id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9975 ISOLDE sim start: OpenMMException: Error compiling kernel: Compile Server Error yangxl@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description I need to use the ISOLDE to refine my cryo-EM structure. However, when I clicked the ""Start simulation"", it reported ""openmm. OpenMMException: Error compiling kernel: Compile Server Error. File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) "". Wish to hear advices for this error, thanks! Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Volumes/Transcend/Experiments/Data Process/20231006-Titan2-EDATP- > DT-1957-W29/cryosparc_P36_J1117_006_volume_map_sharp.mrc"" format mrc Opened cryosparc_P36_J1117_006_volume_map_sharp.mrc as #1, grid size 384,384,384, pixel 0.832, shown at level 0.196, step 2, values float32 > open ""/Volumes/Transcend/Experiments/Data Process/20231006-Titan2-EDATP- > DT-1957-W29/ATP-re1117.pdb"" Chain information for ATP-re1117.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #!1 models > select ~protein 72 atoms, 66 bonds, 18 pseudobonds, 5 residues, 4 models selected > delete sel > show #!1 models > select subtract #1 Nothing selected > isolde start > set selectionWidth 4 Populating font family aliases took 454 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 162 residues in model #2 to IUPAC-IUB standards. Chain information for ATP-re1117.pdb --- Chain | Description 2.2/A | No description available 2.2/B | No description available 2.2/C | No description available 2.2/D | No description available > clipper associate #1 toModel #2 Opened cryosparc_P36_J1117_006_volume_map_sharp.mrc as #2.1.1.1, grid size 384,384,384, pixel 0.832, shown at step 1, values float32 > isolde sim start sel > set selectionWidth 4 ISOLDE: stopped sim > ui tool show ""Ramachandran Plot"" > addh #2.2 Summary of feedback from adding hydrogens to ATP-re1117.pdb #2.2 --- notes | Termini for ATP-re1117.pdb (#2.2) chain A determined from SEQRES records Termini for ATP-re1117.pdb (#2.2) chain B determined from SEQRES records Termini for ATP-re1117.pdb (#2.2) chain C determined from SEQRES records Termini for ATP-re1117.pdb (#2.2) chain D determined from SEQRES records Chain-initial residues that are actual N termini: /A THR 73, /B MET 1, /C MET 1, /D SER 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ARG 591, /B SER 325, /C ARG 288, /D ALA 609 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /B SER 325 Missing OXT added to C-terminal residue /C ARG 288 Missing OXT added to C-terminal residue /D ALA 609 1278 hydrogen bonds 13442 hydrogens added > isolde sim start sel > set selectionWidth 4 Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Applications/ChimeraX-1.5.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 ""/Applications/ChimeraX-1.5.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 ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 893, in start_sim sm.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1624, in start_sim self._prepare_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1582, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: Compile Server Error. openmm.OpenMMException: Error compiling kernel: Compile Server Error. File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Applications/ChimeraX-1.5.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 ""/Applications/ChimeraX-1.5.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 ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 893, in start_sim sm.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1624, in start_sim self._prepare_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1582, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: Compile Server Error. openmm.OpenMMException: Error compiling kernel: Compile Server Error. File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > select /D 9229 atoms, 9299 bonds, 608 residues, 1 model selected > isolde sim start sel Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Applications/ChimeraX-1.5.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 ""/Applications/ChimeraX-1.5.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 ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 893, in start_sim sm.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1624, in start_sim self._prepare_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1582, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: Compile Server Error. openmm.OpenMMException: Error compiling kernel: Compile Server Error. File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Applications/ChimeraX-1.5.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 ""/Applications/ChimeraX-1.5.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 ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/isolde.py"", line 893, in start_sim sm.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1624, in start_sim self._prepare_sim() File ""/Users/yangxl/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1582, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: Compile Server Error. openmm.OpenMMException: Error compiling kernel: Compile Server Error. File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.20 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 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: MacBookPro11,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.2 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: 16 GB Boot ROM Version: 428.40.10.0.0 SMC Version (system): 2.29f24 Software: System Software Overview: System Version: macOS 10.15.7 (19H1519) Kernel Version: Darwin 19.6.0 Time since boot: 64 days 21:34 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.5 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StarMap: 1.2.15 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 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: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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 pyqtgraph: 0.13.3 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect assigned normal Third Party all ChimeraX