[phenixbb] cyclic peptide refinement

Nigel Moriarty nwmoriarty at lbl.gov
Thu Dec 12 11:58:52 PST 2013


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 <weixia1984 at outlook.com> 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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>


-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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