[phenixbb] Peptides bonds in cyclic peptides

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Wed Mar 16 14:58:06 PDT 2011

Hi Chris,
Could you send me (not the list) your pdb file?
A part with the cycling peptide will be sufficient.

>From: Krzysztof Bzymek <kbzymek at gmail.com>
>To: phenixbb at phenix-online.org
>Sent: Wed, March 16, 2011 2:42:08 PM
>Subject: [phenixbb] Peptides bonds in cyclic peptides
>I've been trying to refine a structure of a protein with a cyclic peptide bound 
>to it. Adding LINK/CONECT to the pdb file works in coot but the bonds are not 
>present after refinement in phenix. I tried creating a param file (I followed 
>recommendations for making ASN/NAG bonds posted here a while ago, but changed 
>the names of connected residues) and included it in refinement,  but the bond 
>was not formed and the amino and carboxy groups of respective amino acids were 
>far apart. I also got a message after refinement that a cif file was not 
>specified. What's the solution?
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