<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">… and if you want to find the carbonyls only in GLU residues, you would intersect the specifier with :GLU, <i class="">i.e.</i><span style="font-style: normal;" class="">:</span><div class=""><br class=""></div><div class="">select carbonyl & :glu</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
</div>
<div><br class=""><blockquote type="cite" class=""><div class="">On Dec 11, 2019, at 9:34 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Damien,<br class="">You’ll like this… simply the command: select carbonyl<br class=""><br class="">It selects the atoms as well as the bond between them.<br class=""><br class="">You can specify in the command line any of the functional groups that appear in the menu under Select… Chemistry… functional group. It’s mentioned here:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><blockquote type="cite" class="">On Dec 11, 2019, at 8:02 AM, Damien Larivière <<a href="mailto:damien@fourmentinguilbert.org" class="">damien@fourmentinguilbert.org</a>> wrote:<br class=""><br class="">Dear All,<br class=""><br class="">My question is naive but I have difficulties to figure out how to do it with Chimera.<br class=""><br class="">I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein.<br class=""><br class="">Is there a way, via a command line, to do it?<br class=""><br class="">Thanks for your help on this.<br class=""><br class="">Damien<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>