id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5744 Interfaces: 'ContactPlot' object has no attribute '_handler' jonathan.sheehan@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17 ChimeraX Version: 1.3rc202112040407 (2021-12-04 04:07:47 UTC) Description I finished the Quick Start tutorial, and selected File->Close Session. I got the message: AttributeError: 'ContactPlot' object has no attribute '_handler' I got it again when closing some of the tools. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3rc202112040407 (2021-12-04) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open 2bbv Summary of feedback from opening 2bbv fetched from pdb --- notes | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #1 --- Chain | Description | UniProt A B C | protein (black beetle virus capsid protein) | COAT_BBV D E F | protein (black beetle virus capsid protein) | COAT_BBV N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') | Non-standard residues in 2bbv #1 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain > style /b stick Changed 2382 atom styles > color /n teal > hide /c > ribbon /c > select /B 2382 atoms, 2372 bonds, 2 pseudobonds, 379 residues, 2 models selected > color (#!1 & sel) byhetero > select clear > focus /c Unknown command: focus /c > select /C 2473 atoms, 2469 bonds, 6 pseudobonds, 388 residues, 3 models selected > view sel > view /c > select clear > select /N:4@C5' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > color sel gold > select clear > surface #1 > color /n fromatoms > style solvent sphere Changed 208 atom styles > color solvent red > ui tool show ""Side View"" > sym #1 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly| 60 copies of chains A-F,N 2| icosahedral asymmetric unit| 1 copy of chains A-F,N 3| icosahedral pentamer| 5 copies of chains A-F,N 4| icosahedral 23 hexamer| 6 copies of chains A-F,N 5| icosahedral asymmetric unit, std point frame| 1 copy of chains A-F,N 6| crystal asymmetric unit, crystal frame| 5 copies of chains A-F,N > sym #1 assembly 3 newModel false copies false > view > set bgColor white > set silhouettes true > save /home/jonathan/Desktop/2bbv.png > view > movie record > turn y 2 180 > wait 180 > movie encode /home/jonathan/Desktop/movie1.mp4 Movie saved to /home/jonathan/Desktop/movie1.mp4 > measure buriedarea /a withAtoms2 /b Buried area between /a and /b = 1900.4 area /a = 15385, area /b = 14989, area both = 26573 > measure sasa #1 & ~solvent Solvent accessible area for #1 & ~solvent = 34093 > interfaces #1 & protein 6 buried areas: C A 1675, C B 1671, A B 1663, C F 739, A D 714, B E 699 Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 333, in interceptRequest self._callback(info) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 92, in _intercept return interceptor(request_info, *args) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/help_viewer/tool.py"", line 319, in intercept chimerax_intercept(request_info, *args, session=self.session, File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 468, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 382, in thread_safe func(*args, **kw) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 459, in defer cxcmd(session, topic) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 477, in cxcmd run(session, cmd) File ""/usr/libexec/UCSF-ChimeraX/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 ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/cmd.py"", line 49, in interfaces tool.ContactPlot(session, sg, ba, interface_residue_area_cutoff) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/tool.py"", line 25, in __init__ Graph.__init__(self, session, groups, contacts, File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/graph.py"", line 139, in __init__ self.graph = self._make_graph() File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/graph.py"", line 160, in _make_graph import networkx as nx File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/networkx/__init__.py"", line 57, in from networkx import utils File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/networkx/utils/__init__.py"", line 2, in from networkx.utils.decorators import * File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/networkx/utils/decorators.py"", line 12, in import re, gzip, bz2 File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/bz2.py"", line 18, in from _bz2 import BZ2Compressor, BZ2Decompressor ModuleNotFoundError: No module named '_bz2' ModuleNotFoundError: No module named '_bz2' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/bz2.py"", line 18, in from _bz2 import BZ2Compressor, BZ2Decompressor See log for complete Python traceback. > view > close > set bgColor black > set silhouettes false > open 1080 fromDatabase emdb Summary of feedback from opening 1080 fetched from emdb --- note | Fetching compressed map 1080 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32 > lighting full > volume #1 level 0.9 > volume #1 level 1.1 > volume #1 level 1.3 > ui mousemode right rotate > ui mousemode right translate > ui mousemode right ""contour level"" > volume #1 level 1.685 > volume #1 level 1.771 > volume #1 level 1.508 > volume #1 level 1.3 > volume #1 level 0.6366 > volume #1 level -0.03423 > volume #1 level 0.06584 > volume #1 level 0.4661 > volume #1 level 0.06955 > volume #1 encloseVolume 1e6 step 1 color tan > volume #1 level 0.8287 > volume #1 level 1.07 > set bgColor gray > set silhouettes true > volume #1 level 1.574 > volume #1 level 1.099 > ui mousemode right translate > open 1grl Summary of feedback from opening 1grl fetched from pdb --- note | Fetching compressed mmCIF 1grl from http://files.rcsb.org/download/1grl.cif 1grl title: The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more info...] Chain information for 1grl #2 --- Chain | Description | UniProt A B C D E F G | groel (HSP60 class) | CH60_ECOLI 1grl mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > lighting default > select /E:126@CG1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 202 atoms, 202 bonds, 22 residues, 1 model selected > select up 4182 atoms, 4143 bonds, 518 residues, 1 model selected > select up 29274 atoms, 29001 bonds, 3626 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,47.122,0,1,0,16.128,0,0,1,62.879 > fitmap #2 inMap #1 Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms average map value = 1.044, steps = 104 shifted from previous position = 17.5 rotated from previous position = 24.9 degrees atoms outside contour = 13428, contour level = 1.0993 Position of 1grl (#2) relative to emdb 1080 (#1) coordinates: Matrix rotation and translation 0.90776524 0.41924712 0.01393269 39.70701138 -0.41947454 0.90740126 0.02576956 -18.28427061 -0.00183872 -0.02923712 0.99957081 64.93505013 Axis -0.06543184 0.01876049 -0.99768067 Axis point -20.96735494 -88.75319448 0.00000000 Rotation angle (degrees) 24.85578529 Shift along axis -67.72556908 > volume #1 transparency 0.5 > molmap #2 10 Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level 0.0611, step 1, values float32 > volume #3 style mesh > volume subtract #1 #3 minRms true Opened volume difference as #4, grid size 100,100,100, pixel 2.7, shown at step 1, values float32 Minimum RMS scale factor for ""1grl map 10 #3"" above level 0.061077 is 3.6985 > volume #4 color pink transparency 0 > hide atoms > show ribbons > volume #4 level 0.6499 > close > set bgColor black > set silhouettes false > open 1a0m fromDatabase eds Summary of feedback from opening 1a0m fetched from eds --- note | Fetching map 1a0m from http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4 Opened eds 1a0m as #1, grid size 97,101,88, pixel 0.37,0.37,0.367, shown at level 2.28, step 1, values float32 > open 1a0m Summary of feedback from opening 1a0m fetched from pdb --- note | Fetching compressed mmCIF 1a0m from http://files.rcsb.org/download/1a0m.cif 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #2 --- Chain | Description | UniProt A B | α-conotoxin [TYR15]-epi | CXA1_CONEP Non-standard residues in 1a0m #2 --- NH2 — amino group > hide ribbons > show > volume #1 level 1.0 style mesh > volume zone #1 nearAtoms #2 range 2 > volume #1 level 0.5 transparency 0.6 > show cartoons > hide cartoons > close > open 1273 fromDatabase emdb Summary of feedback from opening 1273 fetched from emdb --- note | Fetching compressed map 1273 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1, values int8 > volume #1 region all showOutlineBox true > close session Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1032, in close_action.triggered.connect(lambda *, s=self, sess=session: s.file_close_cb(sess)) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 680, in file_close_cb run(session, 'close session') File ""/usr/libexec/UCSF-ChimeraX/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 ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/std_commands/close.py"", line 60, in close_session session.reset() File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/session.py"", line 535, in reset sm.reset_state(container, self) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/core/tools.py"", line 292, in reset_state tool_inst.delete() File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/tool.py"", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) AttributeError: 'ContactPlot' object has no attribute '_handler' AttributeError: 'ContactPlot' object has no attribute '_handler' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/tool.py"", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 2251, in dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 654, in close_request tool_instance.delete() File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/tool.py"", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) AttributeError: 'ContactPlot' object has no attribute '_handler' AttributeError: 'ContactPlot' object has no attribute '_handler' File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/chimerax/interfaces/tool.py"", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.43 OpenGL renderer: Quadro RTX 4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: TYAN Model: B7105F48TV8HR-2T-G OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 48 Intel(R) Xeon(R) Gold 5118 CPU @ 2.30GHz Cache Size: 16896 KB Memory: total used free shared buff/cache available Mem: 187G 4.0G 158G 135M 24G 182G Swap: 9G 0B 9G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: ast Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 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: 1.3rc202112040407 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-LinuxSupport: 1.0 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 distro: 1.6.0 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 line-profiler: 3.3.0 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: 21.3 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 tables: 3.6.1 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 Structure Analysis duplicate Eric Pettersen all ChimeraX