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

Young-Jin Cho yjcho at brandeis.edu
Tue Apr 12 07:59:50 PDT 2011

Dear phenix developer and users,

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? 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
Any information or comments are welcome.

Thanks in advance,

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