Dear Tim Gruene,
But how to illustrate the other one half occupancy of peptide?
Disorder ?
Your sincerely
De-Feng Li
lidef...@moon.ibp.ac.cn
2009-04-30
Defeng Li, Dr.,
Email: lidef...@moon.ibp.ac.cn
National Laboratory of Biomacromolecules,
Institute of Biophysics, Chinese Academy of Sciences,
15 Datun Road, Chaoyang District,
Beijing 100101, China
======= 2009-04-29 10:55:00 You writed in your letter：=======
>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
>> ????????lidef...@moon.ibp.ac.cn
>> ??????????2009-04-29
>>
>> Defeng Li, Dr.,
>> Email: lidef...@moon.ibp.ac.cn
>> 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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