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<div><br></div><blockquote type="cite"><div>On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:</div></blockquote><blockquote type="cite">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.</blockquote><div><br></div><div>Hi Gareth,<div>Here is the man page on fetching CASTp data from Chimera:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div>Some of what I describe below is newish, so you would need to get a daily build of Chimera to follow along:</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; "><a href="http://www.cgl.ucsf.edu/chimera/alpha-downloads.html">http://www.cgl.ucsf.edu/chimera/alpha-downloads.html</a></font></div></div></div></div><div><br><div>Although not all protein PDB entries are in the CASTp database, you can upload a structure to the CASTp server directly (not from Chimera):</div><div><a href="http://sts-fw.bioengr.uic.edu/castp/calculation.php">http://sts-fw.bioengr.uic.edu/castp/calculation.php</a></div><div>At least the last time I tried it, if you choose the "E-mail only" output option, one of the files it mails you contains only the atoms that form each pocket. You could look at the text of that file, find the pocket of interest, and then only specify those atoms in the "surface" command in Chimera. (It wouldn't work to just open a file with those atoms and surface them, because the surface would completely enclose the atoms, not just the "real" surface side.) This process is much more tedious than the direct fetch, however.</div><div><br></div><div>Even if you surface only the pocket atoms, there are other issues. One problem is that Chimera only turns on/off surface patches per atom, and sometimes the same atom has surface on one side that is part of the pocket, but also surface on another side that is part of some different pocket or the protein exterior; when you show the surface for all "pocket atoms" there may be some extra bits. Example: use the command "open castp:2gbp" and in the resulting dialog, make sure the Surface option is turned on and click on the second pocket in the list. It may take a few seconds to compute the surface. That pocket is completely enclosed, but some of the same atoms have additional surface. Extra bits can be clipped away to some extent, but you are limited by the planarity of the clipping plane.</div><div><br></div><div>Another possibility in Chimera is to use the Surfnet tool. I find it often makes too many small blobs and requires experimentation. Example: open 2gbp, delete ligand (to make the pocket empty), choose Tools... Surface/Binding Analysis... Surfnet - Selected Atoms. Enter Midas Selection: </div><div> :154 z<5 </div><div>(I know residue 154 is next to the pocket and include other residues within 5 angstroms), set the color if you want to, click Apply. That gives one extra small blob. Actually I tried 8 angstroms first and that gave several extra small blobs. You can close (delete) the entire Surfnet results in the Model Panel (under Favorites). You can Ctrl-click the Surfnet surface to select it. You still can't control the different blobs independently until you split that surface, however (after selecting the surface, use command "ac Sc"). Then you can Ctrl-click an individual blob, open the Selection Inspector (Actions... Inspect), and change the blob's color, type of display (mesh/dot/filled) and lighting, and whether it is displayed at all - thus you can hide the extra blobs.</div><div><br></div><div>In fact, several separate programs have been developed to show pocket or tunnel surface or void volume: </div><div><br></div><div>Hole (can't find a current web page)</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Mole <a href="http://mole.chemi.muni.cz">http://mole.chemi.muni.cz</a>/</font></div></div><div>Caver <a href="http://loschmidt.chemi.muni.cz/caver/">http://loschmidt.chemi.muni.cz/caver/</a></div><div>Hollow <a href="http://hollow.sourceforge.net">http://hollow.sourceforge.net</a>/ (you may enjoy the Munch painting in this page!)</div><div><br></div><div>I haven't had the activation energy to try any of these myself, and unfortunately none have been specifically adapted to work with Chimera (or vice versa). Caver has a Pymol plugin.</div><div>I hope this helps,</div><div>Elaine</div><div><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; 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; 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>-----</div><div>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a></div><div>UCSF Computer Graphics Lab and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a></div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span> </div><br></div></div></div></body></html>