id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4315 Coulombic failure due to unexpected hydrogen name gus.larshyland@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-20.3.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Trying to view structure with electrostatic colouring and it reported a keyerror of 'HXT' Thanks for any help! Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl Traceback (most recent call last): File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/help_viewer/tool.py"", line 389, in download_finished session=self.session) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 903, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolshed_utils/__init__.py"", line 213, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle.name) AttributeError: 'str' object has no attribute 'name' AttributeError: 'str' object has no attribute 'name' File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolshed_utils/__init__.py"", line 213, in _install_bundle raise ToolshedInstalledError(""bundle %r already installed"" % bundle.name) See log for complete Python traceback. > open 6nwv format mmcif fromDatabase pdb Summary of feedback from opening 6nwv fetched from pdb --- warnings | Atom OE1 has no neighbors to form bonds with according to residue template for GLU /C:4 Atom OE2 has no neighbors to form bonds with according to residue template for GLU /C:4 Atom CE2 has no neighbors to form bonds with according to residue template for PHE /F:1 Atom N has no neighbors to form bonds with according to residue template for THR /F:30 Atom OXT has no neighbors to form bonds with according to residue template for THR /F:30 Atom N has no neighbors to form bonds with according to residue template for THR /L:30 Atom OXT has no neighbors to form bonds with according to residue template for THR /L:30 6nwv title: Insulin Lispro Analog [more info...] Chain information for 6nwv #1 --- Chain | Description A C E G I K | Insulin A chain B D F H J L | Insulin Lispro B chain Non-standard residues in 6nwv #1 --- CL — chloride ion CRS — M-cresol GOL — glycerol (glycerin; propane-1,2,3-triol) ZN — zinc ion > mlp Map values for surface ""6nwv_A SES surface"": minimum -26.76, mean -3.309, maximum 21.28 Map values for surface ""6nwv_B SES surface"": minimum -23.39, mean -1.341, maximum 22.07 Map values for surface ""6nwv_C SES surface"": minimum -28.39, mean -5.06, maximum 20.01 Map values for surface ""6nwv_D SES surface"": minimum -21.98, mean -1.476, maximum 21.46 Map values for surface ""6nwv_E SES surface"": minimum -27.15, mean -4.3, maximum 19.64 Map values for surface ""6nwv_F SES surface"": minimum -22.1, mean -1.424, maximum 22.05 Map values for surface ""6nwv_G SES surface"": minimum -23.02, mean -3.498, maximum 20.32 Map values for surface ""6nwv_H SES surface"": minimum -22.46, mean -1.286, maximum 22.31 Map values for surface ""6nwv_I SES surface"": minimum -25.09, mean -3.88, maximum 20.31 Map values for surface ""6nwv_J SES surface"": minimum -22.21, mean -1.501, maximum 21.4 Map values for surface ""6nwv_K SES surface"": minimum -25.48, mean -3.247, maximum 19.19 Map values for surface ""6nwv_L SES surface"": minimum -23.08, mean -1.273, maximum 22.21 > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /L GLU 21 OE1, /H PRO 29 CG, /H PRO 29 CB, /H PRO 29 CD, /H THR 30 C, and 78 other atoms /F THR 30 HXT Traceback (most recent call last): File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 202, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 363, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1273, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1221, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 376, in try_shortcut self.run_shortcut(keys) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 394, in run_shortcut sc.run(self.session, status = self._enabled) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 313, in run f(s) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run_expanded_command run(session, cmd) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 480, in run run_command(session, command, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/cmd.py"", line 97, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 96, in assign_charges assign_residue_charges(charged_residues, his_scheme) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] KeyError: 'HXT' KeyError: 'HXT' File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] See log for complete Python traceback. > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /L GLU 21 OE1, /H PRO 29 CG, /H PRO 29 CB, /H PRO 29 CD, /H THR 30 C, and 78 other atoms /F THR 30 HXT Traceback (most recent call last): File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/toolbar/tool.py"", line 202, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 363, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1273, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/__init__.py"", line 52, in run_provider shortcuts.run_provider(session, name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 1221, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 376, in try_shortcut self.run_shortcut(keys) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 394, in run_shortcut sc.run(self.session, status = self._enabled) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 313, in run f(s) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 537, in run_expanded_command run(session, cmd) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/shortcuts/shortcuts.py"", line 480, in run run_command(session, command, **kw) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/cmd.py"", line 97, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 96, in assign_charges assign_residue_charges(charged_residues, his_scheme) File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] KeyError: 'HXT' KeyError: 'HXT' File ""/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/coulombic/coulombic.py"", line 161, in assign_residue_charges a.charge = res_data[aname] See log for complete Python traceback. OpenGL version: 4.1 INTEL-16.1.11 OpenGL renderer: Intel(R) Iris(TM) Graphics 550 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro13,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.9 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 429.80.1.0.0 SMC Version (system): 2.37f25 Software: System Software Overview: System Version: macOS 11.2.1 (20D74) Kernel Version: Darwin 20.3.0 Time since boot: 15 days 6:31 Graphics/Displays: Intel Iris Graphics 550: Chipset Model: Intel Iris Graphics 550 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1927 Revision ID: 0x000a Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2419H: 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: BC01V13 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 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: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Surface/Binding Analysis not a bug all ChimeraX