<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Yeah, the :127@O behavior is deliberate. If you omit the chain ID, it only matches single-character chain IDs (i.e. not chain ID "water" or "het"). This choice was made so that if your structure has a bunch of waters that so happen to have the same numbers as various polymeric residues, :127 will get the polymeric residue(s) but not the waters. This behavior was more important before the PDB remediation a few years back where such occurrences were commonplace. Now, in standard PDB files waters are frequently assigned specific chain IDs and therefore have different numbers than the polymeric residues. Chimera's behavior still matters for non-standard PDB files generated by various programs.<div><br></div><div>If I were making the decision about Chimera's behavior <i>today</i>, given that the issue no longer affects standard PDB files, it might go the other way (it might not), but I don't feel strongly enough to change anything. A bunch of complaining could change my mind. :-)</div><div><br></div><div>--Eric</div><div><br> Eric Pettersen<br> UCSF Computer Graphics Lab<br> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><br><br></div><div><br><div><div>On Nov 14, 2013, at 7:44 AM, Mark Girvin <<a href="mailto:mark.girvin@einstein.yu.edu">mark.girvin@einstein.yu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div ocsi="0" fpstyle="1" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="direction: ltr; font-family: Tahoma; font-size: 10pt; ">I don't know why that doesn't work, but:<br><br>select :WAT@O<span class="Apple-converted-space"> </span><br><br>seems to (if you only have the one water in your pdb file), as does:<br><br>select :127.water@O <span class="Apple-converted-space"> </span><br><br>(which would presumably limit the selection to the one water molecule)<br><div><br><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "><div style="font-family: Tahoma; font-size: 13px; "> - Mark<br></div></div></div></div><div style="font-family: 'Times New Roman'; font-size: 16px; "><hr tabindex="-1"><div id="divRpF647433" style="direction: ltr; "><font face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>[<a href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a>] on behalf of George Tzotzos [<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, November 14, 2013 8:08 AM<br><b>To:</b><span class="Apple-converted-space"> </span>chimera List<br><b>Subject:</b><span class="Apple-converted-space"> </span>[Chimera-users] Residue selection<br></font><br></div><div></div><div><div class="BodyFragment"><font size="2"><span style="font-size: 10pt; "><div class="PlainText">I'm attaching a pdb file of a protein ligand complex with a single conserve water molecule. The pdb file was constructed with Antechamber Leap. The water molecule is numbered as residue 127. When I try to select using: select :127 nothing happens. Selection works with: select :WAT<br><br>The problem is that I need to monitor the distance between :127@O and a particular atom in the binding site of the protein during an MD trajectory.<br><br>My question is if I'm doing something wrong with the residue selection.<br><br>Many thanks in advance for your help<br><br>Regards<br><br>George<br><br></div></span></font></div><div class="BodyFragment"><font size="2"><span style="font-size: 10pt; "><div class="PlainText">_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></span></font></div></div></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br></div><br><br><div apple-content-edited="true">
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