[phenixbb] peptide ligand refinement problems

Nigel Moriarty nwmoriarty at lbl.gov
Tue Aug 20 12:03:45 PDT 2013


You can use the intra_chain=True option to automatically link the ring. If
that fails send me the model and I'll provide the files used in an older


On Tue, Aug 20, 2013 at 11:32 AM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:

> Dear Phenix Users,
> My colleague has got into trouble when he was refining a peptide ligand
> with a coumarin ring attached via a peptide bond. The peptide part is
> composed of natural amino acids, which does not require a cif file. On the
> other hand, a cif file has been created for the coumarin ring.
> Unfortuantely, after the refinement run, the peptide and the coumarin ring
> fell apart, and we could not figure out why this is happening. We are using
> the Phenix-dev-1370 version. Any help would be appreciated!
> Thank you in advance,
> Mengbin
> --
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
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> phenixbb at phenix-online.org
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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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