[phenixbb] refinement of coordinated ions

Irina PROKHOROVA prokhoro at igbmc.fr
Sun Oct 11 09:18:46 PDT 2015


I have many Osmium ions in my structure. They have 6 coordinated ammonium groups and I would like to refine the B-factors for them: one B-factor for Os in each residue and one B-factor for all 6 ammonium groups in each residue.

For this I have chosen *group_adp with following syntax

    adp {
     group_adp_refinement_mode = one_adp_group_per_residue \
                                  two_adp_groups_per_residue *group_selection
      group = chain O and element Os
      group = chain O and element N

I wanted to refine only B-factor for Osmiums in this refinement. To avoid the bias from previously refined values of B-factor I presetted B-factors for all Osmiums to 50.

As a result I got the change of B-factors for all residues in the model to the same value (which probably means that all model was refined as one group) and R-free increased from 0.25 to 0.34.

What should be the correct syntax for this refinement?

Should I also refine ions coordinates for a good refinement of B-factors?

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