Hello De-Feng Li,
first of all sorry for changing the subject: I think starting a new thread
from an existing one may hamper people who are going to search the
archives in the future, therefore it is good practice to give it its
separate subject line, even though it certainly is be very closely
related.
In your case you can refine two peptides each with an occupancy of 0.5,
one for each direction.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 29 Apr 2009, lidefeng wrote:
> Hi everyone,
>
> Following Chandrika's question, what should I do if one peptide chain crosses a two-fold crystallographic symmetry axis?
> The peptide is not symmetric and the sidechain of one Se-Met (two after CS operation) is determined and conformed by MAD.
>
> Your sincerely
> ????????De-Feng Li
> [log in to unmask]
> ??????????2009-04-29
>
> Defeng Li, Dr.,
> Email: [log in to unmask]
> National Laboratory of Biomacromolecules,
> Institute of Biophysics, Chinese Academy of Sciences,
> 15 Datun Road, Chaoyang District,
> Beijing 100101, China
>
>
> ======= 2009-04-29 17:02:00 You writed in your letter?=======
>
>> Hello everyone,
>>
>> My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve :
>>
>> First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ?
>>
>> Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ?
>>
>> Thanks,
>> Chandrika
>
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