[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
>
> }
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
--
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20131212/e581fff7/attachment-0001.htm>
More information about the phenixbb
mailing list