[phenixbb] cyclic peptide refinement

Ryan Spencer rspencer at uci.edu
Thu Dec 12 08:51:47 PST 2013

Hi Wei,


                I used Custom geometry restraints under the Refinement
settings tab in phenix.refine. Select the bond you want to make, the angle
and the plane you want to set. Should look something like this for the bond:


chain 'A' and resid '   1 ' and name ' N  ' and altloc ' '; chain 'A' and
resid '  16 ' and name ' C  ' and altloc ' '. 


This will create a bond between the amine at position 1 and the carbonyl at
position 16. Enter the appropriate distance (1.329) and sigma (0.06). 


The same can be done for the angle and the plane.




From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of wei xia
Sent: Thursday, December 12, 2013 8:14 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] cyclic peptide refinement



I am trying to refine a structure with a cyclic peptide ligand.

I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic
peptide during refinement.

But there is obvious no bond formed between the two residues in the refined

I checked the geo file and found that there are only angle restraints but no
bond restraints between the two residues

Anyone can help me out?

Thanks in advance!







refinement.pdb_interpretation.apply_cif_link {


       data_link = TRANS


       residue_selection_1 = chain D and resname MVA and resid 5005


       residue_selection_2 = chain D and resname ARG and resid 5001



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