[phenixbb] (Anisotropic ADP vs. isotropic ADP) coupling with occupancy refinement

Pavel Afonine pafonine at lbl.gov
Tue Apr 12 08:24:46 PDT 2011

Hi Young-Jin,

> I am just wondering while I was taking a small molecule X-ray course.
> I used to run refinement with anisotropic ADP when it is high 
> resolution about better than 1.5 or 1.6 A. My question is when you do 
> this with occupancy refinement, does phenix.refine take care the 
> alternative conformations with aniostropic ADP (I guess so) even at 
> low occupancy? 

occupancy refinement in phenix.refine:

> Due to lack of electrons (scattering factor), I experienced that small 
> molecule refinement applies Anisotropic ADP for the atoms (about more 
> than 2 e- in occupancy) while applying isotropic ADP for the less 
> occupied atoms (in an alternative conformation). Would it help if we 
> apply this method to our macro molecular system when you have residues 
> that have low occupied alternative residues? Is so, could we have 
> something like script or else either to modify a pdb file or to make 
> this in consideration during refinement?

I'm sure I see the rationale here: why partially occupied atoms should 
be assumed moving isotropically while fully occupied atoms should be 
refined with anisotropic ADPs ? Am I missing something?


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