[phenixbb] refinement of a ligand with alternate conformations in one region but not the other.

Pavel Afonine PAfonine at lbl.gov
Mon May 25 17:20:19 PDT 2009

Hi Pascal,

> Last question is it possible that for the variable regions I may end 
> up with a sum of occupancies that is not 1 while for the fixed region 
> it might end up being one?

the way it is implemented in phenix.refine - no, the sum of occupancies 
of atoms in alternative conformations is constrained to be 1.

However, if your constrained group has only one selection, for example:

refinement.refine.occupancies {
     constrained_group {
        selection = chain A and resseq 123

than refined occupancies for all atoms in entry number 123 in chain A 
will be refined to a number between 0 and 1 and will be equal to each 
other. Sometime it is useful for refinement of partially occupied ligands.


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