_rs2.pdb > format pdb Chain information for rh_ar15_start_rs2.pdb #2 --- Chain | Description J | No description available K | No description available L | No description available Q | No description available > open > /Users/oc2188/Downloads/rosie_flvcr2/091623_OFS_FLVCR2_MM_Fab_FLV23_ChCl.pdb > format pdb Summary of feedback from opening /Users/oc2188/Downloads/rosie_flvcr2/091623_OFS_FLVCR2_MM_Fab_FLV23_ChCl.pdb --- warning | Ignored bad PDB record found on line 1 REMARK DATE: 2/ 5/21 14:33:49 CREATED BY USER: nathan Chain information for 091623_OFS_FLVCR2_MM_Fab_FLV23_ChCl.pdb #3 --- Chain | Description A | No description available B | No description available D | No description available > ~show #2 > hide #2 > tool show Models > help show > hide #2* Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #2* Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > ~show #2* > hide #2* Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #!2 models > help vseries OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: Z17J00171LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 10151.1.1 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.6 (22G120) Kernel Version: Darwin 22.6.0 Time since boot: 20 hours, 24 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.0 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: 2022.12.7 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: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.11.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.48 ChimeraX-AtomicLibrary: 10.1 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: 2.10.5 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: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309281956 ChimeraX-CoreFormats: 1.2 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: 1.2.2 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: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 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: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.11 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: 1.1.2 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: 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.10 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 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: 2.2.2 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: 1.32.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.1 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: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.12.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.2 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.5 wcwidth: 0.2.7 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " enhancement closed normal UI fixed Elaine Meng Tom Goddard all ChimeraX