Opened 3 years ago
Closed 3 years ago
#7460 closed defect (can't reproduce)
FindHBond: accPhiPsi() takes exactly 8 arguments (9 given)
Reported by: | Owned by: | Eric Pettersen | |
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Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22000 ChimeraX Version: 1.4rc202205200050 (2022-05-20 00:50:00 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4rc202205200050 (2022-05-20) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "D:\Ji Lab Drexel\Data Analysis\DA60000\RelA.pdbqt" format pdbqt Chain information for RelA.pdb #1 --- Chain | Description 8 | No description available Opened RelA.pdbqt containing 1 structures (4792 atoms, 4878 bonds) > open "D:/Ji Lab Drexel/Data > Analysis/Substances/Substance_Ligand_110000/Substance_20220718_1457_mod_9.sdf" > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: RelA.pdb #1/8 PRO 571 N 1 hydrogen bonds found > ui tool show Contacts > contacts intraModel false intraMol false ignoreHiddenModels true 32 contacts > select #2/?:1@C10 1 atom, 1 residue, 1 model selected > select up 33 atoms, 37 bonds, 1 residue, 1 model selected > select sel :< 6 325 atoms, 320 bonds, 33 pseudobonds, 36 residues, 4 models selected > show sel atoms > select clear > close session > open "D:\Ji Lab Drexel\Data Analysis\DA60000\RelA.pdbqt" format pdbqt Chain information for RelA.pdb #1 --- Chain | Description 8 | No description available Opened RelA.pdbqt containing 1 structures (4792 atoms, 4878 bonds) > open "D:/Ji Lab Drexel/Data > Analysis/Substances/Substance_Ligand_110000/Substance_20220718_1457.sdf" > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: RelA.pdb #1/8 PRO 571 N 2 hydrogen bonds found > ui tool show Contacts > contacts intraModel false intraMol false ignoreHiddenModels true 45 contacts > select #2/?:1@H1 1 atom, 1 residue, 1 model selected > select up 29 atoms, 33 bonds, 1 residue, 1 model selected > select sel :< 6 256 atoms, 249 bonds, 47 pseudobonds, 27 residues, 4 models selected > show sel atoms > select clear > close session > open "D:\Ji Lab Drexel\Data Analysis\DA60000\RelA.pdbqt" format pdbqt Chain information for RelA.pdb #1 --- Chain | Description 8 | No description available Opened RelA.pdbqt containing 1 structures (4792 atoms, 4878 bonds) > open "D:/Ji Lab Drexel/Data > Analysis/Substances/Substance_Ligand_110000/Substance_20220718_1457_mod_81.sdf" > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: RelA.pdb #1/8 PRO 571 N 2 hydrogen bonds found > ui tool show Contacts > contacts intraModel false intraMol false ignoreHiddenModels true 44 contacts > select #2/?:1@C9 1 atom, 1 residue, 1 model selected > select up 36 atoms, 40 bonds, 1 residue, 1 model selected > select sel :< 6 294 atoms, 288 bonds, 46 pseudobonds, 31 residues, 4 models selected > show sel atoms > select clear > close session > open "D:\Ji Lab Drexel\Data Analysis\DA60000\RelA.pdbqt" format pdbqt Chain information for RelA.pdb #1 --- Chain | Description 8 | No description available Opened RelA.pdbqt containing 1 structures (4792 atoms, 4878 bonds) > open "D:/Ji Lab Drexel/Data > Analysis/Substances/Substance_Ligand_110000/Substance_20220718_1457_mod_91.sdf" > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false reveal true donor: RelA.pdb #1/8 LYS 254 NZ acceptor: RelA_Substance_20220718_1457_mod_91_opt_0 #2/? UNL 1 N6 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\tool.py", line 52, in run_hbonds run(self.session, " ".join(self.gui.get_command())) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\cmd.py", line 83, in cmd_hbonds result = hb_func(session, struct_info, dist_slop=dist_slop, angle_slop=angle_slop, **base_kw) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): See log for complete Python traceback. > ui tool show H-Bonds > hbonds intraModel false intraMol false intraRes false reveal true donor: RelA.pdb #1/8 LYS 254 NZ acceptor: RelA_Substance_20220718_1457_mod_91_opt_0 #2/? UNL 1 N6 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\tool.py", line 52, in run_hbonds run(self.session, " ".join(self.gui.get_command())) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\cmd.py", line 83, in cmd_hbonds result = hb_func(session, struct_info, dist_slop=dist_slop, angle_slop=angle_slop, **base_kw) File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given File "C:\Program Files\ChimeraX 1.4rc202205200050\bin\lib\site- packages\chimerax\hbonds\hbond.py", line 603, in find_hbonds if not geom_func(donor_atom, donor_hyds, *args): See log for complete Python traceback. OpenGL version: 3.3.0 - Build 30.0.101.1660 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: windows Manufacturer: HP Model: HP Pavilion Laptop 14-dv0xxx OS: Microsoft Windows 11 Home (Build 22000) Memory: 8,344,559,616 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 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: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 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: 1.4rc202205200050 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: 1.1 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: 1.2 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: 1.1.1 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-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.2 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: 4.33.3 funcparserlib: 1.0.0 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: 4.10.0 kiwisolver: 1.4.2 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: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pywin32: 303 pyzmq: 23.0.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 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 WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Structure Analysis |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → FindHBond: accPhiPsi() takes exactly 8 arguments (9 given) |
comment:2 by , 3 years ago
Resolution: | → can't reproduce |
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Status: | accepted → closed |
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Probably something hinky about the structure