id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7169 ISOLDE installed into incompatible ChimeraX chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Updates Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/lewisj/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/lewisj/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE sysconfig: /Users/lewisj/Library/Python/3.9/include/ChimeraX-ISOLDE WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX/bin sysconfig: /Users/lewisj/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX sysconfig: /Users/lewisj/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/lewisj/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/lewisj/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 22.1.2 is available. You should consider upgrading via the '/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-ISOLDE==1.3 Using cached https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.3/ChimeraX_ISOLDE-1.3-cp39-cp39-macosx_10_13_x86_64.whl (81.8 MB) Installing collected packages: ChimeraX-ISOLDE Successfully installed ChimeraX-ISOLDE-1.3 \--- Successfully installed ChimeraX-ISOLDE-1.3 Installed ChimeraX-ISOLDE (1.3) Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 891, in require needed = self.resolve(parse_requirements(requirements)) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 782, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) ChimeraX-ISOLDE (installed) [version: 1.3] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]: custom initialization failed QMainWindowLayout::tabPosition called with out-of-bounds value '0' [Repeated 1 time(s)] > ui tool show ISOLDE Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/lewisj/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 891, in require needed = self.resolve(parse_requirements(requirements)) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 782, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 558, in start_tool api = self._get_api(session.logger) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1685, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show bi.start_tool(session, name) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 564, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) Populating font family aliases took 327 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Error importing bundle ChimeraX-ISOLDE's module: (ChimeraX-AtomicLibrary 7.0 (/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages), Requirement.parse('ChimeraX-AtomicLibrary~=4.2'), {'ChimeraX- ISOLDE'}) File ""/Volumes/ChimeraXInstaller/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 564, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0) OS Loader Version: 540.120.3~6 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 11 days 21:05 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: BenQ EW2780: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: B9K0272101Q Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 0.00 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Tool Shed fixed chimera-programmers Tristan Croll all ChimeraX