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 | |
|---|---|---|---|
| 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 |
|---|---|
| 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 |
|---|---|
| Status: | accepted → closed |
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Probably something hinky about the structure