<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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 class="Apple-style-span" face="Arial">Todd Talley writes:</FONT></DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Arial">Hay,</FONT></DIV><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT class="Apple-style-span" face="Arial"> </FONT></P><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Arial"> I am sure that this is a dumb problem BUT I am unable to “turn on” the disulfide bonds in my structures. They are a crucial part of the structures that I am publishing and I really would like to use Chimera to render the images for our publication but I am not a code guy and none of the combos I have tried worked. If anyone is out there with the answer please let me know! </FONT></DIV><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT class="Apple-style-span" face="Arial"> </FONT></P><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Arial">Thanks!</FONT></DIV></BLOCKQUOTE><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Deposited PDB structures specify disulfide linkages using CONECT records, which Chimera honors. So one way to go is to add such CONECT records to your structures. CONECT records are documented here: <A href="http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html">http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">You can also add the linkages directly in Chimera. If you select a pair of sulfurs that should have the linkage, then the command "bond sel" (Favorites->Command Line) will add the linkage. Sessions and PDB files that you save thereafter will have the linkage information (i.e. a saved PDB file will have the appropriate CONECT record).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">If you have a lot of disulfide bonds or a lot of structures, I could send you a short Python script to add the linkages automatically.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--Eric</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> <BR class="Apple-interchange-newline"> </DIV><BR></BODY></HTML>