id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4609 Problem fetching Modeller scores swamy02_vet@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.8.0-50-generic-x86_64-with-debian-bullseye-sid ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir Summary of feedback from opening /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir --- notes | Alignment identifier is 3ciyA_t3dim.pir Showing conservation header (""seq_conservation"" residue attribute) for alignment 3ciyA_t3dim.pir Opened 2 sequences from 3ciyA_t3dim.pir > open 3ciy 3ciy title: Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA [more info...] Chain information for 3ciy #1 --- Chain | Description A B | Toll-like receptor 3 C | 46-mer D | 46-mer Non-standard residues in 3ciy #1 --- BMA — beta-D-mannopyranose FUC — alpha-L-fucopyranose FUL — beta-L-fucopyranose (6-deoxy-β-L-galactose) MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose Associated 3ciy chain A to 3ciy chain A,B with 0 mismatches Associated 3ciy chain B to 3ciy chain A,B with 0 mismatches > open > /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir Summary of feedback from opening /home/swamy/folder_d/TLR3/modeller_dimer/HKCT3D/chimerax/dimer/success/alignment/3ciyA_t3dim.pir --- notes | Alignment identifier is 3ciyA_t3dim.pir Associated 3ciy chain A to 3ciy chain A,B with 0 mismatches Associated 3ciy chain B to 3ciy chain A,B with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 3ciyA_t3dim.pir Opened 2 sequences from 3ciyA_t3dim.pir > sequence associate /B 3ciyA_t3dim.pir:1 Disassociated 3ciy chain B from 3ciy chain A,B Associated 3ciy chain B to HKCT3 chain A,B with 158 mismatches and/or gaps > ui tool show ""Modeller Comparative"" No target sequence chosen for alignment 3ciyA_t3dim.pir > modeller comparative 3ciyA_t3dim.pir:1 multichain true numModels 5 fast > false hetPreserve false hydrogens false waterPreserve false Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1620426845295728547354 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1620426845295728547354 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service1620426845295728547354 finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence alignment score = 2672 Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence alignment score = 2682.2 RMSD between 1002 pruned atom pairs is 0.941 angstroms; (across all 1329 pairs: 1.979) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence alignment score = 2675 Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence alignment score = 2702.6 RMSD between 1209 pruned atom pairs is 1.195 angstroms; (across all 1329 pairs: 1.310) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence alignment score = 2682.8 Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence alignment score = 2696.6 RMSD between 1061 pruned atom pairs is 1.002 angstroms; (across all 1329 pairs: 1.557) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence alignment score = 2675 Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence alignment score = 2685.2 RMSD between 739 pruned atom pairs is 0.848 angstroms; (across all 1329 pairs: 2.578) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ciy, chain A (#1) with HKCT3_chain_A,B, chain A (#), sequence alignment score = 2675 Matchmaker 3ciy, chain B (#1) with HKCT3_chain_A,B, chain B (#), sequence alignment score = 2685.8 RMSD between 714 pruned atom pairs is 0.756 angstroms; (across all 1329 pairs: 4.892) Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain A to HKCT3 chain A,B with 0 mismatches Associated HKCT3_chain_A,B chain B to HKCT3 chain A,B with 0 mismatches Chain information for HKCT3_chain_A,B --- Chain | Description 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.1/B 2.2/B 2.3/B 2.4/B 2.5/B | No description available > modeller scores #2.1-5 refresh false Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/webservices/httpq.py"", line 115, in run func(*args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 66, in __init__ self.start(session, modeller_host, license_key, structure, refresh, blocking=True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 173, in start self.run(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 283, in run self.launch(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 87, in launch sub_dom = parseString(submission) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py"", line 1968, in parseString return expatbuilder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 925, in parseString return builder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) xml.parsers.expat.ExpatError: syntax error: line 1, column 49 Error generating/processing HTTP request: xml.parsers.expat.ExpatError: syntax error: line 1, column 49 File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/webservices/httpq.py"", line 115, in run func(*args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 66, in __init__ self.start(session, modeller_host, license_key, structure, refresh, blocking=True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 173, in start self.run(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 283, in run self.launch(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 87, in launch sub_dom = parseString(submission) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py"", line 1968, in parseString return expatbuilder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 925, in parseString return builder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) xml.parsers.expat.ExpatError: syntax error: line 1, column 49 Error generating/processing HTTP request: xml.parsers.expat.ExpatError: syntax error: line 1, column 49 File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/webservices/httpq.py"", line 115, in run func(*args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 66, in __init__ self.start(session, modeller_host, license_key, structure, refresh, blocking=True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 173, in start self.run(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 283, in run self.launch(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 87, in launch sub_dom = parseString(submission) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py"", line 1968, in parseString return expatbuilder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 925, in parseString return builder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) xml.parsers.expat.ExpatError: syntax error: line 1, column 49 Error generating/processing HTTP request: xml.parsers.expat.ExpatError: syntax error: line 1, column 49 File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/webservices/httpq.py"", line 115, in run func(*args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 66, in __init__ self.start(session, modeller_host, license_key, structure, refresh, blocking=True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 173, in start self.run(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 283, in run self.launch(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 87, in launch sub_dom = parseString(submission) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py"", line 1968, in parseString return expatbuilder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 925, in parseString return builder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) xml.parsers.expat.ExpatError: syntax error: line 1, column 49 Error generating/processing HTTP request: xml.parsers.expat.ExpatError: syntax error: line 1, column 49 File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/webservices/httpq.py"", line 115, in run func(*args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 66, in __init__ self.start(session, modeller_host, license_key, structure, refresh, blocking=True) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 173, in start self.run(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/tasks.py"", line 283, in run self.launch(*args, **kw) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/modeller/scores.py"", line 87, in launch sub_dom = parseString(submission) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/minidom.py"", line 1968, in parseString return expatbuilder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 925, in parseString return builder.parseString(string) File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) xml.parsers.expat.ExpatError: syntax error: line 1, column 49 Error generating/processing HTTP request: xml.parsers.expat.ExpatError: syntax error: line 1, column 49 File ""/usr/lib/ucsf-chimerax/lib/python3.7/xml/dom/expatbuilder.py"", line 223, in parseString parser.Parse(string, True) See log for complete Python traceback. OpenGL version: 4.6 (Core Profile) Mesa 20.2.6 OpenGL renderer: Mesa Intel(R) HD Graphics 620 (KBL GT2) OpenGL vendor: Intel Manufacturer: Dell Inc. Model: Inspiron 15-3567 OS: Ubuntu 20.04 focal Architecture: 64bit ELF CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz Cache Size: 3072 KB Memory: total used free shared buff/cache available Mem: 7.6Gi 1.7Gi 3.9Gi 546Mi 2.0Gi 5.2Gi Swap: 14Gi 0B 14Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 620 [8086:5916] (rev 02) DeviceName: Onboard IGD Subsystem: Dell HD Graphics 620 [1028:078b] 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 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 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-LinuxSupport: 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 distro: 1.5.0 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 Sequence duplicate all ChimeraX