[phenixbb] Question about restraints in individual B-factor refinement

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Fri May 25 08:44:44 PDT 2007


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
ATOM   2733  C01BINH I   1      30.898  22.496  17.340  0.50 22.15      I

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
ATOM   2733  C01 INH I   2      30.898  22.496  17.340  0.50 22.15      I

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.



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