[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
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
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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