[phenixbb] peptide ligand refinement problems

Mengbin Chen mengbinc at sas.upenn.edu
Tue Aug 20 13:40:40 PDT 2013


Hi

I guess I just rushed to a conclusion. Actually, the peptide bond is not
planar after the refinement run...

Mengbin


On Tue, Aug 20, 2013 at 4:36 PM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:

> 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
>>>
>>> _______________________________________________
>>> 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
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
> --
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
>



-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20130820/50f1346c/attachment.htm>


More information about the phenixbb mailing list