<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Alex,<div><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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: <a href="http://tinyurl.com/mzopva">http://tinyurl.com/mzopva</a></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>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:</div><div><br></div><div>from ESP import colorESP</div><div>colorESP(surf, rgbas, potVals)</div><div><br></div><div>and to get a surface object (assuming exactly one is open):</div><div><br></div><div>import chimera, _surface</div><div>surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0]</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>As to how to call Chimera commands from a Python script:</div><div><br></div><div>from chimera import runCommand</div><div>runCommand("surf")</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>To run a Python script without bringing up the Chimera GUI, look at the --nogui and --script arguments documented here:</div><div><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></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Further questions should probably be sent to the chimera-dev mailing list rather than the chimera-users list.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple"><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceType"><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceName"><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Hello,<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">I’m a student at<span class="Apple-converted-space"> </span><st1:place w:st="on"><st1:placename w:st="on">Carleton</st1:placename><span class="Apple-converted-space"> </span><st1:placetype w:st="on">University</st1:placetype></st1:place><span class="Apple-converted-space"> </span>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?<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Any help would be greatly appreciated!<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Thanks,<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Alex Gawronski<o:p></o:p></span></font></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></o:smarttagtype></o:smarttagtype></o:smarttagtype></div></blockquote></div><br></div></body></html>