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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: [email protected] [mailto:[email protected]] On Behalf Of Troy E Messick Sent: Wednesday, January 16, 2008 1:32 PM To: [email protected] 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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb