id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4152 alt loc starting values Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description If I try to create new altlocs for a set of atoms by: {{{ for a in selected_atoms(session) a.set_alt_loc('A', True) }}} ... then all the coordinates for the new altlocs (or the master coordinates if there were no previous altlocs) are set to (0,0,0). I think it would be more sensible if the new ones inherited the existing coordinates as a starting point. Log: > alias preview_toolshed toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu; toolshed reload available > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu; > toolshed reload available > alias st isolde step $* > alias aw isolde add water $* > alias awsf isolde add water sim false 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 working.pdb Summary of feedback from opening working.pdb --- warnings | Ignored bad PDB record found on line 243 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN Ignored bad PDB record found on line 244 LINKR TYR L 184 LEU L 186 gap Ignored bad PDB record found on line 245 LINKR VAL L 210 GLU L 212 gap Ignored bad PDB record found on line 246 LINKR PRO A 140 GLY A 148 gap working.pdb title: \--- [more info...] Chain information for working.pdb #1 --- Chain | Description A | No description available B | No description available H | No description available L | No description available R | No description available Non-standard residues in working.pdb #1 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) > isolde start > set selectionWidth 4 working.pdb title: \--- [more info...] Chain information for working.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/H | No description available 1.2/L | No description available 1.2/R | No description available Non-standard residues in working.pdb #1.2 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) Done loading forcefield Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > view /B:92 Loading residue template for GOL from internal database Loading residue template for SO4 from internal database Updating bulk solvent parameters... > select clear > select clear Updating bulk solvent parameters... > view /A:59 > select clear Updating bulk solvent parameters... > view /A:213 > select clear Updating bulk solvent parameters... > view /A:179 > view /H:179 > ui tool show Shell /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > select clear > select clear Updating bulk solvent parameters... > save working.pdb #1 > close #1 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_18 Deleting (LIVE) MDFF potential > open working_refine_001.pdb Chain information for working_refine_001.pdb #1 --- Chain | Description A | No description available B | No description available H | No description available L | No description available R | No description available Chain information for working_refine_001.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/H | No description available 1.2/L | No description available 1.2/R | No description available Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > open > /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb Summary of feedback from opening /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb --- warnings | Ignored bad PDB record found on line 243 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN Ignored bad PDB record found on line 244 LINKR TYR L 184 LEU L 186 gap Ignored bad PDB record found on line 245 LINKR VAL L 210 GLU L 212 gap Ignored bad PDB record found on line 246 LINKR PRO A 140 GLY A 148 gap working.pdb title: \--- [more info...] Chain information for working.pdb #2 --- Chain | Description A | No description available B | No description available H | No description available L | No description available R | No description available Non-standard residues in working.pdb #2 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) > close #2 > close #1 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_18 Deleting (LIVE) MDFF potential > open > /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb > format pdb Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1 --- Chain | Description X | No description available Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb --- Chain | Description 1.2/X | No description available > close #1 > open working.pdb Summary of feedback from opening working.pdb --- warnings | Ignored bad PDB record found on line 243 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN Ignored bad PDB record found on line 244 LINKR TYR L 184 LEU L 186 gap Ignored bad PDB record found on line 245 LINKR VAL L 210 GLU L 212 gap Ignored bad PDB record found on line 246 LINKR PRO A 140 GLY A 148 gap working.pdb title: \--- [more info...] Chain information for working.pdb #1 --- Chain | Description A | No description available B | No description available H | No description available L | No description available R | No description available Non-standard residues in working.pdb #1 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) working.pdb title: \--- [more info...] Chain information for working.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/H | No description available 1.2/L | No description available 1.2/R | No description available Non-standard residues in working.pdb #1.2 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) > view /R:449 > delete /R:616 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > set bgColor white Loading residue template for POL from internal database > select clear Updating bulk solvent parameters... > open 6m0j 6m0j title: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 [more info...] Chain information for 6m0j #2 --- Chain | Description A | Angiotensin-converting enzyme 2 E | Spike receptor binding domain Non-standard residues in 6m0j #2 --- CL — chloride ion NAG — N-acetyl-D-glucosamine ZN — zinc ion > matchmaker #2 to #1/R Parameters --- Chain pairing | bb 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 working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence alignment score = 1012.9 RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194 pairs: 0.726) > show #2 > close #2 > view /R:604 > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > select :HOH 1284 atoms, 856 bonds, 428 residues, 1 model selected > clipper isolate sel contextDistance 0 > clipper isolate sel contextDistance 0 > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > select clear Updating bulk solvent parameters... > select :HOH 1281 atoms, 854 bonds, 427 residues, 1 model selected > delete sel > close #1 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_18 Deleting (LIVE) MDFF potential > open working.pdb Summary of feedback from opening working.pdb --- warnings | Ignored bad PDB record found on line 243 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN Ignored bad PDB record found on line 244 LINKR TYR L 184 LEU L 186 gap Ignored bad PDB record found on line 245 LINKR VAL L 210 GLU L 212 gap Ignored bad PDB record found on line 246 LINKR PRO A 140 GLY A 148 gap working.pdb title: \--- [more info...] Chain information for working.pdb #1 --- Chain | Description A | No description available B | No description available H | No description available L | No description available R | No description available Non-standard residues in working.pdb #1 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) working.pdb title: \--- [more info...] Chain information for working.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/H | No description available 1.2/L | No description available 1.2/R | No description available Non-standard residues in working.pdb #1.2 --- CL — (CL) GOL — (GOL) NAG — (NAG) POL — (POL) SO4 — (SO4) Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > select up 6 atoms, 4 bonds, 2 residues, 1 model selected > delete sel > select clear > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > select clear > select #1 17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. > select clear Updating bulk solvent parameters... > view /R:449 > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select clear Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > view /R:449 > awsf > awsf > awsf > awsf > awsf > select clear Updating bulk solvent parameters... > st first > st > st interp 2 > st > st > st > st > st > st > st > st > st > st > st > st > st > st > st > aw > isolde sim start sel Updating bulk solvent parameters... > st > st > st > st > aw > isolde sim start sel > select clear Updating bulk solvent parameters... > aw > isolde sim start sel Updating bulk solvent parameters... > st > st > st > st > st > aw > isolde sim start sel > select clear Updating bulk solvent parameters... > st > aw > isolde sim start sel > select clear Updating bulk solvent parameters... > st > st > st > st > st > st > st > st > st > st > st > st > aw > isolde sim start sel Updating bulk solvent parameters... > awsf > awsf > awsf > select clear Updating bulk solvent parameters... > select up 9 atoms, 6 bonds, 3 residues, 1 model selected > delete sel > st > st > st > st > st > st > aw > isolde sim start sel > select clear Updating bulk solvent parameters... > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > alias al isolde add ligand $* > alias so setattr sel atoms occupancy $* > al SO4 > so 0.7 Assigning occupancy attribute to 5 items > select up 5 atoms, 4 bonds, 1 residue, 1 model selected Updating bulk solvent parameters... > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > so 0.5 Assigning occupancy attribute to 5 items > st > st > st > st > st > awsf > awsf Updating bulk solvent parameters... > st > st > st > al GOL > select clear Updating bulk solvent parameters... > st > aw > isolde sim start sel Updating bulk solvent parameters... > awsf > awsf Updating bulk solvent parameters... > select up 9 atoms, 6 bonds, 3 residues, 1 model selected > delete sel > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > al BMA Deleted the following atoms from residue BMA R710: HO1, O1 > show sel > ui mousemode right ""translate selected atoms"" > delete sel Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 1574, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""/home/tic20/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/menu/menu.py"", line 58, in f module.run_script(session) File ""/home/tic20/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/menu/model_building/make_bond.py"", line 22, in run_script add_bond(*sel) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/struct_edit.py"", line 225, in add_bond \+ all_residues[i1+1:i2] + all_residues[end_range+1:] TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues' TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues' File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/struct_edit.py"", line 225, in add_bond \+ all_residues[i1+1:i2] + all_residues[end_range+1:] See log for complete Python traceback. > select clear > select up 22 atoms, 22 bonds, 1 residue, 1 model selected Updating bulk solvent parameters... > al MAN Deleted the following atoms from residue MAN R711: HO1, O1 > show sel > ui mousemode right ""translate selected atoms"" > delete sel > select clear Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. Updating bulk solvent parameters... > select up 22 atoms, 22 bonds, 1 residue, 1 model selected > delete sel Updating bulk solvent parameters... > delete sel > save working_2.pdb #1 > view /R:449 > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > select sel&sideonly 15 atoms, 15 bonds, 1 residue, 1 model selected OpenGL version: 3.3.0 NVIDIA 455.32.00 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 12G 36G 303M 13G 49G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia 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-Async: 0.1 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-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-Phenix: 0.1 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 graphviz: 0.14.1 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 objgraph: 3.4.1 openvr: 1.12.501 packaging: 20.4 ParmEd: 3.2.0 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 Send2Trash: 1.5.0 SEQCROW: 0.20 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 versioneer: 0.18 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " enhancement closed normal Core fixed all ChimeraX