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).

I don't see why this may not work... Am I missing something?

Pavel.

On 1/16/2008 2:12 PM, Troy E Messick wrote:

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 <crife@slac.stanford.edu> wrote:

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: phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] On Behalf Of Troy E Messick
Sent: Wednesday, January 16, 2008 1:32 PM
To: phenixbb@phenix-online.org
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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