<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Thanks, Elaine. This helps get me started. I will play around a bit with a command file. I bet it will come together easily.</div><div>all the best,</div><div>glenn</div><div><br class="webkit-block-placeholder"></div><br><div><div>On Feb 20, 2008, at 3:55 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Glenn,<br>Although we plan to have user-defined presets in the future, currently there is no reasonably user-friendly way to customize them.<br><br>As a stopgap, if there are a few commands that generate the display you want (and you could start with a preset command), you could:<br><br>- put them in a command file; simply opening the command file in Chimera would execute it<br><br>- alias some word like "mypreset1" to those commands all strung together with semicolons, then later you would only have to type the command "mypreset1"<br><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html</a><br><br>You can have a command file automatically read at Chimera startup. This is specified in the preferences:<br>http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Midas<br><br>You would only put the alias commands there, not the display commands themselves, since you want to control when those commands are executed (and usually at startup no structures have been opened yet anyway).<br><br>There is also a New Molecules section of the preferences in which you can control how structures are displayed when they are first opened:<br>http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules<br><br>However, the New Molecules options are rather limited compared to what you can do with commands. There is nothing about disulfide bonds, for example.<br><br>I would be happy to provide more detailed help with any of this if you would like.<br>Best,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu<br>UCSF Computer Graphics Lab and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> http://www.cgl.ucsf.edu/home/meng/index.html<br><br><br><br><br>On Feb 20, 2008, at 3:31 PM, glenn millhauser wrote:<br><br><blockquote type="cite">Hi Folks,<br></blockquote><blockquote type="cite"> Is there a way to edit the Presets to include additional protein features? Specifically, I work with quite a few disulfide rich proteins and it would be great to select the Preset Interactive 1 and have it automatically draw Cys side chains with disulfide links.<br></blockquote><blockquote type="cite">Many thanks,<br></blockquote><blockquote type="cite">glenn<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Glenn L. Millhauser<br></blockquote><blockquote type="cite">Department of Chemistry & Biochemistry<br></blockquote><blockquote type="cite">UC Santa Cruz<br></blockquote><blockquote type="cite">Santa Cruz, CA 95064<br></blockquote><blockquote type="cite">831 459 2176 voice<br></blockquote><blockquote type="cite">831 566 3337 cell<br></blockquote><blockquote type="cite">831 459 2935 fax<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">http://chemistry.ucsc.edu/~glennm<br></blockquote><blockquote type="cite">http://www.chemistry.ucsc.edu/faculty/millhauser.html<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-users mailing list<br></blockquote><blockquote type="cite">Chimera-users@cgl.ucsf.edu<br></blockquote><blockquote type="cite">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote><br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><br class="Apple-interchange-newline"><br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Glenn L. Millhauser</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Department of Chemistry & Biochemistry</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">UC Santa Cruz</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Santa Cruz, CA 95064</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">831 459 2176 voice</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">831 566 3337 cell</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">831 459 2935 fax</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><br></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="http://chemistry.ucsc.edu/~glennm">http://chemistry.ucsc.edu/~glennm</a></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><a href="http://www.chemistry.ucsc.edu/faculty/millhauser.html">http://www.chemistry.ucsc.edu/faculty/millhauser.html</a></p><br class="Apple-interchange-newline"></span></span></div></span> </div><br></body></html>