[phenixbb] refinement of coordinated ions

Pavel Afonine pafonine at lbl.gov
Sun Oct 18 12:59:38 PDT 2015

Hi Irina,

meaningfulness of what you are trying to do mostly depends on data 
resolution. If data resolution is better than 3A then it is all good to 
refine individual isotropic B factors of all atoms. Since Os is 
electron-rich compared to the rest it may be good to refine anisotropic 
B for Os only (isotropic for the rest). I don't think you need to refine 
group B. Yes, you need to refine all - coordinates, B and likely 
occupancies of Os. Error in one of these parameters will go into other 
parameters. R-factors 25/34 is not good so I guess you are using 
incorrect refinement strategy and/or model parametrization.

If you send me model and data and ligand cif files (if any) off-list I 
might be able to suggest something that may work better.

A good approach is to run with all defaults first, and then if not 
satisfied with results try to find a better way.

Good luck,

On 10/11/15 09:18, Irina PROKHOROVA wrote:
> Hello,
> 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?
> Irina

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