id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6496 Blast failure during AlphaFold search Elaine Meng Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4.dev202203280252 (2022-03-28 02:52:31 UTC) Description following tutorial first had blast fail and then tried to save session also failed the blast is from clicking the Search button on the AlphaFold tool following this tutorial https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-mar2022/alphafold_pae.html Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start tool show $1 > alias whereprefs info path user unversioned config > alias captut open help:user/tutorials/binding-sites.html#cap-example > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html > alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html > alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop- > modeling.html; ui dockable false ""Help Viewer"" executed startup.cxc UCSF ChimeraX version: 1.4.dev202203280252 (2022-03-28) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 30495 fromDatabase emdb Summary of feedback from opening 30495 fetched from emdb --- note | Fetching compressed map 30495 from ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-30495/map/emd_30495.map.gz Opened emdb 30495 as #1, grid size 220,220,220, pixel 1.09, shown at level 0.000223, step 1, values float32 > lighting soft > volume #1 level 1.121 > ui tool show AlphaFold > alphafold match > MQPPPPGPLGDCLRDWEDLQQDFQNIQETHRLYRLKLEELTKLQNNCTSSITRQKKRLQELALALKKCKPSLPAEAEGAAQELENQMKERQGLFFDMEAYLPKKNGLYLSLVLGNVNVTLLSKQAKFAYKDEYEKFKLYLTIILILISFTCRFLLNSRVTDAAFNFLLVWYYCTLTIRESILINNGSRIKGWWVFHHYVSTFLSGVMLTWPDGLMYQKFRNQFLSFSMYQSFVQFLQYYYQSGCLYRLRALGERHTMDLTVEGFQSWMWRGLTFLLPFLFFGHFWQLFNALTLFNLAQDPQCKEWQVLMCGFPFLLLFLGNFFTTLRVVHHKFHSQRHGSKKD Fetching compressed AlphaFold Q9BXJ8 from https://alphafold.ebi.ac.uk/files/AF-Q9BXJ8-F1-model_v2.cif 1 AlphaFold model found using sequence similarity searches: Q9BXJ8 (1 sequences) Sequence Similarity --- AlphaFold Model| Query Sequence| Identity %| Coverage % TACAN_HUMAN | MQPPP...GSKKD | 100.0 | 100.0 Opened 1 AlphaFold model > alphafold search > MQPPPPGPLGDCLRDWEDLQQDFQNIQETHRLYRLKLEELTKLQNNCTSSITRQKKRLQELALALKKCKPSLPAEAEGAAQELENQMKERQGLFFDMEAYLPKKNGLYLSLVLGNVNVTLLSKQAKFAYKDEYEKFKLYLTIILILISFTCRFLLNSRVTDAAFNFLLVWYYCTLTIRESILINNGSRIKGWWVFHHYVSTFLSGVMLTWPDGLMYQKFRNQFLSFSMYQSFVQFLQYYYQSGCLYRLRALGERHTMDLTVEGFQSWMWRGLTFLLPFLFFGHFWQLFNALTLFNLAQDPQCKEWQVLMCGFPFLLLFLGNFFTTLRVVHHKFHSQRHGSKKD Webservices job id: 0RLUUK6DISHKDZKCVWGMWU29LGD16WXOSN0W5MVFIET5WFD77FCRB9D67SDUF2AF Parsing BlastProtein results failed: invalid literal for int() with base 10: '' > save blastfail.cxs Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 147, in take_snapshot , 'table_session': self.table.session_info() File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/item_table.py"", line 463, in session_info sort_info = (self.model().sortColumn(), qt_enum_as_int(self.model().sortOrder())) AttributeError: 'NoneType' object has no attribute 'sortColumn' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> Populating font family aliases took 313 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/blastprotein/ui/results.py"", line 147, in take_snapshot , 'table_session': self.table.session_info() File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/item_table.py"", line 463, in session_info sort_info = (self.model().sortColumn(), qt_enum_as_int(self.model().sortOrder())) AttributeError: 'NoneType' object has no attribute 'sortColumn' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 89, in provider_save saver_info.save(session, path, **provider_kw) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' -> -> File ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > version UCSF ChimeraX version: 1.4.dev202203280252 (2022-03-28) © 2016-2022 Regents of the University of California. All rights reserved. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.6 Locale: UTF-8 Qt version: PyQt6 6.2.3, Qt 6.2.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.3 (21E230) Kernel Version: Darwin 21.4.0 Time since boot: 1:59 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.3 ChimeraX-AtomicLibrary: 6.1.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203280252 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.0.1 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.5 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.31.2 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.4.1 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt6-commercial: 6.2.3 PyQt6-sip: 13.2.0 PyQt6-WebEngine-commercial: 6.2.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Sequence fixed Tom Goddard all ChimeraX