Opened 2 years ago

Closed 2 years ago

#9834 closed defect (can't reproduce)

Coulombic: 'Atom' object has no attribute 'charge'

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-5.15.0-84-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/dell/Yasser-Ribossome/Dados-julho-2023/Electrostatic-Potential-
> Hydrophobicity-24-09-2023/25-Bulky-Flexible-Fitting-40Swt-Manip-MDFF-
> contact-loops-ESs-close-KSRPsite-Post-ManipulativeMDFF-AMBER.pdb

Summary of feedback from opening /home/dell/Yasser-Ribossome/Dados-
julho-2023/Electrostatic-Potential-Hydrophobicity-24-09-2023/25-Bulky-
Flexible-Fitting-40Swt-Manip-MDFF-contact-loops-ESs-close-KSRPsite-Post-
ManipulativeMDFF-AMBER.pdb  
---  
warnings | Ignored bad PDB record found on line 100013  
ATOM 100000 C GLU 4006 262.574 203.401 157.849 1.00 0.00  
  
Ignored bad PDB record found on line 100014  
ATOM 100001 O GLU 4006 261.612 203.924 158.393 1.00 0.00  
  
Ignored bad PDB record found on line 100015  
ATOM 100002 N ALA 4007 262.986 202.184 158.189 1.00 0.00  
  
Ignored bad PDB record found on line 100016  
ATOM 100003 H ALA 4007 263.816 201.826 157.739 1.00 0.00  
  
Ignored bad PDB record found on line 100017  
ATOM 100004 CA ALA 4007 262.274 201.316 159.116 1.00 0.00  
  
50824 messages similar to the above omitted  
  
Chain information for 25-Bulky-Flexible-Fitting-40Swt-Manip-MDFF-contact-
loops-ESs-close-KSRPsite-Post-ManipulativeMDFF-AMBER.pdb #1  
---  
Chain | Description  
? | No description available  
? | No description available  
  

> select clear

> set bgColor white

> hide

[Repeated 1 time(s)]

> ribbon

> show cartoons

> show surfaces

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue G3 (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp4uzfq3d0/ante.in.mol2 -fi mol2 -o /tmp/tmp4uzfq3d0/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(G3) ``  
(G3) `Welcome to antechamber 20.0: molecular input file processor.`  
(G3) ``  
(G3) `Info: Finished reading file (/tmp/tmp4uzfq3d0/ante.in.mol2); atoms read
(40), bonds read (42).`  
(G3) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(G3) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(G3) ``  
(G3) ``  
(G3) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(G3) `Info: Total number of electrons: 196; net charge: -1`  
(G3) ``  
(G3) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(G3) ``  
(G3) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(G3) ``  
(G3) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(G3) ``  
Charges for residue G3 determined  
Assigning partial charges to residue G5 (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpaw3f8zht/ante.in.mol2 -fi mol2 -o /tmp/tmpaw3f8zht/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(G5) ``  
(G5) `Welcome to antechamber 20.0: molecular input file processor.`  
(G5) ``  
(G5) `Info: Finished reading file (/tmp/tmpaw3f8zht/ante.in.mol2); atoms read
(39), bonds read (41).`  
(G5) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(G5) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(G5) ``  
(G5) ``  
(G5) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(G5) `Info: Total number of electrons: 188; net charge: -1`  
(G5) ``  
(G5) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(G5) ``  
(G5) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(G5) ``  
(G5) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(G5) ``  
Charges for residue G5 determined  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 120, in cmd_coulombic  
color_vertices(session, target_surface, offset, charged_atoms, dist_dep,
dielectric, cmap,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in color_vertices  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in <listcomp>  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
AttributeError: 'Atom' object has no attribute 'charge'  
  
AttributeError: 'Atom' object has no attribute 'charge'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
  
See log for complete Python traceback.  
  

> isolde start

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 11.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

> coulombic #1

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 120, in cmd_coulombic  
color_vertices(session, target_surface, offset, charged_atoms, dist_dep,
dielectric, cmap,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in color_vertices  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in <listcomp>  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
AttributeError: 'Atom' object has no attribute 'charge'  
  
AttributeError: 'Atom' object has no attribute 'charge'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 153, in  
charged_atoms.scene_coords, numpy.array([a.charge for a in charged_atoms],
dtype=numpy.double),  
  
See log for complete Python traceback.  
  




OpenGL version: 4.2 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 4000 (IVB GT2)
OpenGL vendor: Intel Open Source Technology Center

Python: 3.9.11
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Latitude E6430
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-3340M CPU @ 2.70GHz
Cache Size: 3072 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          3.7Gi       2.3Gi       231Mi       780Mi       1.2Gi       400Mi
	Swap:         7.4Gi       568Mi       6.9Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation 3rd Gen Core processor Graphics Controller [8086:0166] (rev 09)	
	DeviceName:  Onboard IGD	
	Subsystem: Dell 3rd Gen Core processor Graphics Controller [1028:0534]

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-Clipper: 0.18.0
    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: 1.4
    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-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    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: 1.18.3
    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
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    pyzmq: 23.1.0
    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

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Coulombic: 'Atom' object has no attribute 'charge'

comment:2 by Eric Pettersen, 2 years ago

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

Seems somehow related to the >100,000 atom PDB file, but would need the input to track this down.

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