<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><html>On Apr 7, 2008, at 9:33 AM, Thiruvarangan Ramaraj wrote:</html><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; ">Thanks for your reply.<br>I can find out the residues from one chain that are from certain distances from another chain. But it will give all the residues, instead I want only the residues that are in the surface of the chain. Is there any way to do identify the residues that lie on the surface of a chain.<br><br>I tried to use surfcat, but it is not working, I am sure I am not doing it correct.<span class="Apple-converted-space"> </span><br>Any help would be greatly appreciated.<br>Thank You<br>Sincerely<br>Thiru</span></blockquote></div><br><div>Dear Thiru,</div><div>You can just add another step that says a residue just have a certain amount of surface area. Some new surface-area features were recently added to Chimera, so I recommend getting a daily build. </div><div><br></div><div> First you would need to use "surfcat" and show the surfaces you want.</div><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; ">I don't know what you tried, or what chains are in your structure, so I can't give exact steps. However, here is an example. If you have chains A,B,C and you want one surface around A and another around B,C together, you would use these commands:</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; ">surfcat group1 :.a</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">surfcat group2 :.b:.c</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">surface group1</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">surface group2</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; ">Then, use Select by Attribute ("Select... by Attribute Value" in the Chimera menu): in that tool, choose attributes of "residues" and in the "Attribute" menu, choose the name of the surface area attribute. The name is areaSAS if you want solvent-accessible surface area, areaSES if you want solvent-excluded surface area. The values in the structure are shown in a histogram, and you would move the vertical bars to enclose the range of values you want the residues to have. Lots of residues have a tiny amount of surface area, so you would probably want to set the minimum at some positive number. Click Apply to select that set of residues.</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; ">Then you can narrow the set of residues to only those in the zone, for example:</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 style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">select :.a & :.b zr<4.5 & sel</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; ">(like my previous example plus "& sel" which means "and also already selected"). In the future it should be easier, with a command something like</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; ">select :.a & :.b zr<4.5 & :/areaSES>50.0</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; ">(avoiding the separate "Select by Attribute" step) but currently, there is a bug that prevents using areaSAS and areaSES in the command line.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I hope this helps,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----</div></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>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></body></html>