<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Roberta,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>That preset will depict residues with non-backbone atoms within 3.5 angstroms of: a metal-ion-only residue; a residue classified as ligand (that classification explained here: <A href="http://www.cgl.ucsf.edu/chimera/docs/">http://www.cgl.ucsf.edu/chimera/docs/</A>UsersGuide/midas/surface.html#surfcats). Also, residues involved in a metal-coordination complex will be depicted, though usually that is also covered by the first criteria above. Nucleic acid side chains are always depicted.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>The idea was to quickly get to a view that would be relatively easy to understand yet still useful for analysis. This was my best first approximation. I'm open to suggestions for improvements.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric<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><DIV><DIV>On Jul 17, 2007, at 6:26 AM, Roberta King wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceName"> <O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceType"> <O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place"> <DIV class="Section1"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Hello,<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I have upgraded to Chimera 12417 with the new presets for visualization. What are the criteria within “Interactive 1:setup ribbons” preset for determining which residue side chains are depicted as sticks in the binding pocket? <O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">This is a useful shortcut, but I would like to understand the specific criteria.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Thank you very much,<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Roberta<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P> <DIV><P class="MsoNormal"><FONT size="3" face="Times New Roman"><SPAN style="font-size: 12.0pt">********************************<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Roberta S. King, Ph.D.</SPAN></FONT><O:P></O:P></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Associate Professor<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Department of Biomedical and Pharmaceutical Sciences<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><ST1:PLACE w:st="on"><ST1:PLACETYPE w:st="on"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial">College</SPAN></FONT></ST1:PLACETYPE><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial"> of <ST1:PLACENAME w:st="on">Pharmacy</ST1:PLACENAME></SPAN></FONT></ST1:PLACE><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial"><O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><ST1:PLACE w:st="on"><ST1:PLACETYPE w:st="on"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial">University</SPAN></FONT></ST1:PLACETYPE><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial"> of <ST1:PLACENAME w:st="on">Rhode Island</ST1:PLACENAME></SPAN></FONT></ST1:PLACE><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt;font-family:Arial"><O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><A href="http://www.uri.edu/pharmacy/faculty/king">http://www.uri.edu/pharmacy/faculty/king</A></SPAN></FONT><O:P></O:P></P> </DIV><P class="MsoNormal"><FONT size="2" face="Times New Roman"><SPAN style="font-size: 11.0pt"><O:P> </O:P></SPAN></FONT></P> </DIV> </O:SMARTTAGTYPE></O:SMARTTAGTYPE></O:SMARTTAGTYPE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@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/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>