<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 18, 2009, at 3:55 PM, Gawronski, Alexander wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div> <!-- 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?</font></p></div></blockquote>Hi Alex,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Well, as I said in the initial mail:</div><div><br></div><div><blockquote type="cite"><div><p><font size="2">Given a surface, RGBA values, <br>and corresponding potential values, something like:<br><br>from ESP import colorESP<br>colorESP(surf, rgbas, potVals)</font></p></div></blockquote>'rgbas' would be a list of RGBA tuples (red-green-blue-alpha; Google 'rgba' for more info). 'potVals' would be a list of floating-point electrostatic potential values corresponding to the given RGBAs.<br><blockquote type="cite"><div><p><font size="2">Is there additional information on this functionality that I can look at?<br></font></p></div></blockquote><div><br></div>You can look at the ESP module, included in your Chimera (daily build) distribution in <chimera installation>/share/ESP -- specifically the __init__.py file. The colorESP function is defined there.</div><div><br></div><div>There is user-oriented documentation here: <a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html</a></div><div><br></div><div>--Eric</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div></span></div></div><div><br><blockquote type="cite"><div><p><font size="2"> <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: <a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><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> > <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><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 - <a href="http://www.avg.com">www.avg.com</a><br> Version: 8.5.339 / Virus Database: 270.12.56/2162 - Release Date: 06/18/09 05:53:00<br> <br> </font> </p> </div> _______________________________________________<br>Chimera-dev mailing list<br><a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br></blockquote></div><br></body></html>