[phenixbb] peptide ligand refinement problems

Nigel Moriarty nwmoriarty at lbl.gov
Tue Aug 20 13:52:32 PDT 2013


can you send me the files directly with only the two residues if you desire.

Cheers

Nigel

NB. Any files sent to me will be held in strictest confidence.



On Tue, Aug 20, 2013 at 1:40 PM, Mengbin Chen <mengbinc at sas.upenn.edu>wrote:

> 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
>
> _______________________________________________
> 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
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