<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 4, 2010, at 10:43 AM, Forbes J. Burkowski wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi:<br><br>On Tue, 2 Mar 2010, Elaine Meng wrote:<br><br><blockquote type="cite">I forgot to mention that when you change chain ID, you usually also<br></blockquote><blockquote type="cite">need to change the residue numbering so that residues will be uniquely<br></blockquote><blockquote type="cite">specifiable. For example, if you have two residues both numbered 10<br></blockquote><blockquote type="cite">in chain B, it may be difficult to do something to only one or the<br></blockquote><blockquote type="cite">other in Chimera. Those editing servers allow renumbering in addition<br></blockquote><blockquote type="cite">to changing the chain ID.<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite"><br></blockquote><br>Just a note: If two chains are given the same chain ID, it is not clear<br>how everything will properly work out, even with renumbering. I would<br>imagine that Chimera would see the last residue in the first original<br>chain as the part of a backbone that joins it to the first residue in the<br>second original chain. Would this unfortunate connection occur?</div></blockquote><br></div><div>Hi Forbes,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Assuming that the TER card between the chains is retained, then no, Chimera will treat the two chains as completely separate entities despite the identical chain ID. This can be awkward in some interfaces that list chains since there will be two apparently-identical entries.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>If the TER card is removed then Chimera <i>will</i> treat them as one chain and will add a "missing structure" pseudobond connecting the last residue of one chain to the first residue of the other chain.</div><div><br></div><div>--Eric</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>