<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>So I've been trying to make an 'inverted surface'. Basically I have a cavity inside a protein which is almost completely surrounded and so it is hard to illustrate it to others without removing parts of the protein (which I could of course do). Does Chimera have a function to mark the inside of a cavity with a surface, then allowing the user to remove the protein and just leave the surface so as to illustrate the size and shape of the cavity in relation to the protein.</div><div><br></div><div>Have I explained that clearly enough???</div></span></span></blockquote><br></div><div>Hi Gareth,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If this is a standard PDB you can fetch the structure from the CASTp database (File->Fetch By ID...) which will bring up an interface that will allow you to browse the pockets of the structure, with only the browsed pocket being surfaced.<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If you have a non-standard PDB, you will need to identify some residues near the pocket (let's say they were residues 15 to 19) and then use a command like:<br></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>~surf :15-19 z>5</div><div><br></div><div>to hide surfaces further than 5 angstroms from those residues, which should hide most of the "outside" surface. Then:<br></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>~disp<br></div><div><br></div><div>will hide the structure. If you don't know the pocket residues, you might clip through the outside surface with the Side View clip planes and then use the mouse-hovering popup balloons to identify some residues.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If your pocket has a channel to the outside, you might want to get a clean cut through the channel by using per-model clipping on the surface and orienting the clip plane so that it cuts the channel. The Per-Model Clipping tool is in the Depiction tools category.<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I'd like to get Chimera to handle CASTp results for non-standard PDBs, but haven't gotten to that yet.<br></div><div><br></div><div>--Eric</div><div><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; "><br class="Apple-interchange-newline"> 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><br><div></div></div></body></html>