Hi Keitaro, this sounds like a bug, thanks for reporting! Could you please send me the code diffs off list? Thanks, Pavel On 3/25/19 07:04, Keitaro Yamashita wrote:

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]