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

[Pavel Afonine]

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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