id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4305 ISOLDE residue validation: cannot unpack non-iterable builtin_function_or_method object dilipk@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.16299 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 30210 from EMDB No such database 'EMDB' > open 30210 fromDatabase emdb Summary of feedback from opening 30210 fetched from emdb --- note | Fetching compressed map 30210 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30210/map/emd_30210.map.gz Opened emd_30210.map, grid size 192,192,192, pixel 1.01, shown at level 0.0278, step 1, values float32 > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield > open 7bv2 Summary of feedback from opening 7bv2 fetched from pdb --- notes | Fetching compressed mmCIF 7bv2 from http://files.rcsb.org/download/7bv2.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif Fetching CCD POP from http://ligand-expo.rcsb.org/reports/P/POP/POP.cif Fetching CCD F86 from http://ligand-expo.rcsb.org/reports/F/F86/F86.cif 7bv2 title: The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) [more info...] Chain information for 7bv2 #2 --- Chain | Description A | nsp12 B | nsp8 C | nsp7 P | Primer T | Templete Non-standard residues in 7bv2 #2 --- F86 — [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (Remdesivir, bound form) MG — magnesium ion POP — pyrophosphate 2- ZN — zinc ion 7bv2 title: The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) [more info...] Chain information for 7bv2 --- Chain | Description 2.2/A | nsp12 2.2/B | nsp8 2.2/C | nsp7 2.2/P | Primer 2.2/T | Templete Non-standard residues in 7bv2 #2.2 --- F86 — [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (Remdesivir, bound form) MG — magnesium ion POP — pyrophosphate 2- ZN — zinc ion > volume #1 level 0.1753 > clip assoc #1 to #2 Expected a keyword > clipper associate #1 toModel #2 > set bgColor white > addh Summary of feedback from adding hydrogens to 7bv2 #2.2 --- warnings | Not adding hydrogens to /A LYS 98 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A ASP 100 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 218 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 824 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B ASP 78 CB because it is missing heavy-atom bond partners 5 messages similar to the above omitted notes | Termini for 7bv2 (#2.2) chain A determined from SEQRES records Termini for 7bv2 (#2.2) chain B determined from SEQRES records Termini for 7bv2 (#2.2) chain C determined from SEQRES records Termini for 7bv2 (#2.2) chain P determined from SEQRES records Termini for 7bv2 (#2.2) chain T determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A VAL 31, /A GLU 84, /A ARG 118, /A ASN 911, /B ASP 78, /C LYS 2, /P G 10, /T U 8 Chain-final residues that are actual C termini: /P U 20 Chain-final residues that are not actual C termini: /A LYS 50, /A ASP 100, /A LEU 895, /A THR 929, /B ALA 191, /C GLY 64, /T C 21 962 hydrogen bonds Adding 'H' to /A VAL 31 Adding 'H' to /A GLU 84 Adding 'H' to /A ARG 118 Adding 'H' to /A ASN 911 Adding 'H' to /B ASP 78 1 messages similar to the above omitted /A THR 929 is not terminus, removing H atom from 'C' /B ALA 191 is not terminus, removing H atom from 'C' /C GLY 64 is not terminus, removing H atom from 'C' 8174 hydrogens added > hide HC > restraint ligands #2 Unknown command: isolde restraint ligands #2 > isolde restrain ligands #2 > select #2 16804 atoms, 17042 bonds, 36 pseudobonds, 1047 residues, 17 models selected Loading residue template for POP from internal database Traceback (most recent call last): File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\validation\unparameterised.py"", line 174, in _fix_selected_unparameterised_residue residue, template_name, ccd_template = item.data TypeError: cannot unpack non-iterable builtin_function_or_method object TypeError: cannot unpack non-iterable builtin_function_or_method object File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\validation\unparameterised.py"", line 174, in _fix_selected_unparameterised_residue residue, template_name, ccd_template = item.data See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\validation\unparameterised.py"", line 174, in _fix_selected_unparameterised_residue residue, template_name, ccd_template = item.data TypeError: cannot unpack non-iterable builtin_function_or_method object TypeError: cannot unpack non-iterable builtin_function_or_method object File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\validation\unparameterised.py"", line 174, in _fix_selected_unparameterised_residue residue, template_name, ccd_template = item.data See log for complete Python traceback. File C:/Users/dilipk/Downloads/f86.pdb.cif does not appear to contain any valid residue templates. Traceback (most recent call last): File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 1204, in _add_cif_template_files_gui load_cif_templates(self.session, files) File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\atomic\template_utils.py"", line 601, in load_cif_templates raise RuntimeError('No files successfully loaded.') RuntimeError: No files successfully loaded. RuntimeError: No files successfully loaded. File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\atomic\template_utils.py"", line 601, in load_cif_templates raise RuntimeError('No files successfully loaded.') See log for complete Python traceback. File C:/Users/dilipk/Downloads/f86.cif does not appear to contain any valid residue templates. Traceback (most recent call last): File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\isolde.py"", line 1204, in _add_cif_template_files_gui load_cif_templates(self.session, files) File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\atomic\template_utils.py"", line 601, in load_cif_templates raise RuntimeError('No files successfully loaded.') RuntimeError: No files successfully loaded. RuntimeError: No files successfully loaded. File ""C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site- packages\chimerax\isolde\atomic\template_utils.py"", line 601, in load_cif_templates raise RuntimeError('No files successfully loaded.') See log for complete Python traceback. OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.1008 OpenGL renderer: AMD Radeon HD 6700 Series OpenGL vendor: ATI Technologies Inc. Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Enterprise (Build 16299) Memory: 17,160,163,328 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 WMI: 1.5.1 }}} " defect closed normal Third Party fixed all ChimeraX