[phenixbb] peptide ligand refinement problems

[Mengbin Chen]

Hi Nigel,

It worked! Thanks a lot!

Best,
Mengbin


On Tue, Aug 20, 2013 at 3:03 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> 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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>
>


-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
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