[phenixbb] R-free set for low resolution

Pavel Afonine PAfonine at lbl.gov
Tue Mar 30 10:24:00 PDT 2010


> I do have a data is at very low resolution, so only possible to do 
> rigid body refinement.

it depends what you call "low resolution". In small molecule 
crystallography ~1A resolution is "low resolution" (Acta Cryst. (2007). 
D63, 160-170). So, without knowing what the resolution of your data is I 
can't really tell whether you need to refine individual anisotropic 
B-factors or the whole model as just one TLS group.

Anyway, if by "low resolution" you mean what comes to my mind this very 
minute, you can still try:

- Simulated Annealing refinement in torsion angle space;
- Highly restrained refinement of individual coordinates;
- Optimize weights against Rfree.
- You may need to use secondary-structure restrains (available in recent 
PHENIX versions).
- combined refinement of TLS+individual or group B-factors;
- Highly restrained individual ADP refinement;
- Simple group ADP refinement (where the size of groups depends on 
resolution or/and data-to-parameters ratio)
- Optimize target weights.
- use if available.
- optimize mask parameters (r_solvent and r_shrink) using 
optimize_mask=true (this is will done automatically in future versions 
of phenix.refine).
Multi-Start SA:
- people find it useful (Andrei Korostelev, Martin Laurberg, and Harry 
F. Noller "Multistart simulated annealing refinement of the crystal 
structure of the 70S ribosome". PNAS 2009 106:18195-18200).

Good luck!
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