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
========================================================
