Have you tried adding an altloc to the pdb (I believe it's column 18 in the pdb file format)? If you make one conformer A and the other B then phenix will know that they don't occupy the same space at the same time and keep the atoms in their relative locations.

I hope this helps,
Katherine

On Mon, Jan 28, 2013 at 6:54 AM, Damian Niegowski <Damian.Niegowski@ki.se> wrote:
Hi all,

I´m trying to refine a dataset which seems to have two different ligands with partial occupancy in the same active site. How do you refine this? When I put
them over each other with say 50/50 occupancy Phenix either moves the ligands apart or mashes the two molecules into one strange composite
ligand. In Refmac this works without any special settings, it accepts the occupancy distribution between the ligands. Any ideas?

Regards,

Damian


Damian Niegowski Ph.D.
Institute of Medical Biochemistry and Biophysics
Karolinska Institutet
Scheeles väg 2
171 77 STOCKHOLM
e-mail: damian.niegowski@ki.se
phone: 0046 8 524 876 33
fax: 0046 8 736 04 39

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