Opened 4 years ago
Closed 4 years ago
#6368 closed defect (can't reproduce)
H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Analysis | Version: | |
Keywords: | Cc: | Tristan Croll | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19042 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "C:/Users/sroch/OneDrive/Documents/Academia/RA > MJL/YenTc_ph11/YenTc_pH11_complete_v2.pdb" Chain information for YenTc_pH11_complete_v2.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open "C:/Users/sroch/OneDrive/Documents/Academia/RA > MJL/YenTc_ph11/YenTc_pH11_prepore_3.1_c5.mrc" Opened YenTc_pH11_prepore_3.1_c5.mrc as #2, grid size 512,512,512, pixel 1.41, shown at level 0.127, step 2, values float32 > volume #2 step 1 > volume #2 level 0.3181 > clipper associate #2 toModel #1 Opened YenTc_pH11_prepore_3.1_c5.mrc as #1.1.1.1, grid size 512,512,512, pixel 1.41, shown at level 0.443, step 1, values float32 Chain information for YenTc_pH11_complete_v2.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available > ui tool show ISOLDE > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 209 residues in model #1.2 to IUPAC-IUB standards. Done loading forcefield ISOLDE: stopped sim > addh Summary of feedback from adding hydrogens to YenTc_pH11_complete_v2.pdb #1.2 --- warnings | Not adding hydrogens to /B GLU 1071 CG because it is missing heavy- atom bond partners Not adding hydrogens to /C ASN 68 CG because it is missing heavy-atom bond partners notes | No usable SEQRES records for YenTc_pH11_complete_v2.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for YenTc_pH11_complete_v2.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for YenTc_pH11_complete_v2.pdb (#1.2) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A SER 46, /B SER 2, /C VAL 2 Chain-initial residues that are not actual N termini: /A LYS 132, /B ARG 1276 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 1164, /A ASN 111, /B LYS 1355, /B TYR 1250, /C SER 632 donor: /C ASN 68 N acceptor: /C ASN 68 O Traceback (most recent call last): File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py", line 2784, in start_sim sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel, File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 619, in __init__ raise e File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 597, in __init__ sh = self.sim_handler = Sim_Handler(session, sim_params, sc, File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 1350, in __init__ system = self._system = self._create_openmm_system(ff, top, File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 1433, in _create_openmm_system raise RuntimeError('Unparameterised residue detected') RuntimeError: Unparameterised residue detected During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause self.start_sim() File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py", line 2798, in start_sim self._unparam_mgr._sim_unparam_res_cb() File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\validation\unparameterised.py", line 228, in _sim_unparam_res_cb self._show_main_frame() File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\validation\unparameterised.py", line 50, in _show_main_frame self._update_unparameterised_residues_list() File "C:\Users\sroch\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\validation\unparameterised.py", line 91, in _update_unparameterised_residues_list run(self.session, 'addh') File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\addh\cmd.py", line 62, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\addh\cmd.py", line 169, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\addh\hbond.py", line 249, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File "C:\Program Files\ChimeraX 1.3\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 1.3\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 NVIDIA 497.29 OpenGL renderer: NVIDIA GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 20TKCTO1WW OS: Microsoft Windows 10 Pro (Build 19042) Memory: 16,919,126,016 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz OSLanguage: en-GB Locale: ('en_AU', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: 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: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 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: 1.31 ChimeraX-AtomicLibrary: 4.2 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: 2.6.1 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-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: 1.3 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-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 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: 2.0.4 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: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.6.5 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: 1.0.1 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: 2.4.6 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: 1.6.1 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: 1.13.7 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: 0.11.0 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: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 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: 4.9.1 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: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 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: 3.0.6 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: 1.11.3 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: 2.2.0 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: 5.1.1 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
Change History (2)
comment:1 by , 4 years ago
Cc: | added |
---|---|
Component: | Unassigned → Structure Analysis |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given |
comment:2 by , 4 years ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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This *typically* happens for structures with bad connectivity, but I would need a test case to verify.