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

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. Pavel.