id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15739 "Loading an ESMFold BLAST result gives error ""Expected a keyword""" goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9.dev202407250342 (2024-07-25 03:42:42 UTC) Description Fetching structures from the BLAST output for esmfold is broken. It does not put the ID into the esmfold fetch command. Log: UCSF ChimeraX version: 1.9.dev202407250342 (2024-07-25) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7sx3 7sx3 title: Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conformation 1/2 [more info...] Chain information for 7sx3 #1 --- Chain | Description | UniProt A | Sodium leak channel non-selective protein,Enhanced green fluorescent protein | NALCN_HUMAN 1-1738, A0A7G8ZY66_MUHV1 1760-2000 B | Transmembrane protein FAM155A | F155A_HUMAN 1-458 C | Calmodulin-1 | CALM1_HUMAN 1-149 D | UNC79,Protein unc-79 homolog,Protein unc-79 homolog | UNC79_HUMAN 174-2635 E | Protein unc-80 homolog | UNC80_HUMAN 1-3258 Non-standard residues in 7sx3 #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) PEV — (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (phosphatidylethanolamine; 1-palmitoyl-2-oleoyl-Sn- glycero-3-phosphoethanolamine) PGV — (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate (phosphatidylglycerol; 2-vaccenoyl-1-palmitoyl-Sn- glycerol-3-phosphoglycerol) Y01 — cholesterol hemisuccinate > select #1/D:174-2635 10737 atoms, 10967 bonds, 25 pseudobonds, 1344 residues, 2 models selected > open Q9P2D8 fromDatabase uniprot associate #1/D Summary of feedback from opening Q9P2D8 fetched from uniprot --- notes | Fetching compressed Q9P2D8 UniProt info from https://www.uniprot.org/uniprot/Q9P2D8.xml Alignment identifier is Q9P2D8 Associated 7sx3 chain D to Q9P2D8 with 99 mismatches and/or gaps Opened UniProt Q9P2D8 > select /D:174-2626 10737 atoms, 10967 bonds, 25 pseudobonds, 1344 residues, 2 models selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > select > /D:176-183,187-199,201-205,222-233,237-250,254-264,267-280,282-284,435-437,440-455,498-510,520-537,554-567,569-576,596-613,619-634,644-651,663-666,668-674,679-694,701-715,797-815,826-840,860-878,951-963,969-983,988-995,997-1006,1008-1014,1021-1035,1040-1052,1057-1072,1076-1079,1083-1099,1105-1115,1120-1136,1138-1154,1163-1180,1209-1219,1228-1231,1273-1289,1299-1315,1329-1334,1336-1351,1353-1371,1376-1379,1387-1389,1392-1408,1414-1432,2020-2036,2038-2057,2074-2092,2094-2099,2108-2115,2124-2137,2145-2158,2170-2186,2195-2205,2210-2214,2217-2230,2235-2248,2252-2270,2278-2292,2319-2333,2337-2342,2357-2377,2383-2387,2389-2392,2407-2428,2441-2457,2471-2488,2504-2526,2531-2547,2551-2565,2576-2584,2605-2624 7971 atoms, 8079 bonds, 988 residues, 1 model selected > select /D:174-2626 10737 atoms, 10967 bonds, 25 pseudobonds, 1344 residues, 2 models selected > select /D:174-2626 10737 atoms, 10967 bonds, 25 pseudobonds, 1344 residues, 2 models selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > ~select Nothing selected > select /D:1284 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:2183,2444 13 atoms, 11 bonds, 2 residues, 1 model selected > select /D:174-177 34 atoms, 35 bonds, 4 residues, 1 model selected > select /D:652-655,675-677,1325-1327,1380-1382,2120-2122,2138-2140 162 atoms, 160 bonds, 19 residues, 1 model selected > select /D:2223-2243,2468-2486 324 atoms, 333 bonds, 40 residues, 1 model selected > select /D:638-641,984-986,1221-1223,1320-1322 106 atoms, 103 bonds, 13 residues, 1 model selected > select /C:5-147 926 atoms, 932 bonds, 5 pseudobonds, 114 residues, 2 models selected > select /C:5-147 926 atoms, 932 bonds, 5 pseudobonds, 114 residues, 2 models selected > ui tool show ""Blast Protein"" > blastprotein /C database esmfold cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 > version 0 name bp1 Webservices job id: NYJHI1LX2XPT0KEP > esmfold fetch version 0 alignTo #1/C Expected a keyword > esmfold fetch version 0 alignTo #1/C Expected a keyword OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.0, Qt 6.7.1 Qt runtime version: 6.7.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: MK1H3LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 14 days, 7 hours, 49 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 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: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.14 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.4 ChimeraX-AtomicLibrary: 14.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9.dev202407250342 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepMutationalScan: 1.0 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-Foldseek: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.3 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.7 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.5 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NIHPresets: 1.1.18 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.1.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.13 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.3 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.8 ChimeraX-Ummbas-Anaglyph: 0.1 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.2 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.3 jedi: 0.19.1 Jinja2: 3.1.4 joblib: 1.4.2 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 llvmlite: 0.43.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numba: 0.60.0 numexpr: 2.10.1 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.1.2 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt_toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.17.2 pynmrstar: 3.3.4 pynndescent: 0.5.13 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject_hooks: 1.1.0 PyQt6: 6.7.0 PyQt6-Qt6: 6.7.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.2 PyQt6-WebEngineSubwheel-Qt6: 6.7.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.2 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.32.3 scikit-learn: 1.5.1 scipy: 1.13.0 setuptools: 70.3.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 Sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.6 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.8 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia_utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 tqdm: 4.66.4 traitlets: 5.14.2 typing_extensions: 4.12.2 tzdata: 2024.1 umap-learn: 0.5.6 urllib3: 2.2.2 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Sequence fixed all ChimeraX