Opened 4 years ago

Closed 4 years ago

#5053 closed defect (not a bug)

Coulombic coloring of combined surface

Reported by: wenxiang.cao@… 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-10-10.0.19042
ChimeraX Version: 1.3.dev202108120207 (2021-08-12 02:07:32 UTC)
Description
ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I  generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.

Log:
UCSF ChimeraX version: 1.3.dev202108120207 (2021-08-12)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5ONV format mmcif fromDatabase pdb

5onv title:  
Cryo-EM structure of F-actin in complex with ADP [more info...]  
  
Chain information for 5onv #1  
---  
Chain | Description | UniProt  
A B C D E | Actin, α skeletal muscle | ACTS_RABIT  
  
Non-standard residues in 5onv #1  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
  

> hide solvent

> hide protein

> surface /A-E enclose /A-E

> surface /A-E enclose /A-E & protein

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIC (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\myHP\AppData\Local\Temp\tmp53n10d94\ante.in.mol2 -fi mol2 -o
C:\Users\myHP\AppData\Local\Temp\tmp53n10d94\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
(HIC) ``  
(HIC) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIC) ``  
(HIC) `Info: Finished reading file
(C:\Users\myHP\AppData\Local\Temp\tmp53n10d94\ante.in.mol2); atoms read (32),
bonds read (32).`  
(HIC) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) `Info: Total number of electrons: 120; net charge: 0`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX 1.3.dev202108120207/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
Charges for residue HIC determined  
Coulombic values for 5onv_A SES surface #1.2: minimum, -21.52, mean -2.71,
maximum 12.89  
Coulombic values for 5onv_B SES surface #1.3: minimum, -21.30, mean -2.76,
maximum 13.00  
Coulombic values for 5onv_C SES surface #1.4: minimum, -21.90, mean -2.74,
maximum 13.07  
Coulombic values for 5onv_D SES surface #1.5: minimum, -21.39, mean -2.71,
maximum 12.99  
Coulombic values for 5onv_E SES surface #1.6: minimum, -28.84, mean -2.72,
maximum 12.96  

> close

> open 5ONV format mmcif fromDatabase pdb

5onv title:  
Cryo-EM structure of F-actin in complex with ADP [more info...]  
  
Chain information for 5onv #1  
---  
Chain | Description | UniProt  
A B C D E | Actin, α skeletal muscle | ACTS_RABIT  
  
Non-standard residues in 5onv #1  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
  

> hide solvent

> hide protein

> surface /A-E enclose /A-E & protein

> select #1.2

14500 atoms, 1855 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIC (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\myHP\AppData\Local\Temp\tmpphbw6y6e\ante.in.mol2 -fi mol2 -o
C:\Users\myHP\AppData\Local\Temp\tmpphbw6y6e\ante.out.mol2 -fo mol2 -c bcc -nc
0 -j 5 -s 2 -dr n  
(HIC) ``  
(HIC) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIC) ``  
(HIC) `Info: Finished reading file
(C:\Users\myHP\AppData\Local\Temp\tmpphbw6y6e\ante.in.mol2); atoms read (32),
bonds read (32).`  
(HIC) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) `Info: Total number of electrons: 120; net charge: 0`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX 1.3.dev202108120207/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o
ANTECHAMBER_AM1BCC.AC -f ac -p "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
(HIC) `Running: "D:/program/ChimeraX
1.3.dev202108120207/bin/amber20/bin/atomtype" -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIC) `bash.exe: warning: could not find /tmp, please create!`  
(HIC) ``  
Charges for residue HIC determined  
Coulombic values for 5onv_A SES surface #1.2: minimum, -21.53, mean -2.71,
maximum 12.89  
Coulombic values for 5onv_B SES surface #1.3: minimum, -21.30, mean -2.76,
maximum 13.00  
Coulombic values for 5onv_C SES surface #1.4: minimum, -21.91, mean -2.74,
maximum 13.07  
Coulombic values for 5onv_D SES surface #1.5: minimum, -21.40, mean -2.71,
maximum 12.99  
Coulombic values for 5onv_E SES surface #1.6: minimum, -28.84, mean -2.72,
maximum 12.96  

> select clear

> select /c

2928 atoms, 2992 bonds, 1 pseudobond, 373 residues, 2 models selected  




OpenGL version: 3.3.14739 Core Profile Forward-Compatible Context 21.6.1 27.20.22001.14011
OpenGL renderer: AMD Radeon(TM) RX Vega 10 Graphics 
OpenGL vendor: ATI Technologies Inc.
Manufacturer: HP
Model: HP Laptop 17-ca1xxx
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 14,942,511,104
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 7 3700U with Radeon Vega Mobile Gfx  
OSLanguage: en-US
Locale: ('en_US', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.28.1
    ChimeraX-AtomicLibrary: 4.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.3
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202108120207
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 1.7
    ChimeraX-PDB: 2.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.2
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.11.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    Send2Trash: 1.7.1
    SEQCROW: 1.1.3a1
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 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 coloring of combined surface

comment:2 by Eric Pettersen, 4 years ago

Resolution: → not a bug
Status: accepted → closed

Forwarded to and answered on chimerax-users list

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