[Chimera-users] Electrostatics

sette at uniroma2.it sette at uniroma2.it
Sat Jun 20 02:42:34 PDT 2009


do you think it is possible in future versions of Chimera to read the  
results of APBS calculation for electrostatic properties?


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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