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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Thanks for the info Eric,<br>
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<div style="font-family:Tahoma; font-size:13px"> - Mark<br>
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<div style="direction: ltr;" id="divRpF420543"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Eric Pettersen [pett@cgl.ucsf.edu]<br>
<b>Sent:</b> Thursday, November 14, 2013 3:43 PM<br>
<b>To:</b> Mark Girvin<br>
<b>Cc:</b> George Tzotzos ý[gtzotzos@me.com]ý<br>
<b>Subject:</b> Re: [Chimera-users] Residue selection<br>
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<div>Yeah, waters with a blank chain ID are put in chain "water" and similarly residues in HETATM records with a blank chain ID are put in chain "het". If the chain ID is non-blank, both get assigned the given chain ID rather than "water" or "het".
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<div>--Eric</div>
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<div>On Nov 14, 2013, at 12:22 PM, Mark Girvin <<a href="mailto:mark.girvin@einstein.yu.edu" target="_blank">mark.girvin@einstein.yu.edu</a>> wrote:</div>
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<div style="direction:ltr; font-family:Tahoma; font-size:10pt">Got it. And no problem - just not quite expected.<span class="Apple-converted-space"> </span><br>
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So then chimera sets up internal chain names (like "water") for some entries in PDB files? I don't think George's file had any internal chain entries, or HETATM lines.<br>
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<div style="font-family:Tahoma; font-size:13px"> - Mark<br>
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<div id="divRpF218803" style="direction:ltr"><font face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span>Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>]<br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, November 14, 2013 2:50 PM<br>
<b>To:</b><span class="Apple-converted-space"> </span>Mark Girvin<br>
<b>Cc:</b><span class="Apple-converted-space"> </span>George Tzotzos; chimera List<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Residue selection<br>
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<div>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.
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<div>If I were making the decision about Chimera's behavior<span class="Apple-converted-space"> </span><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>
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<div>--Eric</div>
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Eric Pettersen<br>
UCSF Computer Graphics Lab<br>
<a href="http://www.cgl.ucsf.edu/" target="_blank">http://www.cgl.ucsf.edu</a><br>
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<div>On Nov 14, 2013, at 7:44 AM, Mark Girvin <<a href="mailto:mark.girvin@einstein.yu.edu" target="_blank">mark.girvin@einstein.yu.edu</a>> wrote:</div>
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<div style="direction:ltr; font-family:Tahoma; font-size:10pt">I don't know why that doesn't work, but:<br>
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select :WAT@O<span class="Apple-converted-space"> </span><br>
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seems to (if you only have the one water in your pdb file), as does:<br>
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select :127.water@O <span class="Apple-converted-space"> </span><br>
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(which would presumably limit the selection to the one water molecule)<br>
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<div style="font-family:Tahoma; font-size:13px"> - Mark<br>
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<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" target="_blank">chimera-users-bounces@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>[<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" target="_blank">chimera-users-bounces@cgl.ucsf.edu</a>]
on behalf of George Tzotzos [<a href="mailto:gtzotzos@me.com" target="_blank">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>
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<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>
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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>
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My question is if I'm doing something wrong with the residue selection.<br>
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Many thanks in advance for your help<br>
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Regards<br>
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George<br>
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