<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7654.12">
<TITLE>FW: [Chimera-users] Electrostatics</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Hello,<BR>
<BR>
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?<BR>
<BR>
Thanks!<BR>
Alex Gawronski<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: Eric Pettersen [<A HREF="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</A>]<BR>
Sent: Thu 6/18/2009 2:50 PM<BR>
To: Gawronski, Alexander<BR>
Cc: chimera-users@cgl.ucsf.edu<BR>
Subject: Re: [Chimera-users] Electrostatics<BR>
<BR>
Hi Alex,<BR>
In theory this is doable. In practice, this will not work for some <BR>
of structures in the PDB until our next release. This is because the <BR>
MSMS surfacing library that we're currently using will fail for a <BR>
small fraction of the structures in the PDB. Of course, a "small <BR>
fraction" of the entire PDB is still probably hundreds of structures. <BR>
Our next release (1.4) will include a new surfacing library that will <BR>
be more stable -- though it might not be as fast as MSMS. My best <BR>
guesstimate of when the 1.4 release will be available is September, <BR>
though there's a slight chance it could be earlier.<BR>
Do you intend to compute electrostatics using some Poisson-Boltzmann <BR>
solver? If so, then doing that for the entire PDB seems like a <BR>
Herculean task. Certainly Chimera can show the output once you've <BR>
computed it, but it won't be much help in automating the computation. <BR>
An alternative is that the current daily build includes the Coulombic <BR>
Surface Coloring tool, which unsurprisingly performs the somewhat <BR>
cruder coulombic electrostatics computation for a structure and then <BR>
colors a surface appropriately. Although Poisson-Boltzmann is a more <BR>
accurate computation it has been our experience that qualitatively the <BR>
results are quite similar. You can see an informal comparison here: <A HREF="http://tinyurl.com/mzopva">http://tinyurl.com/mzopva</A><BR>
There is no command line version of Coulombic Surface Coloring, so <BR>
you would have to use the Python API. Given a surface, RGBA values, <BR>
and corresponding potential values, something like:<BR>
<BR>
from ESP import colorESP<BR>
colorESP(surf, rgbas, potVals)<BR>
<BR>
and to get a surface object (assuming exactly one is open):<BR>
<BR>
import chimera, _surface<BR>
surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0]<BR>
<BR>
As to how to call Chimera commands from a Python script:<BR>
<BR>
from chimera import runCommand<BR>
runCommand("surf")<BR>
<BR>
To run a Python script without bringing up the Chimera GUI, look at <BR>
the --nogui and --script arguments documented here:<BR>
<A HREF="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html</A><BR>
<BR>
Further questions should probably be sent to the chimera-dev mailing <BR>
list rather than the chimera-users list.<BR>
<BR>
--Eric<BR>
<BR>
Eric Pettersen<BR>
UCSF Computer Graphics Lab<BR>
<A HREF="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A><BR>
<BR>
<BR>
On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote:<BR>
<BR>
> Hello,<BR>
><BR>
> I'm a student at Carleton University and I need to create meshes <BR>
> with electrostatic coloring for all the proteins in the pdb. I need <BR>
> a way of automating this process with scripts but I can't figure out <BR>
> how. Is this possible to do this through command line? How do I call <BR>
> chimera commands from a script?<BR>
><BR>
> Any help would be greatly appreciated!<BR>
><BR>
> Thanks,<BR>
> Alex Gawronski<BR>
> _______________________________________________<BR>
> Chimera-users mailing list<BR>
> Chimera-users@cgl.ucsf.edu<BR>
> <A HREF="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A><BR>
<BR>
<BR>
No virus found in this incoming message.<BR>
Checked by AVG - www.avg.com<BR>
Version: 8.5.339 / Virus Database: 270.12.56/2162 - Release Date: 06/18/09 05:53:00<BR>
<BR>
</FONT>
</P>
</BODY>
</HTML>