id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8312 "ISOLDE: ""start sim"": No compatible OpenCL platform is available" dolezal@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-6.1.5-060105-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Happens when I press ""Start simulation"" in Isolde michal@mdpc:~$ clinfo Number of platforms 1 Platform Name AMD Accelerated Parallel Processing Platform Vendor Advanced Micro Devices, Inc. Platform Version OpenCL 2.1 AMD-APP (3452.0) Platform Profile FULL_PROFILE Platform Extensions cl_khr_icd cl_amd_event_callback Platform Extensions function suffix AMD Platform Host timer resolution 1ns Platform Name AMD Accelerated Parallel Processing Number of devices 0 NULL platform behavior clGetPlatformInfo(NULL, CL_PLATFORM_NAME, ...) No platform clGetDeviceIDs(NULL, CL_DEVICE_TYPE_ALL, ...) No platform clCreateContext(NULL, ...) [default] No platform clCreateContext(NULL, ...) [other] clCreateContextFromType(NULL, CL_DEVICE_TYPE_DEFAULT) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_CPU) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_GPU) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_ACCELERATOR) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_CUSTOM) No devices found in platform clCreateContextFromType(NULL, CL_DEVICE_TYPE_ALL) No devices found in platform 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 > open > ""/home/michal/Science/CryoEM/Phenix/GuaB1_EM_002/RealSpaceRefine_14/real_space_refined_010-coot-1_after > isolde_ligands_real_space_refined_014.pdb"" Chain information for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb #1 --- Chain | Description A B C D E F G H | No description available > open /home/michal/Desktop/test.mrc Opened test.mrc as #2, grid size 540,540,540, pixel 0.679, shown at level 0.00952, step 4, values float32 > open /home/michal/Desktop/test_sharp100.mrc Opened test_sharp100.mrc as #3, grid size 540,540,540, pixel 0.679, shown at level 0.281, step 4, values float32 > open /home/michal/Desktop/test_blur200.mrc Opened test_blur200.mrc as #4, grid size 540,540,540, pixel 0.679, shown at level 0.00317, step 4, values float32 > open /home/michal/Desktop/test_blur50.mrc Opened test_blur50.mrc as #5, grid size 540,540,540, pixel 0.679, shown at level 0.00289, step 4, values float32 > clipper associate #2 toModel #1 Opened test.mrc as #1.1.1.1, grid size 540,540,540, pixel 0.679, shown at level 0.0312, step 1, values float32 Chain information for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 314 residues in model #1.2 to IUPAC-IUB standards. > clipper associate #3 toModel #1 Opened test_sharp100.mrc as #1.1.1.2, grid size 540,540,540, pixel 0.679, shown at step 1, values float32 > clipper associate #4 toModel #1 Opened test_blur200.mrc as #1.1.1.3, grid size 540,540,540, pixel 0.679, shown at step 1, values float32 > clipper associate #5 toModel #1 Opened test_blur50.mrc as #1.1.1.4, grid size 540,540,540, pixel 0.679, shown at step 1, values float32 > volume #1.1.1.1 level 0.006882 > volume #1.1.1.3 level -0.0001456 > volume #1.1.1.4 level 0.00154 > select clear > view /A:502 > volume #1.1.1.1 level 0.02943 > volume #1.1.1.1 level 0.03094 > volume #1.1.1.2 level 0.2172 > volume show > volume #1.1.1.2 level 0.1617 > show #!1.1.1.1 models > show #!1.1.1.3 models > show #!1.1.1.4 models > hide #!1.1.1.2 models > hide #!1.1.1.3 models > hide #!1.1.1.4 models > select add #1.1.1.1 3 models selected > select subtract #1.1.1.1 Nothing selected > select add #1.1.1.1 3 models selected > select subtract #1.1.1.1 Nothing selected > hide #!1.1.1.1 models > show #!1.1.1.2 models > volume #1.1.1.2 level 0.2888 > volume #1.1.1.2 level 0.2326 > volume #1.1.1.2 step 2 > volume #1.1.1.2 step 1 > volume #1.1.1.2 level 0.2799 > volume #1.1.1.2 level 0.1765 > show #!1.1.1.3 models > volume #1.1.1.3 level 0.008468 > volume #1.1.1.3 level 0.01179 > hide #!1.1.1.3 models > show #!1.1.1.4 models > volume #1.1.1.4 level 0.02085 > color #1.1.1.4 #c061cb models transparency 0 > color #1.1.1.4 #9141ac models transparency 0 > color #1.1.1.3 #57e389 models transparency 0 > color #1.1.1.3 #33d17a models transparency 0 > color #1.1.1.3 #e01b24 models transparency 0 > show #!1.1.1.3 models > volume #1.1.1.3 level 0.008863 > hide #!1.1.1.3 models > hide #!1.1.1.1 models > show #!1.1.1.1 models > hide #!1.1.1.4 models > view /A:501 > show #!1.1.1.2 models > hide #!1.1.1.1 models > volume #1.1.1.2 level 0.4037 > hide #!1.1.1.2 models > show #!1.1.1.1 models > show #!1.1.1.4 models > volume #1.1.1.4 level 0.01819 > hide #!1.1.1.4 models > show #!1.1.1.3 models > volume #1.1.1.3 level 0.007348 > volume #1.1.1.3 level 0.006675 > hide #!1.1.1.4 models > show #!1.1.1.4 models > clipper spotlight > clipper isolate sel maskRadius 4.0 focus false > clipper spotlight > select clear > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 212 atoms, 213 bonds, 13 residues, 1 model selected > clipper isolate sel maskRadius 4.0 focus false > clipper spotlight > isolde sim start sel Loading residue template for 5GP from internal database Loading residue template for ATP from internal database ISOLDE: stopped sim Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif > isolde parameterise sel override true Running ANTECHAMBER command: /usr/lib/ucsf- chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmpyay2orim/ante.in.mol2 -fi mol2 -o /tmp/tmpyay2orim/ante.out.mol2 -fo mol2 -c bcc -nc -14 -j 5 -s 2 -dr n (5GP) `` (5GP) `Welcome to antechamber 20.0: molecular input file processor.` (5GP) `` (5GP) `Info: Finished reading file (/tmp/tmpyay2orim/ante.in.mol2); atoms read (24), bonds read (26).` (5GP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (5GP) `` (5GP) `` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (5GP) `Info: Total number of electrons: 188; net charge: -14` (5GP) `` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (5GP) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!` (5GP) `Cannot properly run ""/usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue 5GP Check reply log for details > isolde parameterise sel override true Running ANTECHAMBER command: /usr/lib/ucsf- chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmps9qlu83f/ante.in.mol2 -fi mol2 -o /tmp/tmps9qlu83f/ante.out.mol2 -fo mol2 -c bcc -nc -14 -j 5 -s 2 -dr n (5GP) `` (5GP) `Welcome to antechamber 20.0: molecular input file processor.` (5GP) `` (5GP) `Info: Finished reading file (/tmp/tmps9qlu83f/ante.in.mol2); atoms read (24), bonds read (26).` (5GP) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (5GP) `` (5GP) `` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (5GP) `Info: Total number of electrons: 188; net charge: -14` (5GP) `` (5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (5GP) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!` (5GP) `Cannot properly run ""/usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue 5GP Check reply log for details > addh Summary of feedback from adding hydrogens to real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb #1.2 --- warnings | Not adding hydrogens to /A GLU 129 CG because it is missing heavy- atom bond partners Not adding hydrogens to /A GLU 138 CG because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 168 CG because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 175 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 188 CB because it is missing heavy-atom bond partners 83 messages similar to the above omitted notes | No usable SEQRES records for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb (#1.2) chain E; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /A VAL 2, /B VAL 2, /C VAL 2, /D VAL 2, /E VAL 2, /F VAL 2, /G VAL 2, /H VAL 2 Chain-initial residues that are not actual N termini: /A SER 402, /B SER 402, /C SER 402, /D SER 402, /E SER 402, /F SER 402, /G SER 402, /H SER 402 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ALA 481, /A ALA 394, /B ALA 481, /B ALA 394, /C ALA 481, /C ALA 394, /D ALA 481, /D ALA 394, /E ALA 481, /E ALA 394, /F ALA 481, /F ALA 394, /G ALA 481, /G ALA 394, /H ALA 481, /H ALA 394 4011 hydrogen bonds /A ALA 481 is not terminus, removing H atom from 'C' /B ALA 481 is not terminus, removing H atom from 'C' /C ALA 481 is not terminus, removing H atom from 'C' /D ALA 481 is not terminus, removing H atom from 'C' /E ALA 481 is not terminus, removing H atom from 'C' 3 messages similar to the above omitted 197 hydrogens added > isolde sim start sel Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/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 ""/usr/lib/ucsf-chimerax/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 ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1286, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 187, in run_provider toolbar_command(session, name) File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/usr/lib/ucsf-chimerax/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 ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/isolde.py"", line 893, in start_sim sm.start_sim() File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1624, in start_sim self._prepare_sim() File ""/home/michal/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1582, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py"", line 5248, in __init__ this = _openmm.new_Context(*args) openmm.OpenMMException: No compatible OpenCL platform is available openmm.OpenMMException: No compatible OpenCL platform is available File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py"", line 5248, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. OpenGL version: 4.6 (Core Profile) Mesa 22.1.0-devel OpenGL renderer: AMD Radeon (TM) R9 380 Series (tonga, LLVM 14.0.1, DRM 3.49, 6.1.5-060105-generic) OpenGL vendor: AMD Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Ubuntu 22.04 jammy Architecture: 64bit ELF Virtual Machine: none CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 31Gi 12Gi 12Gi 50Mi 7.0Gi 18Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 01:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Tonga PRO [Radeon R9 285/380] [1002:6939] (rev f1) Subsystem: Micro-Star International Co., Ltd. [MSI] Radeon R9 380 Gaming 4G [1462:2015] Kernel driver in use: amdgpu Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 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: 0.18.0 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: 1.4 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-LinuxSupport: 1.0 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-NIHPresets: 1.1.9 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 distro: 1.6.0 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: 21.3 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 feedback normal Third Party all ChimeraX