Opened 5 years ago

Closed 5 years ago

#4191 closed defect (fixed)

Coulombic failure due to unexpected hydrogen name

Reported by: cesar.menor@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Trying to color surface by electrostatic potential (Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "J:\My Stuff\BIOQUIMICA\Estructuras PDB\ribosoma.cxs" format session

Log from Fri Jan 15 23:03:03 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified.pdb"

Summary of feedback from opening J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i
modified.pdb  
---  
warnings | Ignored bad PDB record found on line 6465  
END  
  
Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1
9  
Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1
3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187
1 5  
Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198
1 8  
240 messages similar to the above omitted  
CONECT record for nonexistent atom: 6901  
Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1
9  
Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1
3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187
1 5  
Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198
1 8  
240 messages similar to the above omitted  
  
Chain information for 4v4i modified.pdb  
---  
Chain | Description  
1.1/0 | No description available  
1.1/1 | No description available  
1.2/Y | No description available  
1.2/x | No description available  
1.1/z | No description available  
  

> select #1.2/x

560 atoms, 615 bonds, 28 residues, 1 model selected  

> select #1.1/z

1628 atoms, 1818 bonds, 76 residues, 1 model selected  

> select #1.1/0

1621 atoms, 1813 bonds, 76 residues, 1 model selected  

> close session

> open "J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i modified2.pdb"

Summary of feedback from opening J:/My Stuff/BIOQUIMICA/Estructuras PDB/4v4i
modified2.pdb  
---  
warnings | Ignored bad PDB record found on line 160213  
END  
  
Start residue of secondary structure not found: HELIX 1 1 ARG A 9 GLU A 13 1 5  
Start residue of secondary structure not found: HELIX 2 2 GLU A 25 LEU A 33 1
9  
Start residue of secondary structure not found: HELIX 3 3 SER A 55 GLN A 57 1
3  
Start residue of secondary structure not found: HELIX 4 4 PRO A 183 ALA A 187
1 5  
Start residue of secondary structure not found: HELIX 5 5 ARG A 191 GLU A 198
1 8  
240 messages similar to the above omitted  
  
Chain information for 4v4i modified2.pdb  
---  
Chain | Description  
1.1/0 | No description available  
1.1/1 | No description available  
1.2/1 | No description available  
1.2/2 | No description available  
1.1/A | No description available  
1.2/A | No description available  
1.1/B | No description available  
1.1/C | No description available  
1.1/D | No description available  
1.1/E | No description available  
1.1/F | No description available  
1.1/G | No description available  
1.1/H | No description available  
1.1/I | No description available  
1.1/J | No description available  
1.1/K | No description available  
1.1/L | No description available  
1.1/M | No description available  
1.1/N | No description available  
1.1/O | No description available  
1.1/P | No description available  
1.1/Q | No description available  
1.1/R | No description available  
1.1/S | No description available  
1.1/T | No description available  
1.1/U | No description available  
1.1/V | No description available  
1.1/W | No description available  
1.1/X | No description available  
1.2/X | No description available  
1.1/Y | No description available  
1.2/Y | No description available  
1.1/Z | No description available  
1.1/a | No description available  
1.2/a | No description available  
1.1/b | No description available  
1.2/b | No description available  
1.1/c | No description available  
1.2/c | No description available  
1.1/d | No description available  
1.1/e | No description available  
1.1/f | No description available  
1.1/g | No description available  
1.1/h | No description available  
1.1/i | No description available  
1.1/j | No description available  
1.1/k | No description available  
1.1/l | No description available  
1.1/m | No description available  
1.1/n | No description available  
1.1/o | No description available  
1.1/p | No description available  
1.1/q | No description available  
1.1/r | No description available  
1.1/s | No description available  
1.1/t | No description available  
1.1/u | No description available  
1.1/v | No description available  
1.1/w | No description available  
1.1/x | No description available  
1.2/x | No description available  
1.1/y | No description available  
1.1/z | No description available  
  

> select #1.1/0

1621 atoms, 1813 bonds, 76 residues, 1 model selected  

> select add #1.1/1

1743 atoms, 1948 bonds, 82 residues, 1 model selected  

> select add #1.1/Z

2161 atoms, 2374 bonds, 130 residues, 1 model selected  

> select add #1.1/m

3131 atoms, 3360 bonds, 254 residues, 1 model selected  

> select add #1.1/n

4128 atoms, 4368 bonds, 379 residues, 1 model selected  

> select add #1.1/Y

4564 atoms, 4817 bonds, 435 residues, 1 model selected  

> select ~sel

154238 atoms, 167793 bonds, 2 pseudobonds, 10957 residues, 4 models selected  

> hide (#1.2#!1.1 & sel) target a

> select clear

> select add #1.1/1#1.2/1

3012 atoms, 3367 bonds, 141 residues, 2 models selected  

> cartoon sel

> cartoon hide sel

> select add #1.1/1

3012 atoms, 3367 bonds, 141 residues, 2 models selected  

> cartoon sel

> select add #1.1/Z

3430 atoms, 3793 bonds, 189 residues, 2 models selected  

> cartoon hide sel

> hide sel target a

> select add #1.1/0

5051 atoms, 5606 bonds, 265 residues, 2 models selected  

> select add #1.1/z

6679 atoms, 7424 bonds, 341 residues, 2 models selected  

> cartoon sel

> select clear

> select add #1.1/1

122 atoms, 135 bonds, 6 residues, 1 model selected  

> cartoon sel

> surface sel

> select add #1.1/Y

558 atoms, 584 bonds, 62 residues, 2 models selected  

> select #1.2/Y

1647 atoms, 1840 bonds, 77 residues, 1 model selected  

> cartoon sel

> select #1.1/x

2573 atoms, 2878 bonds, 120 residues, 1 model selected  

> cartoon sel

> cartoon hide sel

> select #1.2/x

560 atoms, 615 bonds, 28 residues, 1 model selected  

> cartoon sel

> surface sel

> select #1.1/0

1621 atoms, 1813 bonds, 76 residues, 1 model selected  

> surface sel

> select #1.1/z

1628 atoms, 1818 bonds, 76 residues, 1 model selected  

> surface sel

> select #1.1/n

997 atoms, 1008 bonds, 125 residues, 1 model selected  

> surface sel

> set bgColor white

> select #1.2/Y

1647 atoms, 1840 bonds, 77 residues, 1 model selected  

> surface sel

> select #1.1/Y

436 atoms, 449 bonds, 56 residues, 1 model selected  

> hide sel target a

> select #1.1/Z

418 atoms, 426 bonds, 48 residues, 1 model selected  

> cartoon hide sel

> select #1.1/m

970 atoms, 986 bonds, 124 residues, 1 model selected  

> surface sel

> select clear

> save "J:/My Stuff/BIOQUIMICA/Estructuras PDB/ribosoma.cxs"

opened ChimeraX session  

> select #1.2/2

1057 atoms, 1177 bonds, 50 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #1.2/A

3272 atoms, 3346 bonds, 427 residues, 1 model selected  

> show sel cartoons

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: 4v4i modified2.pdb #1.2/A LYS 164 CG, 4v4i
modified2.pdb #1.2/A LYS 164 CE, 4v4i modified2.pdb #1.2/A LYS 164 CD, 4v4i
modified2.pdb #1.2/A LYS 164 NZ, 4v4i modified2.pdb #1.2/A LYS 39 CG, and 74
other atoms  

copy of 4v4i modified2.pdb #/A SER 337 HB  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 313, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'HB'  
  
KeyError: 'HB'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.89
OpenGL renderer: GeForce GTX 960/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: MICRO-STAR INTERNATIONAL CO., LTD
Model: MS-B08911
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 8,514,162,688
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4460S CPU @ 2.90GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.24b0
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    stripy: 2.0.2
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Coulombic failure due to unexpected hydrogen name

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Hi Cesar,

The version of coulombic you have expects all the atoms in standard residues to have their standard names, including hydrogen atoms. Some of the hydrogens in your structure do not have their standard names. You may be able to work around this problem by deleting the hydrogens in your structure will the command "del H" before running coulombic. Coulombic will compensate for the fact that your structure is missing hydrogens.
The version of coulombic in the daily build can work with non-standard hydrogen names (heavy atoms still must have standard names), but that improved version is only deployed for the Mac platform. We are working on installing the necessary things to deploy in on Windows and Linux but aren't quite there yet. If the workaround I suggested above doesn't completely solve the problem, please let me know and I'll alert you when the new coulombic for Windows is available.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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