<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>On Mar 7, 2006, at 10:01 AM, Elaine Meng wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">Issue (2) can be even more taxing. IF the cofactor residue has the <SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">same name and its atoms have the same names and are in the same <SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">orders in all pairs of structures to be compared, you could then use <SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">EnsembleMatch.<SPAN class="Apple-converted-space"> </SPAN>You'd specify the cofactor residue as the atoms to <SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">match, e.g.</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco"><SPAN class="Apple-converted-space"> </SPAN>:fad</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">(residues named FAD).<SPAN class="Apple-converted-space"> </SPAN>Another approach in this situation would be to <SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">use the match command, e.g.</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco"><SPAN class="Apple-converted-space"> </SPAN>command> match #1:fad #0:fad</FONT></P> </BLOCKQUOTE><BR></DIV><DIV>As of Chimera 1.2184 and later, the restrictions aren't quite as onerous as Elaine outlined. The atom names still do have to correspond, but the atoms need not all be in the same order inside the residue.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><BR><DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> Eric Pettersen</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> UCSF Computer Graphics Lab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> <A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> <A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></DIV></DIV><BR><DIV><BR class="khtml-block-placeholder"></DIV></BODY></HTML>