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<div><br></div><br class="Apple-interchange-newline">On Apr 6, 2008, at 4:53 PM, Thiruvarangan Ramaraj wrote:<blockquote type="cite">Hello,<br>I am new to Chimera, I am trying to identify the residues that lie on the surface of a antigen complex that are within certain distance from the antibody.<br></blockquote><div><br></div>Hi Thiruvarangan,<div>If you want just a certain distance, you can select the residues with a command that includes a "zone" specification. For example, this command would select residues in chain A with any atom within 4.5 angstroms of any atom in chain B:</div><div><br></div><div>select :.a & :.b zr<4.5</div><div><br></div><div>zr is for residue-based cutoff, za for atom-based, and you can use < for less than and > for more than. Once the residues are selected you could do other things to them with the Actions menu including coloring and writing a list of their names to a file. (You can also do the selecting with the menu, but it takes more words to explain.)</div><div><br></div><div>However, there are other ways to find contacts that do not use a single cutoff distance: "Find Clashes/Contacts" and "Intersurf" (both under Tools... Surface/Binding Analysis). For more details on using zone specification or these other tools, please see this previous message:</div><div><br></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/pipermail/chimera-users/2008-March/002425.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002425.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; ">I hope this helps,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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></span></div></div></div></body></html>