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. Ryan From: [email protected] [mailto:[email protected]] On Behalf Of wei xia Sent: Thursday, December 12, 2013 8:14 AM To: [email protected] Subject: [phenixbb] cyclic peptide refinement Hi, 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 structure. 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! Wei P.S. 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 }

Wei I think the problem with the apply_cif_link may be that the atoms are more than 3 angstrom apart. Could you send me the cyclic peptide directly? Nigel NB. Any files sent to me will be held in strictest confidence. On Thu, Dec 12, 2013 at 8:14 AM, wei xia wrote:

Hi, 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 structure. 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!

Wei

P.S.

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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