Actually, I have 2 practical problems (see attachment) which I haven't been able to deal with so far using phenix.refine (latest version).
Ligand A shows 2 stacking modes (A1 and A2) above an FMN cofactor. The A2 conformation also overlaps partially with another partially occupied ligand B. How do I couple the occupancy refinements of these interrelated ligands? Until now, I solved it by refining the occupancy as if ligand A has 3 modes; A1, A2 and A3 (= B). Otherwise, ligand B is always pushed out of its density due to the anti-bumping restraints. This is high res data (~1.5 A), so pretty decisive about atomic positions.
The same question goes for the coupling of conformation C1 of an Ile residue and water D on one hand, and conformation C2 of that Ile on the other hand.
Thus far I've only been able to define these relations in SHELXL, but it's not entirely clear to me how to do this in phenix.refine (which I prefer for this dataset).
Many thanks in advance,
Jonathan Elegheert
PhD Student
L-ProBE, Ghent University
Belgium
Pavel Afonine wrote:
Ralf,
it's not that uncommon. See for example:
http://www.rcsb.org/pdb/files/1ejg.pdb
Also, you may want to couple partially occupied residue's side chain with partially occupied water.
Pavel.
On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote:
Hi Tassos,------------------------------------------------------------------------
However, I want to refine my MET residues in double conformations, one
as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
to start with.
In addition to what Pavel wrote: I just tried out the AMET BMSE mix
without giving any manual atom selections, and it works fine for me.
(P.S.: I'm thrilled to see this use of the
multiple-conformers-with-mixed-residue-names feature,
since it was a lot of work.)
Ralf
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