[phenixbb] MSE gap

[Troy E Messick]

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