[Chimera-users] Electrostatics

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Sat Jun 20 04:46:12 PDT 2009

Hi Marco,

It is already possible, Chimera can read the open dx files generated  
by APBS. You can represent them with the Volume Viewer and/or map them  
on surfaces. In the latter case, it is preferable to use solvent  
accessible surfaces and not molecular surfaces and to use lower  
thresholds (such as 2 kT/e, equivalent to ~ 50 mV at 298 K ) to avoid  
a bias towards local features. Of course, this depends on the purpose  
of your representation. While it is not possible with the current  
implementation of Chimera surfaces (MSMS) to produce solvent  
accessible surfaces, it can be approximated by adding 1.4 A to all van  
der Waals radii ( vdwdefine +1.4) and then set the probe radius to its  
minimum allowed value ( it should be 0 A, because you included the  
probe in the previous command, but at the moment it must be 0.5 A ) It  
will be great to have solvent accessible surfaces in the next 1.4  
release of chimera :-)



Le 20 juin 09 à 11:42, sette at uniroma2.it a écrit :

> Hi,
> do you think it is possible in future versions of Chimera to read the
> results of APBS calculation for electrostatic properties?
> Thanks,
> Marco
> Def. Quota "Eric Pettersen" <pett at cgl.ucsf.edu>:
>> Hi Alex,
>> 	In theory this is doable.  In practice, this will not work for some
>> of structures in the PDB until our next release.  This is because
>> the  MSMS surfacing library that we're currently using will fail for
>> a  small fraction of the structures in the PDB.  Of course, a "small
>> fraction" of the entire PDB is still probably hundreds of
>> structures.   Our next release (1.4) will include a new surfacing
>> library that will  be more stable -- though it might not be as fast
>> as MSMS.  My best  guesstimate of when the 1.4 release will be
>> available is September,  though there's a slight chance it could be
>> earlier.
>> 	Do you intend to compute electrostatics using some
>> Poisson-Boltzmann  solver?  If so, then doing that for the entire
>> PDB seems like a  Herculean task.  Certainly Chimera can show the
>> output once you've  computed it, but it won't be much help in
>> automating the computation.   An alternative is that the current
>> daily build includes the Coulombic  Surface Coloring tool, which
>> unsurprisingly performs the somewhat  cruder coulombic
>> electrostatics computation for a structure and then  colors a
>> surface appropriately.  Although Poisson-Boltzmann is a more
>> accurate computation it has been our experience that qualitatively
>> the  results are quite similar.  You can see an informal comparison
>> here:  http://tinyurl.com/mzopva
>> 	There is no command line version of Coulombic Surface Coloring, so
>> you would have to use the Python API.  Given a surface, RGBA values,
>> and corresponding potential values, something like:
>> from ESP import colorESP
>> colorESP(surf, rgbas, potVals)
>> and to get a surface object (assuming exactly one is open):
>> import chimera, _surface
>> surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0]
>> 	As to how to call Chimera commands from a Python script:
>> from chimera import runCommand
>> runCommand("surf")
>> 	To run a Python script without bringing up the Chimera GUI, look at
>> the --nogui and --script arguments documented here:
>> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html
>> 	Further questions should probably be sent to the chimera-dev
>> mailing  list rather than the chimera-users list.
>> --Eric
>>                        Eric Pettersen
>>                        UCSF Computer Graphics Lab
>>                        http://www.cgl.ucsf.edu
>> On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote:
>>> Hello,
>>> I?m a student at Carleton University and I need to create meshes
>>> with electrostatic coloring for all the proteins in the pdb. I need
>>> a way of automating this process with scripts but I can?t figure
>>> out  how. Is this possible to do this through command line? How do
>>> I call  chimera commands from a script?
>>> Any help would be greatly appreciated!
>>> Thanks,
>>> Alex Gawronski
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> Dr.Marco Sette, Ph.D.
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        sette at uniroma2.it
> e-mail:        m77it at yahoo.it
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
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Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2

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