[phenixbb] MSE gap

Rife, Christopher L crife at slac.stanford.edu
Wed Jan 16 14:02:12 PST 2008

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). 


-----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


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,
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