Hi Katya,

I'd like to refine group adps for my protein

there are three modes for refinement of group ADP: one or two B per residue and user selected groups. The default is one ADP per residue. The example below will do it: phenix.refine model.pdb data.hkl params.txt where the file params.txt contains the following lines: refinement { refine { strategy = *individual_sites rigid_body individual_adp *group_adp tls \ occupancies group_anomalous adp { group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection } } } Since one HOH molecules is considered as one "residue", there will be one refinable B per HOH, which is equivalent to refinement of individual ADP. Or (probably better): refinement { refine { strategy = *individual_sites rigid_body *individual_adp *group_adp tls \ occupancies group_anomalous adp { individual { isotropic = water anisotropic = not all } group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection } } } Pavel. On 3/23/09 11:01 AM, Katya Heldwein wrote:

Hi,

I'd like to refine group adps for my protein and individual adps for the solvent while refining coordinates for all atoms. How can I set that up in the command line mode?

Katya