id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20790 Douse: name 'compare_model' is not defined borgosch@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-26.5.2-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description NameError: name 'compare_model' is not defined NameError: name 'compare_model' is not defined File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/check_waters/tool.py"", line 124, in _finalize_init self.compared_waters = compare_waters(compare_model, check_model) ^^^^^^^^^^^^^ Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/maxbo/Desktop/wt/forEVL/Coot/260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb Summary of feedback from opening /Users/maxbo/Desktop/wt/forEVL/Coot/260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO a 2 ILE a 6 1 5 Start residue of secondary structure not found: HELIX 2 2 PRO a 9 LYS a 29 1 21 Start residue of secondary structure not found: HELIX 3 3 ALA a 54 VAL a 61 1 8 Start residue of secondary structure not found: HELIX 4 4 THR a 62 ILE a 65 1 4 Start residue of secondary structure not found: HELIX 5 5 GLU a 66 ASN a 68 1 3 234 messages similar to the above omitted Chain information for 260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb #1 --- Chain | Description Aa | No description available Ab | No description available Ac | No description available Computing secondary structure > open > /Users/maxbo/Desktop/wt/forEVL/CryoSPARC/J315/cryosparc_P2_J315_localfilter.mrc Opened cryosparc_P2_J315_localfilter.mrc as #2, grid size 384,384,384, pixel 0.837, shown at level 0.0142, step 2, values float32 > lighting soft > set bgColor white > volume #2 step 1 > volume #2 level 0.03667 > volume #2 level 0.04546 > ui tool show ""Water Placement"" Populating font family aliases took 89 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > phenix douse #2 nearModel #1 keepInputWater false verbose true resolution > 2.4 Command: /Users/maxbo/Applications/phenix-2.0-5936/phenix_bin/phenix.douse map.mrc model.pdb resolution=2.4 stdout: Starting phenix.douse on Fri Jul 24 14:09:38 2026 by maxbo =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, map.mrc Found model, model.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- resolution=2.4 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = ""model.pdb"" } default_model = ""model.pdb"" real_map_files = ""map.mrc"" default_real_map = ""map.mrc"" } resolution = 2.4 Starting job =============================================================================== Removing water in input model number of water in input model to remove: 0 time (s): 0.280 (total time: 0.280) Process per chain (mode=per_chain) Working on chain Aa: Normalize and re-sample input map input map (min,max,mean): -0.182 0.362 0.008 re-scaled map (min,max,mean): 0.000 13.703 0.363 input map dimenstions: 125 88 172 input map grid steps (A): 0.837 0.837 0.837 input map (min,max,mean): 0.000 13.703 0.363 time (s): 0.390 (total time: 0.670) Get cutoff mean density at atom centers: 2.574 density cutoff for peak search: 0.644 time (s): 0.330 (total time: 1.000) Mask out molecule/solvent regions time (s): 0.340 (total time: 1.340) Find peaks total peaks found: 5530 B factors set to : 39.469 time (s): 0.400 (total time: 1.740) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 5530 final: 733 time (s): 0.440 (total time: 2.180) Filter peaks by sphericity peaks left: 671 time (s): 1.920 (total time: 4.100) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 671 final: 650 time (s): 0.340 (total time: 4.440) Refine ADP B (min/max/mean) start: 39.469 39.469 39.469 B (min/max/mean) final: 0.000 24.806 16.162 time (s): 3.120 (total time: 7.560) Filter peaks by CC_mask start: 650 final: 496 time (s): 0.800 (total time: 8.360) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 496 final: 468 time (s): 0.340 (total time: 8.700) Filter peaks by CC_mask and number start: 468 final: 461 time (s): 0.770 (total time: 9.470) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 461 final: 460 time (s): 0.330 (total time: 9.800) Add to model and reset internals new water chain ID: 'Aa' B (min/max/mean): 0.000 24.806 13.192 time (s): 0.490 (total time: 10.290) Working on chain Ab: Normalize and re-sample input map input map (min,max,mean): -0.182 0.362 0.009 re-scaled map (min,max,mean): 0.000 13.441 0.370 input map dimenstions: 110 112 162 input map grid steps (A): 0.837 0.837 0.837 input map (min,max,mean): 0.000 13.441 0.370 time (s): 0.350 (total time: 0.630) Get cutoff mean density at atom centers: 2.263 density cutoff for peak search: 0.566 time (s): 0.340 (total time: 0.970) Mask out molecule/solvent regions time (s): 0.350 (total time: 1.320) Find peaks total peaks found: 5322 B factors set to : 44.588 time (s): 0.390 (total time: 1.710) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 5322 final: 687 time (s): 0.440 (total time: 2.150) Filter peaks by sphericity peaks left: 627 time (s): 1.820 (total time: 3.970) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 627 final: 610 time (s): 0.340 (total time: 4.310) Refine ADP B (min/max/mean) start: 44.588 44.588 44.588 B (min/max/mean) final: 0.000 21.159 14.096 time (s): 4.800 (total time: 9.110) Filter peaks by CC_mask start: 610 final: 434 time (s): 0.780 (total time: 9.890) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 434 final: 392 time (s): 0.340 (total time: 10.230) Filter peaks by CC_mask and number start: 392 final: 383 time (s): 0.740 (total time: 10.970) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 383 final: 380 time (s): 0.330 (total time: 11.300) Add to model and reset internals new water chain ID: 'Ab' B (min/max/mean): 0.000 21.159 11.103 time (s): 0.460 (total time: 11.760) Working on chain Ac: Normalize and re-sample input map input map (min,max,mean): -0.182 0.343 0.008 re-scaled map (min,max,mean): 0.000 13.918 0.350 input map dimenstions: 81 125 170 input map grid steps (A): 0.837 0.837 0.837 input map (min,max,mean): 0.000 13.918 0.350 time (s): 0.340 (total time: 0.620) Get cutoff mean density at atom centers: 2.514 density cutoff for peak search: 0.629 time (s): 0.340 (total time: 0.960) Mask out molecule/solvent regions time (s): 0.350 (total time: 1.310) Find peaks total peaks found: 5527 B factors set to : 47.112 time (s): 0.380 (total time: 1.690) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 5527 final: 739 time (s): 0.450 (total time: 2.140) Filter peaks by sphericity peaks left: 676 time (s): 1.940 (total time: 4.080) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 676 final: 657 time (s): 0.350 (total time: 4.430) Refine ADP B (min/max/mean) start: 47.112 47.112 47.112 B (min/max/mean) final: 0.000 25.002 17.007 time (s): 2.540 (total time: 6.970) Filter peaks by CC_mask start: 657 final: 458 time (s): 0.790 (total time: 7.760) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 458 final: 414 time (s): 0.330 (total time: 8.090) Filter peaks by CC_mask and number start: 414 final: 409 time (s): 0.740 (total time: 8.830) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 409 final: 407 time (s): 0.340 (total time: 9.170) Add to model and reset internals new water chain ID: 'Ac' B (min/max/mean): 0.000 25.002 12.854 time (s): 0.470 (total time: 9.640) time (s): 47.280 (total time: 47.560) Attribute water to chains time (s): 11.910 (total time: 59.470) Summary Number of water added: 1118 time (s): 0.070 (total time: 59.540) =============================================================================== Job complete usr+sys time: 62.81 seconds wall clock time: 62.91 seconds Placed 1116 waters in map ""cryosparc_P2_J315_localfilter.mrc"" near model ""260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 873, in customEvent func(*args, **kw) File ""/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/chimerax/phenix_ui/douse.py"", line 194, in map_range=map_range, d_ref=d: _process_results(session, douse_model, shift, near_model, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/chimerax/phenix_ui/douse.py"", line 219, in _process_results DouseResultsViewer(session, ""Water Placement Results"", near_model, model, compared_waters, map) File ""/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site- packages/chimerax/phenix_ui/tool.py"", line 275, in __init__ super().__init__(session, tool_name, douse_model, compare_info=(orig_model, compared_waters), File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/check_waters/tool.py"", line 105, in __init__ self._finalize_init(check_model, compare_info, model_labels, compare_map, category_tips) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/check_waters/tool.py"", line 124, in _finalize_init self.compared_waters = compare_waters(compare_model, check_model) ^^^^^^^^^^^^^ NameError: name 'compare_model' is not defined NameError: name 'compare_model' is not defined File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/check_waters/tool.py"", line 124, in _finalize_init self.compared_waters = compare_waters(compare_model, check_model) ^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z15W0045PD/A Chip: Apple M2 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 16 GB System Firmware Version: 18000.121.3 OS Loader Version: 18000.121.3 Software: System Software Overview: System Version: macOS 26.5.2 (25F84) Kernel Version: Darwin 25.5.0 Time since boot: 8 days, 3 hours, 50 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 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: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 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: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMalign: 0.1.3 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-LigandRecognizer: 0.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.6.4 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 finufft: 2.5.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 MolecularDynamicsViewer: 1.6 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Editing fixed all ChimeraX