<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">After the 1.2065 production release, a bug crept into the code that determines secondary structure when HELIX and SHEET records are absent. I'm guessing your structure is lacking these records and therefore the helices aren't being properly identified. You can manually identify them to Chimera by using the procedure Elaine outlined, quoted below.<DIV><BR><DIV> <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>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>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="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></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> </DIV><BR><DIV><DIV>On Aug 30, 2005, at 11:21 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">You can change assignments</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>(a) manually (by selecting the desired parts, then clicking the button</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">reporting what is selected on the bottom right corner of the Chimera window</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">to open the Selection Inspector, Inspect "Residue" instead of "Atom," setting</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Monaco" size="4" style="font: 14.0px Monaco">"in helix" to "true" and "in strand" to "false")</FONT></P> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>