If you have a ligand sitting on a four-fold axis, let's call the four
residues 1, 2, 3, 4. Residues 2, 3, and 4 are generated by the
refinement program using symmetry so the occupancy of 1 should be set to
0.25 to generate a total occupancy of 1.0.
Now you say that residue 1 has four conformations. Let's call them
1.A, 1.B, 1.C and 1.D. The sum of the occupancies of these
conformations have to add up to the occupancy of 1. If their
occupancies are equal you have to set them to 0.0625 (or 1/16).
The refinement program will generate 2.A, 3.C and all the rest.
Dale Tronrud
On 2/6/2016 11:41 AM, Appu kumar wrote:
> Dear CCp4 Users,
> I am refining a tetrameric protein which has ligand placed at the center
> axis. There is one tetramer in ASU. I added the ligand with 0.25
> occupancy and performed the refinement using both phenix and refmac.
> Refinement leaves lots of green density around the ligand inferring that
> there may be four different conformation of the ligand. When i made four
> different conformation of ligand (each with 0.25 occupancy) and started
> refinement, there is lot of clashes in ligand itself. Is there a ways to
> refine the four different conformation of ligand with different
> conformation with 0.25 occupancy avoiding clashes in ligands?
>
> I appreciate your input, suggestions on the refinement.
>
> Thank you
> Appu
|