[phenixbb] scattering_table in phenix.real_space_refine

Keitaro Yamashita keitaro.yamashita at bs.s.u-tokyo.ac.jp
Mon Mar 25 07:06:59 PDT 2019

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
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,

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