id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5354 Crystal Contacts: name 'm' is not defined macbas@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open C:\\\Users\\\Maciek\\\Desktop\\\k-turn.cxs Log from Tue Oct 5 12:34:16 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4cs1 Summary of feedback from opening 4cs1 fetched from pdb --- note | Fetching compressed mmCIF 4cs1 from http://files.rcsb.org/download/4cs1.cif 4cs1 title: Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound. [more info...] Chain information for 4cs1 #1 --- Chain | Description A | 5'-(*GP*GP*CP*GP*ap*ap*GP*ap*ap*CP*CP*GP*GP*GP *GP*ap*GP*CP*CP)-3' Non-standard residues in 4cs1 #1 --- MG — magnesium ion 4cs1 mmCIF Assemblies --- 1| author_and_software_defined_assembly > sym #1 assembly 1 > view > hide #!2.1 models > show #!2.1 models > color #1 green > color #2.1 green > color #2.2 red > delete solvent > delete mg Missing or invalid ""atoms"" argument: invalid atoms specifier > delete MG Missing or invalid ""atoms"" argument: invalid atoms specifier > delete atoms MG Expected a keyword > delete magnesiu Missing or invalid ""atoms"" argument: invalid atoms specifier > delete magnesium Missing or invalid ""atoms"" argument: invalid atoms specifier > delete metal Missing or invalid ""atoms"" argument: invalid atoms specifier > delete ions > color #!2.1-2 bynucleotide > nucleotides #!2.1-2 fill > style nucleic & #!2.1-2 stick Changed 834 atom styles > hbonds 87 hydrogen bonds found > select clear > hbonds 87 hydrogen bonds found > select clear > select clear > !hbonds Unknown command: !hbonds > ~hbonds > select up 22 atoms, 24 bonds, 1 residue, 1 model selected > show #!1 models > hide #!2 models > hide #!2.2 models > hide #!2.1 models > show #!2.1 models > hide #!2.1 models > show #!2.1 models > hide #!2 models > hide #!1 models > select #2.1 417 atoms, 468 bonds, 19 residues, 1 model selected > select #2 834 atoms, 936 bonds, 38 residues, 3 models selected > ~select #2 Nothing selected > show #!2 models > select #2.1/A:6 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #2.1/A:5 44 atoms, 48 bonds, 2 residues, 1 model selected > select clear > select #2.1/A:4 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #2.1/A:5 45 atoms, 49 bonds, 2 residues, 1 model selected > select add #2.1/A:6 67 atoms, 73 bonds, 3 residues, 1 model selected > color sel blue > select clear > hbonds 87 hydrogen bonds found > contacts 5823 contacts > ~contacts > color @@color=blue purple > select #2.1/A:3 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #2.1/A:2 43 atoms, 46 bonds, 2 residues, 1 model selected > color sel yellow > select clear > select #2.1/A:7 23 atoms, 25 bonds, 1 residue, 1 model selected > select #2.1/A:8 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #2.1/A:7 45 atoms, 49 bonds, 2 residues, 1 model selected > color sel green > select clear > ui tool show H-Bonds > hbonds reveal true 87 hydrogen bonds found > hbonds reveal true 87 hydrogen bonds found > hbonds reveal true 87 hydrogen bonds found > hbonds reveal true 87 hydrogen bonds found > hbonds dashes 6 reveal true retainCurrent true 87 hydrogen bonds found > hbonds twoColors true reveal true 87 hydrogen bonds found 59 strict hydrogen bonds found > select #2.1/A:11 20 atoms, 21 bonds, 1 residue, 1 model selected > hbonds twoColors true reveal true 87 hydrogen bonds found 59 strict hydrogen bonds found > hbonds twoColors true reveal true 87 hydrogen bonds found 59 strict hydrogen bonds found > hbonds twoColors true reveal true 87 hydrogen bonds found 59 strict hydrogen bonds found > show #!2.2 models > hide #!2 models > hide #1.1 models > show #1.1 models > show #!2 models > hide #!1 models > hide #1.1 models > hide #3 models > show #3 models > hide #3 models > save C:/Users/Maciek/Desktop/k-turn.cxs ——— End of log from Tue Oct 5 12:34:16 2021 ——— opened ChimeraX session > hide #!2 models > hide #!2.1 models > hide #!2.2 models > show #!1 models > show #!2 models > hide #!1 models > show #!2.1 models > show #!2.2 models > select #2.1/A:4 23 atoms, 25 bonds, 1 residue, 1 model selected > select #2.1/A:5 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #2.1/A:6 44 atoms, 48 bonds, 2 residues, 1 model selected > select add #2.1/A:4 67 atoms, 73 bonds, 3 residues, 1 model selected > show sel atms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show atoms sel Expected ',' or a keyword > color sel cpk Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select #2.1/A:3 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #2.1/A:2 43 atoms, 46 bonds, 2 residues, 1 model selected > select add #2.1/A:4 66 atoms, 71 bonds, 3 residues, 1 model selected > select add #2.1/A:5 88 atoms, 95 bonds, 4 residues, 1 model selected > select add #2.1/A:6 110 atoms, 119 bonds, 5 residues, 1 model selected > select add #2.1/A:7 133 atoms, 144 bonds, 6 residues, 1 model selected > select add #2.1/A:8 155 atoms, 168 bonds, 7 residues, 1 model selected > select add #2.1/A:9 177 atoms, 192 bonds, 8 residues, 1 model selected > color ~sel grey > select clear > select clear > select #2.1/A:7 23 atoms, 25 bonds, 1 residue, 1 model selected > select #2.2/A:16 22 atoms, 24 bonds, 1 residue, 1 model selected > select clear Drag select of 210 atoms, 15 residues, 235 bonds, 39 shapes > hide ~sel > hide ~sel cartoons > select clear > save C:/Users/Maciek/Desktop/k-turn.cxs > tool show si > contacts 5823 contacts > hbonds 87 hydrogen bonds found > ~contacts > crystalcontacts Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 280, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. > crystalcontacts Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 280, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. > ui tool show ""Crystal Contacts"" > crystalcontacts #2.1 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalgui.py"", line 130, in _show_contacts run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. > crystalcontacts #2.2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalgui.py"", line 130, in _show_contacts run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. > crystalcontacts #2.2 distance 5 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalgui.py"", line 130, in _show_contacts run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. > crystalcontacts #2.2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalgui.py"", line 130, in _show_contacts run(self.session, cmd) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystalcmd.py"", line 59, in crystalcontacts show_crystal_contacts(m, distance, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) NameError: name 'm' is not defined NameError: name 'm' is not defined File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\crystal_contacts\crystal.py"", line 36, in show_crystal_contacts raise UserError('No unit cell parameters for %s' % m.name) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.9664 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: OptiPlex 7070 OS: Microsoft Windows 10 Pro (Build 19042) Memory: 8,361,283,584 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz OSLanguage: pl-PL Locale: ('pl_PL', 'cp1250') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 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: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 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: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 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: 0.29.21 decorator: 5.0.9 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: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Analysis fixed all ChimeraX