[phenixbb] peptide ligand refinement problems

[Nigel Moriarty]

Mengbin

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
method.

Nigel


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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>
>


-- 
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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