Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4301 closed defect (duplicate)

coulombic failure due to unexpected hydrogen name

Reported by: idocaspy@… 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:        Linux-5.4.0-52-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Tried to show electrostatics of PDB and got this error message

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

> open /home/ido/Downloads/Chlamy_TSP4_10LHC_164_real_space_refined_164.pdb

Chain information for Chlamy_TSP4_10LHC_164_real_space_refined_164.pdb #1  
---  
Chain | Description  
1 Z | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> set bgColor white

> lighting soft

> hide atoms

> show surfaces

> style sphere

Changed 52213 atom styles  

> style ball

Changed 52213 atom styles  

> close session

> open /home/ido/Downloads/Chlamy_TSP4_10LHC_164_real_space_refined_164.pdb
> format pdb

Chain information for Chlamy_TSP4_10LHC_164_real_space_refined_164.pdb #1  
---  
Chain | Description  
1 Z | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> lighting soft

> save /home/ido/Downloads/esrf0620/Pics/TSP4_model.png width 912 height 686
> supersample 3

> save /home/ido/Downloads/esrf0620/Pics/TSP4_model2.png width 912 height 686
> supersample 3

> hide surfaces

> hide atoms

> show cartoons

> cartoon style modeHelix tube sides 20

> select
> ::name="3PH"::name="BCR"::name="C7Z"::name="CA"::name="CHL"::name="CL0"::name="CLA"::name="DAO"::name="DGA"::name="DGD"::name="HOH"::name="LHG"::name="LMG"::name="LMT"::name="LPX"::name="LUT"::name="NKP"::name="OCA"::name="PLM"::name="PQN"::name="QTB"::name="RRX"::name="SF4"::name="SNC"::name="SPH"::name="SQD"::name="T7X"

18482 atoms, 19126 bonds, 808 pseudobonds, 692 residues, 2 models selected  

> show sel atoms

> select clear

> ui tool show "Basic Actions"

> save /home/ido/Downloads/esrf0620/Pics/TSP4_model3.png width 912 height 686
> supersample 3

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> cartoon style xsection rectangle modeHelix default

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> cartoon style modeHelix tube sides 20

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> close session

> open /home/ido/Downloads/PSII_Duna_C2S2_29_RSR_addHOH_Nathan.pdb

Chain information for PSII_Duna_C2S2_29_RSR_addHOH_Nathan.pdb #1  
---  
Chain | Description  
A a | No description available  
B b | No description available  
C c | No description available  
D d | No description available  
E e | No description available  
F f | No description available  
G g | No description available  
H h | No description available  
I i | No description available  
J j | No description available  
K k | No description available  
L l | No description available  
M m | No description available  
N n | No description available  
O o | No description available  
P p | No description available  
R r | No description available  
S s | No description available  
T t | No description available  
U u | No description available  
V v | No description available  
W w | No description available  
X x | No description available  
Y y | No description available  
Z z | No description available  
  

> hide atoms

> show surfaces

> coulombic

/s ARG 285 HN  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'HN'  
  
KeyError: 'HN'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  

> hide surfaces

> coulombic

/s ARG 285 HN  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'HN'  
  
KeyError: 'HN'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/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 (Core Profile) Mesa 20.0.8
OpenGL renderer: llvmpipe (LLVM 10.0.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X299 AORUS MASTER
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 20 Intel(R) Core(TM) i9-9820X CPU @ 3.30GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         49G        6.1G        188M         69G         74G
	Swap:          2.0G        1.8G        217M

Graphics:
	17:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1e04] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. Device [19da:2503]	
	Kernel driver in use: nvidia
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-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-Label: 1.0
    ChimeraX-LinuxSupport: 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
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    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
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    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
    ptyprocess: 0.6.0
    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
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    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
    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

Change History (4)

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

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed
Summary: coulombic → coulombic failure due to unexpected hydrogen name

Hi Ido,

The Coulombic included in ChimeraX 1.1 requires that hydrogen names match the standard PDB name for those hydrogens. The hydrogen names in your structure do not match. The Coulombic in the ChimeraX daily build is more forgiving in that regard, so if you use the daily build you should be able to run coulombic on your structure.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by fulusi@…, 5 years ago 

Hi Eric,

Thank you for your reply, I corrected the structure and now everything
works properly.
If their error comes back I'll use the daily build as you suggested.

Best wishes,
Ido

On Mon, Mar 1, 2021 at 11:25 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by Eric Pettersen, 5 years ago

Glad to hear you got things working!

--Eric

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