Hi,

I have a question about the handling of restraints in the individual B-factor refinement routine.

What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...)

My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e.

ATOM   2724  C01AINH I   1      27.808  26.376  23.301  0.50 27.77      I    C
ATOM   2733  C01BINH I   1      30.898  22.496  17.340  0.50 22.15      I    C
...

vs. scenario B) where the same ligand is modeled as 2 different residues
ATOM   2724  C01 INH I   1      27.808  26.376  23.301  0.50 27.77      I    C
ATOM   2733  C01 INH I   2      30.898  22.496  17.340  0.50 22.15      I    C
....

Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of?

Many thanks for any input.

Cheers

        Carsten