The principle difference between occ=0 and omitting the atom entirely is
that occ=0 atoms exclude bulk solvent. Or at least they do for typical
operation of contemporary refinement programs. So, by defining occ=0
you are forcing all map voxels within ~0.6A or so of your invisible
atom to
Hi, all,
I am glad to see these matters being discussed. I think we all believe that
protein crystallographers should be concerned with producing models that
modelers and chemists can respect and use.
Schrödinger spends a lot of time thinking about ligands; its refinement
program, PrimeX,
Hi James,
a remark: different programs may treat occ=0 differently. In phenix.refine
(phenix.maps, etc) atoms with zero occupancy will be ignored for
bulk-solvent mask calculation, unless you ask to do otherwise. For example,
this means that if you want to calculate a ligand OMIT map both options
