id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10300 Crash adding Volume menu chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001d0f6000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001c0f3000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File 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""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001a0ed000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000190ea000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000180e7000 (most recent call first): File 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""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000160e1000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00007000150de000 (most recent call first): File 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""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000352 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold search > GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Webservices job id: 8KBVQ80443G5LWH2 > alphafold match > GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH Fetching compressed AlphaFold A0A2V5LC98 from https://alphafold.ebi.ac.uk/files/AF-A0A2V5LC98-F1-model_v4.cif 1 AlphaFold model found using sequence similarity searches: A0A2V5LC98 (1 sequences) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A2V5LC98_9MICC | GSATL...HHHHH | 41.2 | 89.3 Opened 1 AlphaFold model > alphafold match > GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH 1 AlphaFold model found using sequence similarity searches: A0A2V5LC98 (1 sequences) | Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % A0A2V5LC98_9MICC | GSATL...HHHHH | 41.2 | 89.3 Opened 1 AlphaFold model > close #2 > alphafold predict > GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction > volume flip #6 Running AlphaFold prediction AlphaFold prediction finished Results in /Users/tilpap/Downloads/ChimeraX/AlphaFold/prediction_1 > open /Users/tilpap/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb | Chain information for best_model.pdb #2 --- Chain | Description A | No description available > hide #2 models > show #2 models > hide #1 models > show #1 models > toolshed show Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.3.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tilpap/Downloads/ChimeraX_PDBImages-1.2-py3-none-any.whl Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDBImages==1.2) (2.12) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDBImages==1.2) (1.10.3) Requirement already satisfied: ChimeraX-Core~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDBImages==1.2) (1.6.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.5.1) Requirement already satisfied: ChimeraX-Atomic~=1.34 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.43.10) Requirement already satisfied: ChimeraX-PDB~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (2.7.2) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.2) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.10.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.1) Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (10.0.6) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.2.3) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.0) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.0) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.1.1) Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.4) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.3) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.34->ChimeraX-mmCIF~=2.0->ChimeraX- PDBImages==1.2) (2.0.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.34->ChimeraX-mmCIF~=2.0->ChimeraX- PDBImages==1.2) (2.0.1) Requirement already satisfied: ChimeraX-IO~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX- PDBImages==1.2) (1.0.1) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX- PDBImages==1.2) (2.0) Requirement already satisfied: ChimeraX-Map~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX- PDBImages==1.2) (1.1.4) Requirement already satisfied: ChimeraX-UI~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX- PDBImages==1.2) (1.28.4) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.0->ChimeraX-MapFit~=2.0->ChimeraX- StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.1.1) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.0->ChimeraX-MapFit~=2.0->ChimeraX- StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.2) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.0->ChimeraX-MapFit~=2.0->ChimeraX- StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.34->ChimeraX- mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.0->ChimeraX-OpenCommand~=1.0->ChimeraX- mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX- OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.1) Installing collected packages: ChimeraX-PDBImages Successfully installed ChimeraX-PDBImages-1.2 \--- Successfully installed ChimeraX-PDBImages-1.2 Installed ChimeraX-PDBImages (1.2) Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl > select add #2 4453 atoms, 4547 bonds, 560 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.96421,-0.20983,0.16206,-1.5295,0.21546,0.97635,-0.017767,-8.0458,-0.1545,0.052048,0.98662,6.24 > view matrix models > #2,0.41111,0.90962,0.059811,43.614,-0.3259,0.20793,-0.92225,-24.097,-0.85134,0.35965,0.38193,27.481 > view matrix models > #2,0.57481,0.80996,-0.11645,32.81,-0.4968,0.23234,-0.83619,-16.414,-0.65022,0.5385,0.53594,27.811 > view matrix models > #2,0.57481,0.80996,-0.11645,4.8277,-0.4968,0.23234,-0.83619,-21.72,-0.65022,0.5385,0.53594,33.395 > view matrix models > #2,0.57481,0.80996,-0.11645,-13.13,-0.4968,0.23234,-0.83619,-1.6484,-0.65022,0.5385,0.53594,22.914 > view matrix models > #2,0.57481,0.80996,-0.11645,-2.6914,-0.4968,0.23234,-0.83619,2.6437,-0.65022,0.5385,0.53594,7.874 > ui tool show ""Fit in Map"" > ui tool show ""Volume Viewer"" > ui tool show Updates Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.3.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-ISOLDE==1.6.0 Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.6.0/ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl (87.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.7/87.7 MB 3.5 MB/s eta 0:00:00 Collecting ChimeraX-PhenixUI==1.2.0 Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxphenixui/releases/1.2.0/ChimeraX_PhenixUI-1.2.0-py3-none- any.whl (236 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 236.8/236.8 kB 1.2 MB/s eta 0:00:00 Installing collected packages: ChimeraX-PhenixUI, ChimeraX-ISOLDE Successfully installed ChimeraX-ISOLDE-1.6.0 ChimeraX-PhenixUI-1.2.0 \--- Successfully installed ChimeraX-ISOLDE-1.6.0 ChimeraX-PhenixUI-1.2.0 Installed ChimeraX-ISOLDE (1.6.0) Installed ChimeraX-PhenixUI (1.2.0) Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/tilpap/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/tilpap/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 956, in require needed = self.resolve(parse_requirements(requirements)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 815, in resolve dist = self._resolve_dist( File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 856, in _resolve_dist raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is required by ChimeraX-ISOLDE ChimeraX-ISOLDE (installed) [version: 1.6.0] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot [categories: Validation] [synopsis: Interactive Ramachandran plot]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]: custom initialization failed > view matrix models > #2,0.32066,0.81227,-0.48723,-0.14818,-0.454,-0.31964,-0.83169,-12.713,-0.8313,0.4879,0.26628,8.2717 > view matrix models > #2,0.25702,0.79691,-0.5467,0.62083,-0.56071,-0.33778,-0.75598,-8.4099,-0.78711,0.50084,0.36002,8.6391 > view matrix models > #2,0.27809,0.75768,-0.59042,-1.7777,-0.64201,-0.3106,-0.70097,-4.1337,-0.71449,0.57398,0.40006,8.7255 > ui mousemode right ""rotate selected models"" > view orient > view matrix models > #2,0.29051,0.78738,-0.54373,-0.68629,-0.62096,-0.2772,-0.73319,-4.5038,-0.72802,0.55063,0.4084,8.7167 > view Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl > toolshed show Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl > toolshed show Downloading bundle ChimeraX_PhenixUI-1.2.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.3.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tilpap/Downloads/ChimeraX_PhenixUI-1.2.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Geometry~=1.3 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.3) Requirement already satisfied: ChimeraX-CheckWaters~=1.3 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.3.1) Requirement already satisfied: ChimeraX-Core~=1.5dev1 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.6.1) Requirement already satisfied: ChimeraX-Atomic~=1.32 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.43.10) Requirement already satisfied: ChimeraX-PDB~=2.6 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (2.7.2) Requirement already satisfied: ChimeraX-MapFilter~=2.0.1 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (2.0.1) Requirement already satisfied: ChimeraX-UI~=1.21 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.28.4) Requirement already satisfied: ChimeraX-MapData~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (2.0) Requirement already satisfied: ChimeraX-Map~=1.1.3 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PhenixUI==1.2.1) (1.1.4) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0.3) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (1.1.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (2.12) Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (10.0.6) Requirement already satisfied: ChimeraX-Arrays~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (1.1) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0.1) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (1.0.2) Requirement already satisfied: ChimeraX-HBonds~=2.3 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-CheckWaters~=1.3->ChimeraX-PhenixUI==1.2.1) (2.4) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.5.1) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.2) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (2.1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.10.1) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-MapData~=2.0->ChimeraX-PhenixUI==1.2.1) (1.2.3) Requirement already satisfied: ChimeraX-IO~=1.0.1 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-PDB~=2.6->ChimeraX-PhenixUI==1.2.1) (1.0.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-UI~=1.21->ChimeraX-PhenixUI==1.2.1) (1.0) Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-HBonds~=2.3->ChimeraX-CheckWaters~=1.3->ChimeraX- PhenixUI==1.2.1) (2.0.1) Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-HBonds~=2.3->ChimeraX-CheckWaters~=1.3->ChimeraX- PhenixUI==1.2.1) (2.0.1) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.1.3->ChimeraX- PhenixUI==1.2.1) (2.0) Requirement already satisfied: ChimeraX-Surface~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX- PhenixUI==1.2.1) (1.0.1) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.21->ChimeraX- PhenixUI==1.2.1) (1.0.1) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (1.10.3) Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (1.4) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0) Installing collected packages: ChimeraX-PhenixUI Attempting uninstall: ChimeraX-PhenixUI Found existing installation: ChimeraX-PhenixUI 1.2.0 Uninstalling ChimeraX-PhenixUI-1.2.0: Successfully uninstalled ChimeraX-PhenixUI-1.2.0 Successfully installed ChimeraX-PhenixUI-1.2.1 \--- Successfully installed ChimeraX-PhenixUI-1.2.1 Installed ChimeraX-PhenixUI (1.2.1) Downloading bundle ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip is available: 23.0 -> 23.3.1 [notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tilpap/Downloads/ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl Requirement already satisfied: ChimeraX-Core>=1.5 in /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages (from ChimeraX-QScore==1.0) (1.6.1) Installing collected packages: ChimeraX-QScore Successfully installed ChimeraX-QScore-1.0 \--- Successfully installed ChimeraX-QScore-1.0 Installed ChimeraX-QScore (1.0) > select subtract #2 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > ui tool show ""Show Volume Menu"" Alignment identifier is 1/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > select > #1/A:8-10,27-28,86-89,92-97,123-131,178-182,194,207-214,291,324-325,339,341,352-354,391-410,428-479,499-506,512-526,534-564 1388 atoms, 1395 bonds, 172 residues, 1 model selected > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > hide #1 models > show #2 models > select > #2/A:58-63,66-71,97-107,180-187,324-342,359-391,395-450,467-475,480-491,498-543 1674 atoms, 1690 bonds, 206 residues, 1 model selected > select add #2 4453 atoms, 4547 bonds, 560 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 4453 atoms, 4547 bonds, 560 residues, 1 model selected > select subtract #2 Nothing selected > select > #2/A:4-6,16-18,26-28,31-33,50-52,78-81,112-114,128-133,136-138,143-145,156-161,167-176,194-197,202-205,221-229,234-239,244-246,248-252,258-261,273-275,278-280,307-309,451-453,458-461 802 atoms, 795 bonds, 101 residues, 1 model selected > open /Users/tilpap/Downloads/cryosparc_P144_J39_009_volume_map_sharp(1).mrc Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc as #3, grid size 512,512,512, pixel 0.867, shown at level 0.142, step 2, values float32 > hide #2 models > view > surface dust #3 size 8.67 > volume #3 step 1 > view > surface dust #3 size 8.67 > ui tool show ""Hide Dust"" > help help:user/tools/hidedust.html > surface dust #3 size 8.75 > surface dust #3 size 14.55 > surface dust #3 size 8.86 > surface dust #3 size 16.15 > surface dust #3 size 8.86 > surface dust #3 size 16.37 > ui tool show ""Map Coordinates"" > ui tool show ""Map Eraser"" > ui tool show ""Hide Dust"" > view > volume #3 level 0.4856 > save /Users/tilpap/Desktop/Template_model.mrc models #3 > open /Users/tilpap/Desktop/Template_model.mrc Opened Template_model.mrc as #4, grid size 512,512,512, pixel 0.827, shown at level 0.142, step 2, values float32 > view > surface dust #3 size 8.27 > surface dust #4 size 8.27 > close #4 > ui tool show ""Map Eraser"" > view > volume erase #3 center 210.32,208.32,215.54 radius 74 outside true Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc copy as #5, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > close #3 > close #4 > volume #5 level 0.362 > ui tool show ""Map Statistics"" > measure mapstats Map cryosparc_P144_J39_009_volume_map_sharp(1).mrc copy #5, minimum -3.526, maximum 5.634, mean 0.0005955, SD 0.05409, RMS 0.0541 > ui tool show ""Map Coordinates"" > save /Users/tilpap/Desktop/Template_model.mrc models #5 > open /Users/tilpap/Desktop/Template_model.mrc Opened Template_model.mrc as #3, grid size 512,512,512, pixel 0.827, shown at level 0.0145, step 2, values float32 > close #5 > volume #3 step 1 > surface dust #3 size 8.27 > volume #3 level 0.193 > ui tool show ""Hide Dust"" > surface dust #3 size 8.41 > surface dust #3 size 11.81 > transparency 50 > transparency 0 > lighting full > close #3 > open /Users/tilpap/Downloads/cryosparc_P144_J39_009_volume_map_sharp(1).mrc Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc as #3, grid size 512,512,512, pixel 0.867, shown at level 0.142, step 2, values float32 > ui tool show ""Map Eraser"" > ui tool show ""Map Coordinates"" > surface dust #3 size 8.67 > view > select add #3 802 atoms, 795 bonds, 101 residues, 3 models selected > select add #2 4453 atoms, 4547 bonds, 560 residues, 3 models selected > select subtract #2 2 models selected > save /Users/tilpap/Desktop/Template_pixel.mrc models #3 > select subtract #3 Nothing selected > open /Users/tilpap/Downloads/cryosparc_P144_J94_011_volume_map_sharp.mrc Opened cryosparc_P144_J94_011_volume_map_sharp.mrc as #4, grid size 512,512,512, pixel 0.827, shown at level 0.327, step 2, values float32 > volume #4 color #78b3ff > volume #4 step 1 > volume #4 level 1.091 > view > volume #3 step 1 > volume flip #4 Opened cryosparc_P144_J94_011_volume_map_sharp.mrc z flip as #5, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > volume #3 level 0.3674 > select add #5 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models #5,1,0,0,11.25,0,1,0,3.4608,0,0,1,15.259 > view matrix models #5,1,0,0,12.123,0,1,0,3.7138,0,0,1,21.82 > view > lighting full > view matrix models > #5,0.98958,0.14396,-0.00055933,-16.081,-0.14395,0.98957,0.0049578,34.775,0.0012672,-0.0048257,0.99999,22.581 > view matrix models > #5,0.93332,0.35876,-0.014195,-47.05,-0.35876,0.93343,0.0025647,91.752,0.01417,0.002699,0.9999,18.329 > view matrix models > #5,0.84479,0.53444,-0.026452,-63.324,-0.53456,0.84512,0.0030066,146.85,0.023962,0.0116,0.99965,14.463 > view matrix models > #5,0.75034,0.66007,-0.036024,-68.328,-0.66036,0.75093,0.0050803,192.48,0.030405,0.019977,0.99934,11.416 > view matrix models > #5,0.75034,0.66007,-0.036024,-69.344,-0.66036,0.75093,0.0050803,199.07,0.030405,0.019977,0.99934,11.114 > view matrix models > #5,0.75034,0.66007,-0.036024,-69.937,-0.66036,0.75093,0.0050803,202.85,0.030405,0.019977,0.99934,10.94 > select subtract #5 Nothing selected > ui tool show ""Fit in Map"" > fitmap #5 inMap #3 Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points correlation = 0.3466, correlation about mean = 0.1197, overlap = 1.184e+05 steps = 68, shift = 1.58, angle = 3.63 degrees Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates: Matrix rotation and translation 0.70736438 0.70598306 -0.03497933 -70.33781613 -0.70596274 0.70808925 0.01504069 221.11143351 0.03538696 0.01405485 0.99927485 11.58309161 Axis -0.00069734 -0.04977461 -0.99876023 Axis point 230.84538258 195.34053078 0.00000000 Rotation angle (degrees) 44.97913456 Shift along axis -22.52541635 > fitmap #5 inMap #3 Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points correlation = 0.3466, correlation about mean = 0.1198, overlap = 1.184e+05 steps = 40, shift = 0.00995, angle = 0.009 degrees Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates: Matrix rotation and translation 0.70740058 0.70594243 -0.03506723 -70.31923972 -0.70591919 0.70813020 0.01515684 221.07979672 0.03553202 0.01403267 0.99927001 11.56279291 Axis -0.00079524 -0.04994195 -0.99875181 Axis point 230.83229388 195.31133072 0.00000000 Rotation angle (degrees) 44.97620409 Shift along axis -22.53359617 > view > select add #5 2 models selected > view matrix models > #5,0.67894,0.73322,-0.037663,-69.649,-0.73317,0.67981,0.017956,232.15,0.038769,0.015422,0.99913,10.626 > view matrix models > #5,0.64618,0.76212,-0.040407,-68.395,-0.76202,0.64721,0.021174,244.37,0.042289,0.017109,0.99896,9.5735 > view matrix models > #5,0.64618,0.76212,-0.040407,-69.278,-0.76202,0.64721,0.021174,243.59,0.042289,0.017109,0.99896,9.6687 > fitmap #5 inMap #3 Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points correlation = 0.6153, correlation about mean = 0.3637, overlap = 2.52e+05 steps = 64, shift = 1.93, angle = 2.73 degrees Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates: Matrix rotation and translation 0.63748007 0.77046681 0.00025641 -76.16794974 -0.77046680 0.63748011 -0.00014962 250.13809629 -0.00027873 -0.00010217 0.99999996 21.18116524 Axis 0.00003079 0.00034728 -0.99999994 Axis point 227.73451656 206.01225219 0.00000000 Rotation angle (degrees) 50.39583000 Shift along axis -21.09664013 > fitmap #5 inMap #3 Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points correlation = 0.6153, correlation about mean = 0.3639, overlap = 2.52e+05 steps = 28, shift = 0.014, angle = 0.0205 degrees Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates: Matrix rotation and translation 0.63749232 0.77045671 0.00005837 -76.13875137 -0.77045671 0.63749231 0.00014751 250.08110464 0.00007644 -0.00013901 0.99999999 21.10400615 Axis -0.00018594 -0.00001173 -0.99999998 Axis point 227.68368502 205.95544995 0.00000000 Rotation angle (degrees) 50.39491972 Shift along axis -21.09278192 > select subtract #5 Nothing selected > transparency #3.1#5.1 50 > show #2 models > view > hide #2 models > view > surface dust #5 size 8.27 > transparency #5.1 0 > view > volume #4 level 1.481 > volume #4 level 4.289 > view > transparency #5.1 50 > transparency #5.1 0 > open /Users/tilpap/Desktop/IEVA_FINAL/RealSpaceRefine_1/6wxb_Ieva- > coot_manualfit-coot-11_real_space_refined_001.pdb Chain information for 6wxb_Ieva-coot_manualfit- coot-11_real_space_refined_001.pdb #6 --- Chain | Description A B C | No description available > select add #6 12433 atoms, 12740 bonds, 2 pseudobonds, 1534 residues, 2 models selected > view matrix models #6,1,0,0,66.057,0,1,0,82.334,0,0,1,32.561 > view matrix models #6,1,0,0,91.134,0,1,0,116.14,0,0,1,56.843 > view > view matrix models #6,1,0,0,78.294,0,1,0,102.87,0,0,1,62.176 > view matrix models #6,1,0,0,73.415,0,1,0,72.028,0,0,1,67.004 > view matrix models > #6,0.93478,-0.35083,0.055714,128.28,0.35235,0.93566,-0.019885,32.587,-0.045153,0.038218,0.99825,68.129 > view matrix models > #6,0.59674,-0.78886,0.14697,231.66,0.79831,0.60217,-0.0092049,15.916,-0.08124,0.12282,0.9891,61.908 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 0.3386, steps = 88 shifted from previous position = 3.8 rotated from previous position = 4.21 degrees atoms outside contour = 10000, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.30404502 -0.94826858 0.09134185 385.88090492 0.94809837 -0.29182648 0.12628061 95.64462646 -0.09309196 0.12499605 0.98778028 45.11093558 Axis -0.00067420 0.09679965 0.99530366 Axis point 159.76946495 187.25777936 0.00000000 Rotation angle (degrees) 107.70075457 Shift along axis 53.89728586 > view matrix models > #6,0.5369,-0.83498,0.12062,249.72,0.83243,0.54756,0.085143,2.7693,-0.13714,0.054696,0.98904,83.326 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 0.3286, steps = 120 shifted from previous position = 1.95 rotated from previous position = 3.47 degrees atoms outside contour = 10007, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.34607559 -0.93713009 0.04493208 398.55940282 0.92906755 -0.33564292 0.15549056 99.61443454 -0.13063375 0.09555643 0.98681498 53.95082594 Axis -0.03195813 0.09361535 0.99509539 Axis point 166.95982175 187.19443851 0.00000000 Rotation angle (degrees) 110.33153281 Shift along axis 50.27444654 > view matrix models > #6,0.49518,-0.85601,0.1485,254.68,0.85889,0.50806,0.064651,5.9688,-0.13079,0.095531,0.9868,82.398 > view matrix models > #6,0.46514,-0.88265,0.067636,275.59,0.88515,0.46267,-0.049512,26.498,0.012409,0.082899,0.99648,61.614 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 0.4337, steps = 92 shifted from previous position = 3.35 rotated from previous position = 4.53 degrees atoms outside contour = 9457, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.45421105 -0.88813785 0.07002486 401.24159261 0.89047660 -0.45499970 0.00516759 147.91925122 0.02727176 0.06470267 0.99753186 39.94887948 Axis 0.03344434 0.02401692 0.99915197 Axis point 155.11484390 195.65580904 0.00000000 Rotation angle (degrees) 117.11895860 Shift along axis 56.88682875 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 0.4331, steps = 44 shifted from previous position = 0.0315 rotated from previous position = 0.113 degrees atoms outside contour = 9461, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.45594649 -0.88727920 0.06963061 401.45758588 0.88959247 -0.45672525 0.00522397 148.29000161 0.02716694 0.06432472 0.99755917 40.02658725 Axis 0.03323326 0.02387798 0.99916235 Axis point 155.20772266 195.64674027 0.00000000 Rotation angle (degrees) 117.22953117 Shift along axis 56.87566996 > view matrix models > #6,0.39473,-0.91752,0.048472,292.63,0.9184,0.39246,-0.05017,34.035,0.027008,0.06432,0.99756,61.022 > view matrix models > #6,0.39473,-0.91752,0.048472,296.22,0.9184,0.39246,-0.05017,30.891,0.027008,0.06432,0.99756,60.772 > view matrix models > #6,0.39473,-0.91752,0.048472,294.39,0.9184,0.39246,-0.05017,29.362,0.027008,0.06432,0.99756,60.129 > view matrix models > #6,0.29445,-0.95372,0.060973,312.97,0.95517,0.29163,-0.051051,39.48,0.030907,0.073271,0.99683,58.287 > view matrix models > #6,0.19886,-0.97734,0.072534,329.05,0.97939,0.19552,-0.050668,50.554,0.035338,0.081116,0.99608,56.54 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 2.872, steps = 88 shifted from previous position = 3.02 rotated from previous position = 5.93 degrees atoms outside contour = 2354, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.66966311 -0.74266496 -0.00029198 423.24879435 0.74266500 -0.66966312 -0.00005650 200.78773879 -0.00015357 -0.00025468 0.99999996 52.80702091 Axis -0.00013343 -0.00009319 0.99999999 Axis point 166.97170419 194.52827874 0.00000000 Rotation angle (degrees) 132.04107081 Shift along axis 52.73183766 > fitmap #6 inMap #5 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433 atoms average map value = 2.872, steps = 28 shifted from previous position = 0.0131 rotated from previous position = 0.00384 degrees atoms outside contour = 2358, contour level = 1.0908 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.66964668 -0.74267975 -0.00033751 423.25389191 0.74267981 -0.66964669 -0.00010054 200.78927035 -0.00015135 -0.00031798 0.99999994 52.82920489 Axis -0.00014639 -0.00012533 0.99999998 Axis point 166.97254962 194.53398331 0.00000000 Rotation angle (degrees) 132.03980421 Shift along axis 52.74207646 > select subtract #6 Nothing selected > view > volume #5 level 0.873 > volume #5 level 0.752 > show #!6 cartoons > rainbow #!6 > transparency #5.1 50 > show #!6 atoms > view > ui tool show ""Volume Viewer"" > volume #5 level 2.142 > transparency #5.1 0 > volume #5 level 0.4934 > transparency #5.1 50 > color #!6 bychain > view > open /Users/tilpap/Downloads/cryosparc_P144_J100_010_volume_map_sharp.mrc Opened cryosparc_P144_J100_010_volume_map_sharp.mrc as #7, grid size 512,512,512, pixel 0.827, shown at level 0.0327, step 2, values float32 > volume flip #7 Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip as #8, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > close #7 > close #4 > volume #8 level 0.07744 > surface dust #5 size 8.27 > surface dust #8 size 8.27 > view > ui tool show ""Model Panel"" > select add #8 2 models selected > view matrix models #8,1,0,0,17.275,0,1,0,9.3595,0,0,1,-4.1556 > view matrix models #8,1,0,0,10.418,0,1,0,11.296,0,0,1,21.823 > view matrix models #8,1,0,0,-2.6968,0,1,0,15.88,0,0,1,47.692 > view matrix models #8,1,0,0,-4.8533,0,1,0,19.108,0,0,1,43.561 > view matrix models #8,1,0,0,2.1203,0,1,0,5.882,0,0,1,43.468 > view matrix models #8,1,0,0,4.0235,0,1,0,3.3618,0,0,1,43.477 > view matrix models #8,1,0,0,7.7544,0,1,0,9.278,0,0,1,26.775 > view matrix models #8,1,0,0,7.7567,0,1,0,9.1237,0,0,1,22.031 > view matrix models > #8,0.99098,0.13388,0.0053013,-20.229,-0.13395,0.99088,0.014729,36.434,-0.003281,-0.015306,0.99988,26.045 > view matrix models > #8,0.98893,0.10903,0.10063,-34.063,-0.12631,0.9745,0.18546,3.211,-0.077845,-0.19612,0.97749,85.352 > view matrix models > #8,0.97543,0.2196,-0.017463,-30.693,-0.21795,0.97355,0.068496,46.896,0.032043,-0.063007,0.9975,29.314 > view matrix models > #8,0.93825,0.34533,-0.020574,-49.228,-0.34309,0.93648,0.072718,80.515,0.04438,-0.061169,0.99714,26.378 > view matrix models > #8,0.91968,0.39207,-0.021616,-55.135,-0.3896,0.91797,0.074438,93.998,0.049028,-0.060038,0.99699,25.18 > ui tool show ""Fit in Map"" > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.1876, correlation about mean = 0.03582, overlap = 1.081e+04 steps = 84, shift = 2.61, angle = 2.47 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.88543959 -0.46040116 -0.06346264 134.45640129 0.46063513 0.88751158 -0.01176737 -73.46224731 0.06174154 -0.01881382 0.99791484 -8.79599391 Axis -0.00758063 -0.13469563 0.99085802 Axis point 217.53332221 237.91622919 0.00000000 Rotation angle (degrees) 27.69514593 Shift along axis 0.16019847 > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.1876, correlation about mean = 0.03584, overlap = 1.081e+04 steps = 44, shift = 0.00386, angle = 0.00241 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.88545079 -0.46038471 -0.06342566 134.44121736 0.46061822 0.88752042 -0.01176281 -73.46322400 0.06170698 -0.01879962 0.99791724 -8.79478709 Axis -0.00757060 -0.13462486 0.99086772 Axis point 217.53483056 237.89662619 0.00000000 Rotation angle (degrees) 27.69376230 Shift along axis 0.15770505 > view matrix models > #8,0.91936,0.3903,-0.049438,-43.061,-0.38855,0.92049,0.041515,101.02,0.061711,-0.018958,0.99791,12.543 > view matrix models > #8,0.88044,0.47122,-0.052821,-51.527,-0.4694,0.88191,0.043504,126.04,0.067083,-0.013508,0.99766,10.285 > ui tool show ""Fit in Map"" > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.2047, correlation about mean = 0.04911, overlap = 1.219e+04 steps = 80, shift = 0.699, angle = 2.7 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.93653359 -0.34120415 -0.08052678 103.54324139 0.34308405 0.93924753 0.01036405 -60.05953890 0.07209832 -0.03733373 0.99669856 -6.26639293 Axis -0.06787563 -0.21719094 0.97376640 Axis point 221.54841481 262.23756222 0.00000000 Rotation angle (degrees) 20.57061795 Shift along axis -0.08567774 > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.2048, correlation about mean = 0.04919, overlap = 1.22e+04 steps = 44, shift = 0.0194, angle = 0.0135 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.93647009 -0.34135654 -0.08061943 103.60616398 0.34324944 0.93918571 0.01048936 -60.09243656 0.07213600 -0.03749555 0.99668976 -6.22427286 Axis -0.06824953 -0.21726594 0.97372353 Axis point 221.58230641 262.25919035 0.00000000 Rotation angle (degrees) 20.58155097 Shift along axis -0.07575321 > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.2047, correlation about mean = 0.04912, overlap = 1.219e+04 steps = 44, shift = 0.0165, angle = 0.00569 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.93649818 -0.34127935 -0.08061989 103.58467455 0.34316851 0.93921583 0.01044049 -60.08421321 0.07215635 -0.03744371 0.99669024 -6.25096488 Axis -0.06812144 -0.21734386 0.97371511 Axis point 221.59474536 262.26983057 0.00000000 Rotation angle (degrees) 20.57676805 Shift along axis -0.08406151 > view matrix models > #8,0.80732,0.58971,-0.021792,-67.359,-0.58684,0.80618,0.075508,160.37,0.062097,-0.048171,0.99691,19.234 > view matrix models > #8,0.66576,0.74593,0.019003,-79.371,-0.74457,0.66246,0.082233,223.33,0.048751,-0.068896,0.99643,26.618 > view matrix models > #8,0.65446,0.75583,0.020208,-79.356,-0.75454,0.65116,0.081575,228,0.048497,-0.068635,0.99646,26.609 > ui tool show ""Fit in Map"" > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.97, correlation about mean = 0.9154, overlap = 9.164e+04 steps = 112, shift = 1.25, angle = 4.9 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.99998675 -0.00514666 0.00005815 1.08549866 0.00514666 0.99998675 0.00006222 -1.09282105 -0.00005847 -0.00006192 1.00000000 0.17330457 Axis -0.01205947 0.01132894 0.99986310 Axis point 213.20362866 210.71068577 0.00000000 Rotation angle (degrees) 0.29492370 Shift along axis 0.14780980 > fitmap #8 inMap #5 Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points correlation = 0.97, correlation about mean = 0.9155, overlap = 9.16e+04 steps = 24, shift = 0.0102, angle = 0.00529 degrees Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation 0.99998679 -0.00514036 -0.00003301 1.09253131 0.00514036 0.99998679 0.00007480 -1.09231530 0.00003262 -0.00007497 1.00000000 0.16067979 Axis -0.01456665 -0.00638317 0.99987353 Axis point 212.85543994 212.42271076 0.00000000 Rotation angle (degrees) 0.29455951 Shift along axis 0.15171738 > ui tool show ""Model Panel"" > select subtract #8 Nothing selected > volume #8 level 0.06065 > volume #8 level 0.1166 > volume #8 level 0.1558 > volume #8 level 0.04385 > volume #8 level 0.04 > ui tool show ""Fit in Map"" > fitmap #6 inMap #8 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) using 12433 atoms average map value = 0.2414, steps = 28 shifted from previous position = 0.0285 rotated from previous position = 0.0348 degrees atoms outside contour = 1035, contour level = 0.04 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) coordinates: Matrix rotation and translation -0.66626061 -0.74571889 -0.00037366 423.21428798 0.74571896 -0.66626064 -0.00005095 199.82839059 -0.00021096 -0.00031259 0.99999993 52.70876822 Axis -0.00017543 -0.00010909 0.99999998 Axis point 166.89484434 194.62188074 0.00000000 Rotation angle (degrees) 131.77911239 Shift along axis 52.61272510 > fitmap #6 inMap #8 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) using 12433 atoms average map value = 0.2414, steps = 28 shifted from previous position = 0.0228 rotated from previous position = 0.00297 degrees atoms outside contour = 1052, contour level = 0.04 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) coordinates: Matrix rotation and translation -0.66629689 -0.74568646 -0.00038035 423.20551252 0.74568653 -0.66629692 -0.00006771 199.83152932 -0.00020293 -0.00032873 0.99999993 52.69205639 Axis -0.00017502 -0.00011896 0.99999998 Axis point 166.89254447 194.61556026 0.00000000 Rotation angle (degrees) 131.78190059 Shift along axis 52.59421279 > transparency #8.1 50 > view > surface dust #8 size 8.27 > ui tool show ""Map Eraser"" > volume erase #8 center 224.99,229.05,357.13 radius 30.518 Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip copy as #7, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > surface dust #7 size 8.27 > volume erase #7 center 221.6,233.53,373.55 radius 30.487 > volume erase #7 center 215.01,211.18,385.14 radius 30.487 > volume erase #7 center 237.91,273.32,358.91 radius 30.487 > view > open /Users/tilpap/Downloads/cryosparc_P144_J102_006_volume_map_sharp.mrc Opened cryosparc_P144_J102_006_volume_map_sharp.mrc as #4, grid size 512,512,512, pixel 0.827, shown at level 0.0465, step 2, values float32 > volume flip #4 Opened cryosparc_P144_J102_006_volume_map_sharp.mrc z flip as #9, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > close #4 > surface dust #7 size 8.27 > surface dust #9 size 8.27 > ui tool show ""Map Eraser"" Can only have one displayed volume when erasing > volume #9 level 0.06903 > ui tool show ""Model Panel"" > select add #9 2 models selected > view > ui mousemode right ""rotate selected models"" > view matrix models #9,1,0,0,4.8209,0,1,0,-2.3742,0,0,1,14.405 > view matrix models #9,1,0,0,8.4096,0,1,0,-4.0268,0,0,1,24.425 > view matrix models #9,1,0,0,8.1749,0,1,0,-3.5191,0,0,1,21.325 > view matrix models #9,1,0,0,16.675,0,1,0,9.9479,0,0,1,21.765 > view matrix models > #9,0.9814,0.19055,0.023426,-25.159,-0.19105,0.98134,0.021589,49.82,-0.018875,-0.025663,0.99949,31.365 > view matrix models > #9,0.95896,0.2816,0.032992,-41.955,-0.28257,0.95879,0.029528,72.339,-0.023318,-0.037639,0.99902,34.973 > view matrix models > #9,0.90839,0.41526,0.048908,-63.274,-0.4172,0.90794,0.039813,109.55,-0.027873,-0.05657,0.99801,40.209 > view matrix models > #9,0.87873,0.47393,0.056686,-71.223,-0.47643,0.87812,0.043749,127.64,-0.029043,-0.065451,0.99743,42.482 > view matrix models > #9,0.8334,0.54901,0.063541,-79.195,-0.55097,0.83434,0.017682,158.15,-0.043307,-0.049745,0.99782,42.038 > view matrix models > #9,0.74194,0.66718,0.066267,-85.842,-0.66749,0.74433,-0.020504,209.95,-0.063005,-0.02902,0.99759,41.791 > view matrix models > #9,0.75474,0.65586,0.014378,-75.414,-0.6556,0.7533,0.052158,190.53,0.023378,-0.048792,0.99854,27.614 > view matrix models > #9,0.67262,0.73858,0.045656,-82.3,-0.73979,0.66974,0.064413,223.72,0.016996,-0.077101,0.99688,35.383 > view matrix models > #9,0.67262,0.73858,0.045656,-84.852,-0.73979,0.66974,0.064413,223.62,0.016996,-0.077101,0.99688,35.705 > ui tool show ""Fit in Map"" > fitmap #9 inMap #8 Fit map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip in map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip using 198494 points correlation = 0.9914, correlation about mean = 0.9794, overlap = 9487 steps = 132, shift = 1.6, angle = 5.14 degrees Position of cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#9) relative to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) coordinates: Matrix rotation and translation 0.99999814 0.00193008 -0.00002018 -0.41174072 -0.00193008 0.99999814 -0.00000369 0.40752431 0.00002017 0.00000373 1.00000000 -0.02898894 Axis 0.00192263 -0.01045415 -0.99994351 Axis point 211.06782868 213.55641856 0.00000000 Rotation angle (degrees) 0.11059147 Shift along axis 0.02393536 > select subtract #9 Nothing selected > transparency #7.1#9.1 0 > ui tool show ""Model Panel"" > hide #!7 models > hide #!6 models > ui tool show ""Model Panel"" > show #!6 models > transparency #9.1 50 > open /Users/tilpap/Downloads/cryosparc_P144_J104_map_locres.mrc Opened cryosparc_P144_J104_map_locres.mrc as #4, grid size 512,512,512, pixel 0.827, shown at level 6.6, step 2, values float32 > ui tool show ""Volume Viewer"" > volume flip #4 Opened cryosparc_P144_J104_map_locres.mrc z flip as #10, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > close #4 > surface dust #9 size 8.27 > surface dust #10 size 8.27 > show #!6 surfaces > hide #!6 surfaces > volume #!9-10 style mesh > volume #!9-10 style surface > ui tool show ""Color Zone"" QMainWidget::resizeDocks: all sizes need to be larger than 0 Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 2 maps. > volume #!9-10 hide > volume show > close #10 > ui tool show ""Volume Viewer"" > close #7 > ui tool show ""Map Eraser"" Can only have one displayed volume when erasing > ui windowfill toggle > ui mousemode right ""map eraser"" Can only have one displayed volume when erasing > ui mousemode right ""map eraser"" > ui tool show ""Volume Viewer"" > ui tool show ""Model Panel"" > select add #8 2 models selected > ui tool show ""Map Eraser"" > volume erase #8 center 232.47,236.73,378.2 radius 30.518 Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip copy as #7, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > volume erase #7 center 232.47,236.73,378.2 radius 30.487 > surface dust #7 size 8.27 > volume erase #7 center 265.87,242.31,370.42 radius 39.802 > volume erase #7 center 174.3,206.21,387.63 radius 39.802 > volume erase #7 center 215.32,222.14,381.43 radius 39.802 > view > ui mousemode right zoom > transparency #6.2-4#7.1 0 > ui tool show ""Surface Color"" > open /Users/tilpap/Downloads/cryosparc_P144_J104_map_locres.mrc Opened cryosparc_P144_J104_map_locres.mrc as #4, grid size 512,512,512, pixel 0.827, shown at level 6.6, step 2, values float32 > color sample #9.1 map #4 palette #ff0000:#ffffff:#0000ff Map values for surface ""surface"": minimum 0, mean 2.427, maximum 43.23 > color sample #9.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff Map values for surface ""surface"": minimum 0, mean 2.427, maximum 43.23 > color sample #9.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff Map values for surface ""surface"": minimum 0, mean 2.427, maximum 43.23 > ui tool show ""Model Panel"" > color sample #7.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff Map values for surface ""surface"": minimum 0, mean 1.779, maximum 44.38 > color sample #7.1 map #4 palette #0000ff:#00ff00:#ff0000:#808080:#808080 Map values for surface ""surface"": minimum 0, mean 1.779, maximum 44.38 > color sample #7.1 map #4 palette #0000ff:#59e2f9:#31ff25:#eee34f:#e8181d Map values for surface ""surface"": minimum 0, mean 1.779, maximum 44.38 > volume flip #4 Opened cryosparc_P144_J104_map_locres.mrc z flip as #10, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > color sample #7.1 map #4 palette > 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d Map values for surface ""surface"": minimum 0, mean 1.779, maximum 44.38 > ui tool show ""Model Panel"" > hide #!10 models > select subtract #8 Nothing selected > open /Users/tilpap/Downloads/cryosparc_P144_J102_006_volume_map_sharp.mrc Opened cryosparc_P144_J102_006_volume_map_sharp.mrc as #11, grid size 512,512,512, pixel 0.827, shown at level 0.0465, step 2, values float32 > surface dust #7 size 8.27 > surface dust #11 size 8.27 > volume flip #11 Opened cryosparc_P144_J102_006_volume_map_sharp.mrc z flip as #12, grid size 512,512,512, pixel 0.827, shown at step 1, values float32 > surface dust #12 size 8.27 > color sample #7.1 map #10 palette > 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d Map values for surface ""surface"": minimum 0, mean 1.713, maximum 40.53 > color sample #12.1 map #10 palette > 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d Map values for surface ""surface"": minimum 0, mean 0.7784, maximum 44.73 > color sample #12.1 map #10 palette > 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d Map values for surface ""surface"": minimum 0, mean 0.7784, maximum 44.73 > ui tool show ""Model Panel"" > show #!12 models > ui tool show ""Fit in Map"" > fitmap #2 inMap #12 Fit molecule best_model.pdb (#2) to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 4453 atoms average map value = 3.114e-06, steps = 568 shifted from previous position = 3.28 rotated from previous position = 5.64 degrees atoms outside contour = 4453, contour level = 0.04651 Position of best_model.pdb (#2) relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates: Matrix rotation and translation 0.23275852 0.80649914 -0.54349113 -1.07359348 -0.68437071 -0.26122679 -0.68073291 -4.88240916 -0.69098495 0.53039579 0.49114163 11.23787951 Axis 0.62867824 0.07656177 -0.77388756 Axis point 1.99880654 -4.36415796 0.00000000 Rotation angle (degrees) 105.58474229 Shift along axis -9.74560596 > fitmap #2 inMap #12 Fit molecule best_model.pdb (#2) to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 4453 atoms average map value = 3.09e-06, steps = 76 shifted from previous position = 0.0526 rotated from previous position = 0.0967 degrees atoms outside contour = 4453, contour level = 0.04651 Position of best_model.pdb (#2) relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates: Matrix rotation and translation 0.23264762 0.80720495 -0.54248986 -1.05661673 -0.68338822 -0.26120075 -0.68172921 -4.87611477 -0.69199395 0.52933386 0.49086662 11.20398099 Axis 0.62867694 0.07760931 -0.77378427 Axis point 2.00106879 -4.35288911 0.00000000 Rotation angle (degrees) 105.59544533 Shift along axis -9.71216678 > view > ui tool show ""Volume Viewer"" > volume #12 level 0.07438 > select add #2 4453 atoms, 4547 bonds, 560 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 4453 atoms, 4547 bonds, 560 residues, 1 model selected > select add #1 8949 atoms, 9127 bonds, 1134 residues, 2 models selected > select subtract #2 4496 atoms, 4580 bonds, 574 residues, 1 model selected > select subtract #1 Nothing selected > select add #6 12433 atoms, 12740 bonds, 2 pseudobonds, 1534 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.14468,-0.98948,-0.00020096,343.39,0.98948,0.14468,0.00046899,49.695,-0.00043498,-0.0002667,1,61.856 > view matrix models > #6,0.14468,-0.98948,-0.00020096,332.78,0.98948,0.14468,0.00046899,46.697,-0.00043498,-0.0002667,1,57.408 > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.14468,-0.98948,-0.00020096,335.48,0.98948,0.14468,0.00046899,47.2,-0.00043498,-0.0002667,1,57.226 > view matrix models > #6,0.33541,-0.94205,-0.0069956,301.11,0.94202,0.33531,0.012944,23.148,-0.0098484,-0.010932,0.99989,60.263 > view matrix models > #6,0.41757,-0.9086,-0.0087215,284.14,0.90856,0.41738,0.017878,14.783,-0.012604,-0.015389,0.9998,61.365 > view matrix models > #6,0.54509,-0.83831,-0.010587,254.85,0.83822,0.5447,0.026251,4.4151,-0.01624,-0.023184,0.9996,63.125 > view matrix models > #6,0.64481,-0.76426,-0.011203,228.9,0.76412,0.6442,0.033541,-0.97755,-0.018417,-0.030188,0.99937,64.552 > view matrix models > #6,0.79021,-0.6128,-0.0067924,183.61,0.61265,0.78964,0.03369,-0.886,-0.015282,-0.030783,0.99941,64.175 > view matrix models > #6,0.94148,-0.33707,-0.00035547,118.13,0.3369,0.94099,0.032187,16.895,-0.010515,-0.030423,0.99948,63.405 > view matrix models > #6,0.91848,-0.34305,0.19675,92.369,0.32097,0.93729,0.13589,3.9922,-0.23103,-0.061661,0.97099,105.08 > view matrix models > #6,0.93305,-0.34153,0.11304,102.76,0.32937,0.93737,0.11337,6.1754,-0.14467,-0.068547,0.9871,90.925 > view matrix models > #6,0.93979,-0.33543,-0.065378,128.05,0.33894,0.93933,0.052737,13.713,0.043722,-0.071721,0.99647,62.176 > view matrix models > #6,0.90501,-0.32963,-0.26891,163.34,0.34325,0.93923,0.0039019,20.54,0.25128,-0.095835,0.96316,40.311 > view matrix models > #6,0.89205,-0.32775,-0.31116,171.41,0.34284,0.93937,-0.0065869,22.181,0.29445,-0.1008,0.95034,36.655 > view matrix models > #6,0.92726,-0.33307,-0.17106,145.66,0.34245,0.93913,0.027717,17.043,0.15142,-0.084281,0.98487,49.97 > view matrix models > #6,0.93471,-0.33437,-0.12044,137.03,0.3411,0.93918,0.039792,15.391,0.099806,-0.078274,0.99192,55.594 > view matrix models > #6,0.93614,-0.33465,-0.10796,134.96,0.34067,0.93921,0.042742,15,0.087092,-0.076791,0.99324,57.043 > view > ui tool show ""Model Panel"" > select subtract #6 3 models selected > ui tool show ""Fit in Map"" > fitmap #6 inMap #12 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 12433 atoms average map value = 0.04192, steps = 72 shifted from previous position = 1.12 rotated from previous position = 1.74 degrees atoms outside contour = 8993, contour level = 0.074378 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates: Matrix rotation and translation 0.92540790 -0.36081908 -0.11588708 142.73175856 0.36655256 0.92984830 0.03195887 13.86156265 0.09622603 -0.07205370 0.99274811 55.13564170 Axis -0.13600423 -0.27735378 0.95109291 Axis point 17.23278134 403.01433899 0.00000000 Rotation angle (degrees) 22.48163407 Shift along axis 29.18243870 > fitmap #6 inMap #12 Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 12433 atoms average map value = 0.04192, steps = 48 shifted from previous position = 0.01 rotated from previous position = 0.00753 degrees atoms outside contour = 8990, contour level = 0.074378 Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6) relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates: Matrix rotation and translation 0.92540013 -0.36087074 -0.11578825 142.73543521 0.36660337 0.92982609 0.03202203 13.85087090 0.09610712 -0.07208156 0.99275761 55.15315033 Axis -0.13611443 -0.27705114 0.95116535 Axis point 17.29041027 402.96782995 0.00000000 Rotation angle (degrees) 22.48316845 Shift along axis 29.19401340 > volume #!12 hide > hide #!6 atoms > volume show > ui tool show ""Show Volume Menu"" > view > ui tool show ""Show Volume Menu"" ===== Log before crash end ===== Log: Startup Errors --- error | Bundle 'ChimeraX-ISOLDE' custom initialization failed warning | Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/tilpap/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/tilpap/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 956, in require needed = self.resolve(parse_requirements(requirements)) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 815, in resolve dist = self._resolve_dist( File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 856, in _resolve_dist raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is required by ChimeraX-ISOLDE You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.6 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2,8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 486.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.29f24 Software: System Software Overview: System Version: macOS 12.7.1 (21G920) Kernel Version: Darwin 21.6.0 Time since boot: 41 days 19:11 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.1 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.0 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX