Opened 3 years ago

Closed 3 years ago

#7460 closed defect (can't reproduce)

FindHBond: accPhiPsi() takes exactly 8 arguments (9 given)

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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
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    sfftk-rw: 0.7.2
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    sphinxcontrib-devhelp: 1.0.2
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    tifffile: 2021.11.2
    tinyarray: 1.2.4
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    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 Eric Pettersen, 3 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → FindHBond: accPhiPsi() takes exactly 8 arguments (9 given)

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed

Probably something hinky about the structure

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