[phenixbb] Group ADP refinement
pafonine at lbl.gov
Tue Jul 23 12:20:01 PDT 2013
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..
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,
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