Opened 2 years ago

Closed 2 years ago

#10098 closed defect (duplicate)

DockPrep not catching ChargeError

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.2.0-36-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/zain/Desktop/MD Simulations/ECSb1-RBD/ECSb1-RBD.pdb"

ECSb1-RBD.pdb title:  
Crystal structure of sars-cov-2 spike RBD In complex with the D27 neutralizing
antibody fab fragment [more info...]  
  
Chain information for ECSb1-RBD.pdb #1  
---  
Chain | Description  
A | No description available  
R | No description available  
  

> select /A:1-120

1812 atoms, 1827 bonds, 120 residues, 1 model selected  

> toolshed show

> ui tool show "Dock Prep"

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/R PRO 521: phi -71.7, psi none trans  
/A SER 120: phi -89.1, psi none trans  
Applying PRO rotamer (chi angles: 27.0 -34.6) to /R PRO 521  
Applying SER rotamer (chi angles: 65.3) to /A SER 120  
Summary of feedback from adding hydrogens to ECSb1-RBD.pdb #1  
---  
notes | No usable SEQRES records for ECSb1-RBD.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for ECSb1-RBD.pdb (#1) chain R; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 1, /R CYS 336  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 120, /R PRO 521  
Chain-final residues that are not actual C termini:  
237 hydrogen bonds  
11 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 118, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
KeyError: ('PRO', 'c')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 120, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen /R PRO 521 HXT bonded to atom
that should not have hydrogens (/R PRO 521 C)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /R PRO 521 HXT bonded to atom
that should not have hydrogens (/R PRO 521 C)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 120, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  

> ui tool show "Dock Prep"

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/R PRO 521: phi -71.7, psi none trans  
/A SER 120: phi -89.1, psi none trans  
Applying PRO rotamer (chi angles: 8.7) to /R PRO 521  
Applying SER rotamer (chi angles: -49.7) to /A SER 120  
Summary of feedback from adding hydrogens to ECSb1-RBD.pdb #1  
---  
notes | No usable SEQRES records for ECSb1-RBD.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for ECSb1-RBD.pdb (#1) chain R; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 1, /R CYS 336  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 120, /R PRO 521  
Chain-final residues that are not actual C termini:  
237 hydrogen bonds  
9 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 118, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
KeyError: ('PRO', 'c')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 120, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen /R PRO 521 HXT bonded to atom
that should not have hydrogens (/R PRO 521 C)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /R PRO 521 HXT bonded to atom
that should not have hydrogens (/R PRO 521 C)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 120, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
Cache Size: 10240 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       3.7Gi       6.8Gi       280Mi       5.0Gi        11Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. GP107 [GeForce GTX 1050 Ti] [19da:1456]	
	Kernel modules: nvidiafb, nouveau

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
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    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
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    platformdirs: 3.5.0
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    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
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    python-dateutil: 2.8.2
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    tzdata: 2023.3
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    wheel-filename: 1.4.1
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Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: UnassignedStructure Editing
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionDockPrep not catching ChargeError

addcharge does, so dockprep probably should.

comment:2 by Eric Pettersen, 2 years ago

Resolution: duplicate
Status: acceptedclosed

Duplicate of #9960

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