[phenixbb] Group ADP refinement

[Pavel Afonine]

Hi Joe,

hard to tell without looking at the files... Could you please send me 
the eff and pdb files off list (I don't need the data file as I can 
simulate it!), then I will be able to comment more meaningfully?

 From your description of what you are trying to do it should just work 
fine, so yes, I need to look at the files..

Thanks,
Pavel

On 7/23/13 8:36 AM, joseph Lyons wrote:
> Dear phenixbb.
>
> I am currently running phenix 1.8.2-1309.
>
> My goal is to use group ADP with 2 b-factors per residue for the 
> protein and individual b-factors for solvent.
>
> However, this does not seem to be working even though the system seems 
> to recognise what I want to do. The refinement output gives what looks 
> like individual b-factor refinement...
>
> ================== Extract refinement strategy and selections 
> =================
>
> Refinement flags and selection counts:
>   individual_sites       =  True (4048 atoms)
>   torsion_angles         = False (0 atoms)
>   rigid_body             = False (0 atoms in 0 groups)
>   individual_adp         =  True (iso = 127 aniso = 0)
>   group_adp              =  True (3921 atoms in 967 groups)
>   tls                    = False (0 atoms in 0 groups)
>   occupancies            = False (0 atoms)
>   group_anomalous        = False
>
> In troubleshooting it appears that with Group ADP with 2 b-factors per 
> residue, the solvent B-factors are not being refined, i.e., remaining 
> at the Wilson B that I set previously. For Group ADP with 1 b-factors 
> per residue - everything appears to refine OK.
>
> Any help would be greatly appreciated,
>
> Regards,
>
> Joe
>