On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine
In the example below I see residue #30 has two conformations, A and B, and they are automatically constrained-refined in phenix.refine and their sum adds up to 1 (0.52+0.48). Same for residue #451.
Although I see that occupancy of "AGLU A 30 " = occupancy of "AALA A 451 ", it is not guaranteed in refinement, since otherwise that would be a double-constrained refinement:
constraint #1: occupancy(AGLU A 30) + occupancy(BGLU A 30)=1 constraint #2: occupancy(AGLU A 30) = occupancy(AALA A 451)
which is not currently available.
Wait, now I'm confused too - isn't this the entire point of the constrained_group setting? For example, the parameters below: refinement.refine.occupancies.constrained_group { selection = "chain A and resseq 30" selection = "chain A and resseq 451" } If both selections have alternate conformers A and B, and the occupancies for A and B are both 0.5, what would phenix.refine do? -Nat