Re: [phenixbb] ADP settings for protein and solvent

23 Mar 2009

      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

Re: [phenixbb] ADP settings for protein and solvent

Pavel Afonine