Dear Eric,<br><br>Thank you so much for your quick response. We were using the minimization routines in Chimera, and needed consistency in the atom numbering to integrate with other components of our application.<br><br>George<br>
<br><div class="gmail_quote">On Mon, Jun 27, 2011 at 6:18 PM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word">Hi George,<div><span style="white-space:pre-wrap"> </span>The short answer is no. Generally speaking, unless your structure is unmodified (in which case, why not use the original file?) there is no way to write a standard-conformant PDB file while preserving original serial numbers. Let's say you opened a structure, added hydrogens, and wanted to write it out with unchanged serial numbers. Well, the hydrogens are going to have serial numbers larger than any heavy atom, so since they will be written along with their residue-mates in the file (else TER card conventions would be violated), the serial numbers will not be... serial.</div>
<div><span style="white-space:pre-wrap"> </span>Nonetheless, I can imagine scenarios where you would be willing to ignore the not-strictly-legal nature of such a file, so I'll add a feature-request ticket to the Chimera Trac database with you on the recipient list. If anyone else would also like to be on the notification list, send me an email...</div>
<div><br></div><div>--Eric</div><div><br><div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:16px"><font face="Helvetica" size="5"> Eric Pettersen</font></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:16px"><font face="Helvetica" size="5"> UCSF Computer Graphics Lab</font></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:16px">
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<div>On Jun 27, 2011, at 5:14 PM, George White wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5">Hi,<br><br>I am wondering is there any way to write a pdb from Chimera that preserves the original atom serial numbering of the input pdb. Chimera seems to apply its own renumbering (i.e. making the number of the 1st atom #1 etc.) .<br>
<br>Thanks in advance,<br>George<br></div></div> _______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
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