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If you just do what I suggested in my previous email, then I presume
you will get what you want: a new PDB file with fixed gap and
accordingly updated statistics in its header (statistics in REMARK 3 is
what is supposed to go for PDB deposition).<br>
<br>
I don't see why this may not work... Am I missing something?<br>
<br>
Pavel.<br>
<br>
<br>
On 1/16/2008 2:12 PM, Troy E Messick wrote:
<blockquote
cite="mid:3f3aea4a0801161412k56175573n41c07702c37afbc4@mail.gmail.com"
type="cite">
<pre wrap="">That's what I've used to bring them back together in previous rounds
of refinement. The only problem is that I want to finalize the pdb so
I can deposit it. If I'm making modifications to the pdb file (by
regularizing), then I think the stats in the log file aren't accurate.
Troy
On Jan 16, 2008 5:02 PM, Rife, Christopher L <a class="moz-txt-link-rfc2396E" href="mailto:crife@slac.stanford.edu"><crife@slac.stanford.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">If it's close together, just open the file in coot and use the regularize command to put them where they should be. Or, better yet, use real-space-refine to optimize it (note, this needs a map).
Regards,
Chris
-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> [<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] On Behalf Of Troy E Messick
Sent: Wednesday, January 16, 2008 1:32 PM
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
Subject: [phenixbb] MSE gap
Hello,
I seem to be having a problem with phenix.refine and the
seleno-methionine residue (resname MSE).
It seems that I have a gap in the peptide bond between the C atoms and
the N atom of the subsequent residue. Is there something I could add
to the restraints_edits.params file to get it to click together? What
is the distance_ideal and sigma for a peptide bond?
Thanks for your help,
Troy
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