id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5550 Alphafold match: 'Structure' object has no attribute 'num_observed_residues' Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC) Description open 7cfd alphafold match #1 MatchMaker throws an error on chain O (which has a UniProt ID but only a single residue modelled), and the session ends up pretty borked - atoms from the AF models appear to be added to the session, but don't appear in the Models panel and are drawn as featureless white spheres. Log: UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7cfd structureFactors true Summary of feedback from opening 7cfd fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Fetching compressed mmCIF 7cfd from http://files.rcsb.org/download/7cfd.cif Fetching CCD 2MR from http://ligand-expo.rcsb.org/reports/2/2MR/2MR.cif Fetching compressed 7cfd structure factors from http://files.rcsb.org/download/7cfd-sf.cif Resolution: 2.703675434227976 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 30,32,28, pixel 0.899,0.845,0.886, shown at level 0.258, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 30,32,28, pixel 0.899,0.845,0.886, shown at level -0.121,0.121, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 30,32,28, pixel 0.899,0.845,0.886, shown at level 0.473, step 1, values float32 7cfd title: Drosophila melanogaster Krimper eTud2-AubR15me2 complex [more info...] Chain information for 7cfd --- Chain | Description | UniProt 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | FI20010p1 | A1ZAC4_DROME 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M 1.2/N 1.2/O 1.2/Z | Protein aubergine | AUB_DROME 7cfd mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 5| author_defined_assembly 6| author_defined_assembly 7| author_defined_assembly 8| author_defined_assembly > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 106 residues in model #1.2 to IUPAC-IUB standards. Opened (LIVE) MDFF potential as #1.1.1.5, grid size 30,32,28, pixel 0.899,0.845,0.886, shown at level 0.276, step 1, values float32 Done loading forcefield > alphafold match #1 Fetching compressed AlphaFold A1ZAC4 from https://alphafold.ebi.ac.uk/files/AF-A1ZAC4-F1-model_v1.cif Fetching compressed AlphaFold O76922 from https://alphafold.ebi.ac.uk/files/AF-O76922-F1-model_v1.cif Fewer than 3 residues aligned; cannot match 7cfd, chain O with AlphaFold O76922, chain O 2 AlphaFold models found using UniProt identifiers: A1ZAC4 (chains B,C,D,E,F,A,G,H), O76922 (chains I,J,K,L,N,M,Z,O) Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py"", line 53, in alphafold_match session.models.add(mlist) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py"", line 676, in add m.added_to_session(session) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py"", line 405, in group.added_to_session = lambda session, g=group: _log_alphafold_chain_info(g) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py"", line 418, in _log_alphafold_chain_info _log_alphafold_chain_table(am.child_models(), struct_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\alphafold\match.py"", line 438, in _log_alphafold_chain_table m.num_residues, m.num_observed_residues, pct_id)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\attributes.py"", line 61, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\attributes.py"", line 57, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Structure' object has no attribute 'num_observed_residues' AttributeError: 'Structure' object has no attribute 'num_observed_residues' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\attributes.py"", line 85, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > select #1/O 13 atoms, 12 bonds, 1 residue, 1 model selected > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #1 > show #1 > hide #2 > show #2 OpenGL version: 3.3.0 NVIDIA 471.11 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Notebook Model: P7xxTM1 OS: Microsoft Windows 10 Education (Build 19041) Memory: 68,654,501,888 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-GB Locale: ('en_GB', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: -himerax-clipper: 0.17.0 alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 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: 2.1.1 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202110222254 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 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-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 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-ISOLDE: 1.3.dev33 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.2 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.4 ChimeraX-ModelPanel: 1.2 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-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.5 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: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.6 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.5.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.8.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.21 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.0 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.0 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Prediction fixed Eric Pettersen all ChimeraX