[phenixbb] Group ADP refinement

joseph Lyons josephalyons at gmail.com
Tue Jul 23 08:36:08 PDT 2013

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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