[phenixbb] scattering_table in phenix.real_space_refine

[Keitaro Yamashita]

Dear PHENIX developers,

For the refinement of CryoEM structure, I changed scattering_table to
electron from default (n_gaussian in phenix-1.13), but the resultant
coordinates and ADPs were exactly same while map-model CCs were
improved. Looking into the code, I noticed scattering_table is not
passed to the ADP refinement code
(mmtbx.refinement.real_space.adp.real_space_group_adp_refinery_via_reciprocal_space)
and xray_structure is newly constructed from a pdb_hierarchy object;
therefore a default table in
scattering_type_registry() (which is n_gaussian) is always used. Is
this an intended behavior?

I modified the code to use the scattering table of electron in ADP
refinement, and CCs were improved (CC_mask 0.7566 to 0.7813; both
evaluated with scattering_table=electron).

Best regards,
Keitaro