Hello Chandrika,
you can either set the occupancy of the molecule to 0.5 and refine it as
a whole molecule or leave the occupancy at 1, refine only one half of the
molecule and let the symmetry operator do the rest.
Chemically the first way makes more sense to me: even though the PEG
molecule sits on the symmetry axis, it may nevertheless not follow the
two-fold symmetry. The lattice is built by the macromolecule, and much can
happen in the space inbetween - even though in that case you would
probably have to deal with disorder.
When you deposit the structure you should do it depending on which of the
two above methods you chose.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 29 Apr 2009, Chandrika Deshpande wrote:
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
