<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">A related tool in Chimera is Intersurf, for showing interface surfaces:<div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/intersurf/intersurf.html">http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/intersurf/intersurf.html</a></div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><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-size: 16px; "><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-size: 16px; "><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><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Oct 11, 2012, at 6:31 PM, Tom Goddard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><br><blockquote type="cite">Hi Tom,<br></blockquote><blockquote type="cite">I have a non-EM density question!<br></blockquote><blockquote type="cite">Is there a way to display the buried surface between two PDB chains in Chimera? Something like what GRASP does:<br></blockquote><blockquote type="cite"><a href="http://www.csb.yale.edu/poststructure/grasp/grasp2.html">http://www.csb.yale.edu/poststructure/grasp/grasp2.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I know I can measure the area with:<br></blockquote><blockquote type="cite">"measure buriedArea :.A :.B"<br></blockquote><blockquote type="cite">but is there a way to display the buried surfaces?<br></blockquote><blockquote type="cite">Thanks!<br></blockquote><blockquote type="cite">-gabe<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br>Hi Gabe,<br><br> The measure buriedArea command sets a value for each atom giving the<br>area buried (square Angstroms). So you can use<br><br> measure buriedArea :.A :.B<br> surfcat a :.A<br> surfcat b :.B<br> color pink :.A<br> color lightblue :.B<br> surface @/buriedSESArea>1<br><br>The surfcat command just defines chains A and B as two different objects<br>for surfacing and the surface command show the surface patches<br>associated with all atoms having buried solvent excluded surface area<br>greater than 1 square Angstrom. It shows the entire patch of area for<br>those atoms, not just the part that is buried. So it is pretty ugly and<br>a bigger surface then just the buried part.<br><br> For a much prettier picture but a slightly different measurement you<br>might try instead<br><br> split #0<br> surface<br> measure contactArea #0.1 #0.2 2 slab 0.5<br><br>The split puts chains A and B in two models #0.1 and #0.2. The<br>"surface" makes surfaces on each. And the "measure contactArea..."<br>finds all points on one surface within 2 Angstroms of any point on the<br>other surface and displays a pretty looking slab depicting the surface<br>(attached picture). This is a different definition of buried area but<br>might do.<br><br><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#contactArea">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#contactArea</a><br><br> Tom<br><br><span><contactArea.jpg></span>_______________________________________________<br>Chimera-users mailing list<br>Chimera-users@cgl.ucsf.edu<br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div><br><br><div>
</div>
<br></body></html>