<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 12, 2010, at 5:05 AM, Guy Nimrod wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello, <br>When I load complex structure (e.g., pdb 3mht) and show the surface of one chain (e.g. selectchainA; action->surface->show), the generated surface does not cover the interface between the query protein and the other chains. Consequently, the interface appears as a hole in the surface (see attached figure). <br>Is there an easy way to visualize the whole surface (i.e. the generated surface on a selected chain will disregard chains which are not selected)?</div></blockquote><br></div><div><br></div><img height="812" width="747" src="cid:35AA7848-2769-4375-8E86-3E2C05B2C76E@cgl.ucsf.edu"><div><br></div><div>Hi Guy,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>When you surface some subset of atoms in Chimera, Chimera still considers all atoms in the same "surface category" as the subset for purposes of computing the surface -- it just doesn't show the surface of the atoms not in the subset. So for example if you ask for a surface on a single residue Chimera doesn't make a surface that completely encloses the residue -- the surface is "open" where the residue connects to the rest of the molecule. Similarly, a single chain of a multi-chain molecule may not be completely enclosed if Chimera considers other chains of the molecule to be in the same surface category.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>That is what has happened here. Chain A (the protein) and the chains C and D (the nucleic acid) have been classified into the same surface category (main). To get the enclosed surface that you want you need to put chain A into a surface category of its own and surface that. These two commands will accomplish that:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>surfcat prot :.a</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>surf prot</div><div><br></div><div>The surface actually inter-penetrates the nucleic acid because of the flipped-out base, like this:</div><div><img height="668" width="747" apple-width="yes" apple-height="yes" src="cid:B3F3A836-F43F-4A23-A738-BB6252469672@cgl.ucsf.edu"></div><div><br></div><div><br></div><div>--Eric</div><div><br></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></body></html>