Opened 4 years ago

Closed 4 years ago

#4933 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:        Linux-3.10.0-1160.6.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202107180729 (2021-07-18 07:29:18 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202107180729 (2021-07-18)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open rec.crg.pdb

Summary of feedback from opening rec.crg.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
443 messages similar to the above omitted  
  
Chain information for rec.crg.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open 1000_summary/poses.mol2

Opened poses.mol2 containing 1000 structures (42561 atoms, 44759 bonds)  

> open 100_summary/poses.mol2

Opened poses.mol2 containing 1000 structures (41082 atoms, 43155 bonds)  

> open 300_summary/poses.mol2

Opened poses.mol2 containing 1000 structures (41738 atoms, 43880 bonds)  

> open 600_summary/poses.mol2

Opened poses.mol2 containing 1000 structures (42309 atoms, 44490 bonds)  

> open omega_summary/poses.mol2

Opened poses.mol2 containing 997 structures (40866 atoms, 42944 bonds)  

> open rdkit2_summary/poses.mol2

Opened poses.mol2 containing 627 structures (24792 atoms, 26010 bonds)  

> open rdkit3_summary/poses.mol2

Opened poses.mol2 containing 688 structures (27704 atoms, 29052 bonds)  

> open rdkit41_summary/poses.mol2

Opened poses.mol2 containing 1000 structures (41665 atoms, 43712 bonds)  

> open rdkit4_summary/poses.mol2

Opened poses.mol2 containing 999 structures (41632 atoms, 43675 bonds)  

> open rdkit_summary/poses.mol2

Opened poses.mol2 containing 667 structures (26262 atoms, 27541 bonds)  

> open Ruth_summary/poses.mol2

Opened poses.mol2 containing 692 structures (28901 atoms, 30413 bonds)  

> hide #!2 models

> show #!2 models

> ~display H

> delete H

> help viewdockx

> viewdockx #1 Cate1

No suitable models found for ViewDockX  

> viewdockx #!1 Cate1

No suitable models found for ViewDockX  

> viewdockx #!1.* Cate1

No suitable models found for ViewDockX  

> viewdockx #!1.* name Cate1

No suitable models found for ViewDockX  

> viewdockx #0 name Cate1

No suitable models found for ViewDockX  

> viewdockx name Cate1

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> viewdockx name Cate1

> viewdockx #2 name Cate2

> hide #2.1-1000 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> viewdockx

> viewdockx

> viewdockx #2

> hbonds #2.1-1000 restrict
> #1#3.1-1000#4.1-1000#5.1-1000#6.1-997#7.1-627#8.1-688#9.1-1000#10.1-999#11.1-667#12.1-692
> reveal true interSubmodel true

donor: ZINC000000627692 none #9.2/? UNK 1 N acceptor: ZINC000000940984 none
#9.766/? UNK 1 N  
Traceback (most recent call last):  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 380, in handle_scheme  
method(query)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 432, in _cb_hb  
self._count_pbonds(query, "hbonds", "hydrogen bonds", "HBonds")  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/viewdockx/tool.py", line 444, in _count_pbonds  
run(self.session, cmd)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/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 "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 606, 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 "/home/fuqy/Software/chimerax-2021.07.18/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> hide #2.2 models

> show #2.5 models




OpenGL version: 3.3.0 NVIDIA 460.27.04
OpenGL renderer: GeForce GTX 750 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Scientific Linux 7.9 Nitrogen
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        5.5G        3.3G        142M        6.9G        9.7G
	Swap:            0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2)	
	Subsystem: NVIDIA Corporation Device [10de:105f]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
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: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.26.1
    ChimeraX-AtomicLibrary: 3.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107180729
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    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: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 1.6.2
    ChimeraX-PDB: 2.4.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    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
    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: 1.10.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    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: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 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, 4 years ago

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

Don't know why you would be looking for H-bonds _between_ docked compounds, but nonetheless I can't reproduce this without have the compounds in their positions relative to each other.

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