Question about restraints in individual B-factor refinement
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
Hi Carsten, for the refinement of b-factors there is no difference between two options. We use the sphere b-factors restraints which are calculated based on interatomic distances and the information about alternative conformations is not used at that point. However if you refine the coordinates, the difference is significant: if you refine it as two separate residues then they will "see" each other for non-bonded interactions term calculation and hence will be pushed apart. Please let me know if you still have questions! Pavel. Schubert, Carsten [PRDUS] wrote:
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
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participants (2)
-
Pavel Afonine -
Schubert, Carsten [PRDUS]