[chimera-dev] FW: [Chimera-users] Electrostatics

Gawronski, Alexander Alexander.Gawronski at nrc-cnrc.gc.ca
Thu Jun 18 15:55:39 PDT 2009


I sent an email to Eric Pettersen about automating coloring by electrostatics (see below). He told me to direct further questions to the chimera-dev list. So my question is, in the function colorESP(surf, rgbas, potVals) what should rgbas and potVals be specifically? Is there additional information on this functionality that I can look at?

Alex Gawronski

-----Original Message-----
From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Thu 6/18/2009 2:50 PM
To: Gawronski, Alexander
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Electrostatics
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

	To run a Python script without bringing up the Chimera GUI, look at  
the --nogui and --script arguments documented here:

	Further questions should probably be sent to the chimera-dev mailing  
list rather than the chimera-users list.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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

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