[phenixbb] peptide ligand refinement problems
mengbinc at sas.upenn.edu
Tue Aug 20 13:40:40 PDT 2013
I guess I just rushed to a conclusion. Actually, the peptide bond is not
planar after the refinement run...
On Tue, Aug 20, 2013 at 4:36 PM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:
> Hi Nigel,
> It worked! Thanks a lot!
> On Tue, Aug 20, 2013 at 3:03 PM, Nigel Moriarty <nwmoriarty at lbl.gov>wrote:
>> 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 Chen
>>> Department of Chemistry
>>> University of Pennsylvania
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
Department of Chemistry
University of Pennsylvania
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