[phenixbb] ADP settings for protein and solvent
Pavel Afonine
PAfonine at lbl.gov
Mon Mar 23 11:18:59 PDT 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
>
>
More information about the phenixbb
mailing list