id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4555 ISOLDE/Clipper: Spgr_descr: No such HM symbol arronsullivan@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description attepted to use ISOLDE for the first time and got the error in the log attached. Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open C:\Users\robot\Desktop\Modeling\Herceptin_FC_Lys_v1.cxs format session Log from Mon Apr 19 13:13:53 2021UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6IQG Summary of feedback from opening 6IQG fetched from pdb --- notes | Fetching compressed mmCIF 6iqg from http://files.rcsb.org/download/6iqg.cif Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif Fetching CCD HCS from http://ligand-expo.rcsb.org/reports/H/HCS/HCS.cif 6iqg title: X-ray crystal structure of Fc and peptide complex [more info...] Chain information for 6iqg #1 --- Chain | Description A B | Immunoglobulin gamma-1 heavy chain C D | 18-mer peptide G(HCS)DCAYHRGELVWCT(HCS)H(NH2) Non-standard residues in 6iqg #1 --- BMA — beta-D-mannopyranose CL — chloride ion FUC — alpha-L-fucopyranose HCS — 2-amino-4-mercapto-butyric acid MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > select /C/D 228 atoms, 236 bonds, 28 residues, 1 model selected > remove Unknown command: remove > remove selected Unknown command: remove selected > remove /c Unknown command: remove /c > hide /c > select clear > hide /c > select /C:613 14 atoms, 15 bonds, 1 residue, 1 model selected > select /C/D 228 atoms, 236 bonds, 28 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 > select ::name=""LYS"" 324 atoms, 288 bonds, 36 residues, 1 model selected > show sel atoms > style sel ball Changed 324 atom styles > surface sel > transparency (#!1 & sel) 50 > surface style mesh > select clear > select /B:246@CE 1 atom, 1 residue, 1 model selected > select /B:246@NZ 1 atom, 1 residue, 1 model selected > select /B:248@NZ 1 atom, 1 residue, 1 model selected > ui tool show Distances > distance /B:246@NZ /B:248@NZ Distance between /B LYS 246 NZ and LYS 248 NZ: 11.620Å Drag select of 2 residues > select /B:246@CE 1 atom, 1 residue, 1 model selected > distance /B:246@CE /B:290@CE Distance between /B LYS 246 CE and LYS 290 CE: 13.306Å > select clear > select ::name=""LYS"" 324 atoms, 288 bonds, 2 pseudobonds, 36 residues, 2 models selected > surface style dot > surface style solid > transparency (#!1 & sel) 80 > select clear > select /B:290@CE 1 atom, 1 residue, 1 model selected > select /B:246@CG 1 atom, 1 residue, 1 model selected > select clear > hide #2.1 models > show #2.1 models > hide #!2 models > select /B:274@CE 1 atom, 1 residue, 1 model selected > distance /B:274@CE /B:322@CE Distance between /B LYS 274 CE and LYS 322 CE: 7.003Å > show #!2 models > select /B:274@CE 1 atom, 1 residue, 1 model selected > distance /B:274@CE /B:326@NZ Distance between /B LYS 274 CE and LYS 326 NZ: 11.172Å > select /B:322@CE 1 atom, 1 residue, 1 model selected > select /B:274@CD 1 atom, 1 residue, 1 model selected > select /B:288@CE 1 atom, 1 residue, 1 model selected > distance /B:288@CE /B:290@CE Distance between /B LYS 288 CE and LYS 290 CE: 9.280Å > select /B:322@CE 1 atom, 1 residue, 1 model selected > distance /B:320@NZ /B:322@CE Distance between /B LYS 320 NZ and LYS 322 CE: 9.849Å > select /B:320@NZ 1 atom, 1 residue, 1 model selected > select /B:320@NZ 1 atom, 1 residue, 1 model selected > distance /B:317@CE /B:320@NZ Distance between /B LYS 317 CE and LYS 320 NZ: 12.281Å > select clear > select /B:317@CE 1 atom, 1 residue, 1 model selected > distance /B:317@CE /B:340@NZ Distance between /B LYS 317 CE and LYS 340 NZ: 14.146Å > select /B:340@NZ 1 atom, 1 residue, 1 model selected > distance /B:338@NZ /B:340@NZ Distance between /B LYS 338 NZ and LYS 340 NZ: 9.588Å Drag select of 6iqg_A SES surface, 15 of 202702 triangles, 6iqg_B SES surface, 414 of 203562 triangles, 5 atoms, 2 residues, 3 bonds > select /B:439@CE 1 atom, 1 residue, 1 model selected > distance /A:360@CE /B:439@CE Distance between /A LYS 360 CE and /B LYS 439 CE: 9.669Å > select /B:370@NZ 1 atom, 1 residue, 1 model selected > distance /A:409@NZ /B:370@NZ Distance between /A LYS 409 NZ and /B LYS 370 NZ: 5.420Å > select /A:414@CE 1 atom, 1 residue, 1 model selected > select clear > select /B:414@CE 1 atom, 1 residue, 1 model selected > distance /B:360@CG /B:414@CE Distance between /B LYS 360 CG and LYS 414 CE: 8.721Å > select /B:392@NZ 1 atom, 1 residue, 1 model selected > distance /B:392@NZ /B:409@NZ Distance between /B LYS 392 NZ and LYS 409 NZ: 9.394Å > select /B:409@NZ 1 atom, 1 residue, 1 model selected > distance /A:370@CE /B:409@NZ Distance between /A LYS 370 CE and /B LYS 409 NZ: 4.309Å > view sel > select clear > rotate Unknown command: rotate > wobble > stop > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\robot\Desktop\movie3.mp4 Movie saved to \C:Users\\...\Desktop\movie3.mp4 > save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs > set bgColor white > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > distance style color black > distance style color #005500 > distance style color #aaaa00 > distance style color black > distance style color #00007f > distance style color #550000 > distance style color #55007f > distance style color #005500 > distance style color #d7eaf8 > distance style color #cccccc > distance style color #f0f0f0 > distance style color #fafafa > distance style color white > distance style color black > distance style color white > distance style color #ffefc3 > distance style color white > distance style color #ff1a1a > distance style color black > distance style color white > distance style color #c52a2a > distance style color white > distance style color #c72e2e > distance style color white > distance style color #7a5656 > distance style color #eddcdc > distance style color #f2e1e1 > distance style color #2d1b1b > distance style color #6769d2 > distance style color #6b72de > distance style color #6565c3 > distance style color #554a6d > distance style color #eddede > distance style color white > distance style color black > distance style color #62594e > distance style color white > distance style color black > distance style color #ff3939 > distance style color #ff3535 > distance style color black > distance style color #f13131 > distance style color #ff3535 > distance style color #ff3636 > distance style color #b02d2d > distance style color #9e2c2c > distance style color black > distance style color white > distance style color black > distance style color #6c2b2b > distance style color #b22d2d > distance style color #ff3232 > distance style color #ff3d3d > distance style color #ff3535 > distance style color black > distance style color white > distance style color #e4d7d7 > distance style color #d7d4e9 > distance style color #d2cfe2 > distance style color #d7d4e9 > distance style color #dbd7ef > distance style color #c0bcd8 > distance style color #bfbbd7 > distance style color #5e515a > distance style color #f0f0f0 > distance style color black > distance style color #828790 > distance style color #f0f0f0 > distance style color #aa0000 > distance style color #f0f0f0 > distance style color #005500 > lighting full > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\robot\Desktop\movie4.mp4 Movie saved to \C:Users\\...\Desktop\movie4.mp4 > select /B:320@CD 1 atom, 1 residue, 1 model selected > select /B:317@CG 1 atom, 1 residue, 1 model selected > select /B:274@CD 1 atom, 1 residue, 1 model selected > select /B:290@CG 1 atom, 1 residue, 1 model selected > select /B:288@CG 1 atom, 1 residue, 1 model selected > select /B:334@CD 1 atom, 1 residue, 1 model selected > distance /B:334@CD /B:340@NZ Distance between /B LYS 334 CD and LYS 340 NZ: 14.834Å > select /B:360@O 1 atom, 1 residue, 1 model selected > select /B:360@O 1 atom, 1 residue, 1 model selected > select /B:360@CG 1 atom, 1 residue, 1 model selected > ~distance /B:360@CG /B:414@CE > select /B:414@NZ 1 atom, 1 residue, 1 model selected > distance /B:360@CE /B:414@NZ Distance between /B LYS 360 CE and LYS 414 NZ: 9.752Å > distance style color #aa0000 > distance style color #005500 > select /B:414@NZ 1 atom, 1 residue, 1 model selected > select /A:439@CE 1 atom, 1 residue, 1 model selected > select /B:360@CE 1 atom, 1 residue, 1 model selected > distance /A:439@CE /B:360@CE Distance between /A LYS 439 CE and /B LYS 360 CE: 10.094Å > distance style color #aa0000 > distance style color #005500 > select /B:414@CE 1 atom, 1 residue, 1 model selected > select clear > select /B:414@CB 1 atom, 1 residue, 1 model selected > select /A:409@NZ 1 atom, 1 residue, 1 model selected > select /B:409@CG 1 atom, 1 residue, 1 model selected > select /A:370@NZ 1 atom, 1 residue, 1 model selected > select /B:392@CG 1 atom, 1 residue, 1 model selected > select /B:409@CG 1 atom, 1 residue, 1 model selected > select /B:409@CD 1 atom, 1 residue, 1 model selected > select /B:409@CA 1 atom, 1 residue, 1 model selected > select /A:370@CE 1 atom, 1 residue, 1 model selected > select /B:409@NZ 1 atom, 1 residue, 1 model selected > select /B:360@CD 1 atom, 1 residue, 1 model selected > select /A:360@CG 1 atom, 1 residue, 1 model selected > save C:/Users/robot/Desktop/Modeling/Herceptin_FC_Lys_v1.cxs opened ChimeraX session > open 1HZH Summary of feedback from opening 1HZH fetched from pdb --- notes | Fetching compressed mmCIF 1hzh from http://files.rcsb.org/download/1hzh.cif Fetching CCD GAL from http://ligand-expo.rcsb.org/reports/G/GAL/GAL.cif 1hzh title: Crystal structure of the intact human igg B12 with broad and potent activity against primary hiv-1 isolates: A template for hiv vaccine design [more info...] Chain information for 1hzh #3 --- Chain | Description H K | immunoglobulin heavy chain L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein Non-standard residues in 1hzh #3 --- BMA — beta-D-mannopyranose FUC — alpha-L-fucopyranose GAL — beta-D-galactopyranose MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose > hide #2.1 models > hide #!2 models > hide #!1 models > view orient > select ::name=""LYS"" 1117 atoms, 997 bonds, 16 pseudobonds, 124 residues, 3 models selected > show sel & #!3 atoms > color sel & #!3 bychain > select clear > select clear > color #!3 bychain > show #!3 atoms > hide #!3 models > show #!1 models > show #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/H #3/K Alignment identifier is 2 > sequence chain #3/L #3/M Alignment identifier is 3 > select clear > hide atoms > close session > open C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb Summary of feedback from opening C:/Users/robot/Desktop/Modeling/1igt_eaaak_tails_2_AF488.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK BIOVIA PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-04-23T12:35:55Z Chain information for 1igt_eaaak_tails_2_AF488.pdb #1 --- Chain | Description A C | No description available B | No description available D | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /A /C Alignment identifier is 1 > sequence chain /B Alignment identifier is 1/B > sequence chain /D Alignment identifier is 1/D > show sel atoms > show sel atoms > show sel surfaces > select clear > color bychain > select ::name=""KAF"" 6540 atoms, 6852 bonds, 102 residues, 1 model selected > show sel surfaces > close session > open C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb format pdb Summary of feedback from opening C:\Users\robot\Desktop\Modeling\1igt_eaaak_tails_2_AF488.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK BIOVIA PDB file Ignored bad PDB record found on line 2 REMARK Created: 2021-04-23T12:45:44Z Chain information for 1igt_eaaak_tails_2_AF488.pdb #1 --- Chain | Description A C | No description available B | No description available D | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > sequence chain /D Alignment identifier is 1/D > select ::name=""KAF"" 6538 atoms, 6850 bonds, 102 residues, 1 model selected > show sel atoms > show sel surfaces > hide sel surfaces > color (#!1 & sel) lime > show sel surfaces > show sel atoms > color sel lime > show sel surfaces > color (#!1 & sel) lime > hide sel atoms > show sel atoms > ui tool show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 531, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1253, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\\__init__.py"", line 139, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\tools.py"", line 193, in get_singleton tinst = tool_class(session, tool_name, **kw) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\tool.py"", line 186, in __init__ self.isolde = isolde.Isolde(self) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 312, in __init__ self._start_gui(gui) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 456, in _start_gui self._populate_menus_and_update_params() File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 559, in _populate_menus_and_update_params self._update_model_list(None, None, force=True) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 1027, in _update_model_list self._change_selected_model(model=current_model) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 2486, in _change_selected_model sh = get_symmetry_handler(m, create=True, auto_add_to_session=True) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 159, in get_symmetry_handler sh = _get_symmetry_handler(structure, create) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 170, in _get_symmetry_handler return SymmetryManager(structure.session, model=structure) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 573, in __init__ spotlight_mode=spotlight_mode) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 601, in add_model self.cell, self.spacegroup, self.grid, self.resolution, self._has_symmetry = f(*args) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 202, in symmetry_from_model_metadata return symmetry_from_model_metadata_pdb(model) File ""C:\Users\robot\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\clipper\symmetry.py"", line 447, in symmetry_from_model_metadata_pdb spgr_descr = Spgr_descr(symstr, symstr_type) RuntimeError: Spgr_descr: No such HM symbol During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 1501, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\run.py"", line 31, in run results = command.run(text, log=log) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\cmd.py"", line 187, in ui_tool_show bi.start_tool(session, name) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 537, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Spgr_descr: No such HM symbol chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Spgr_descr: No such HM symbol File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 537, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 461.92 OpenGL renderer: GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Home (Build 19043) Memory: 68,586,754,048 MaxProcessMemory: 137,438,953,344 CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor "" 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: 2.1.3 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-Clipper: 0.15.0 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: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 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 gdcm: 2.8.8 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+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 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 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 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 Send2Trash: 1.5.0 SEQCROW: 0.25.2 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 WMI: 1.5.1 }}} " defect assigned normal Third Party all ChimeraX