[phenixbb] TLS + anisotropic ADP mixed refinement

Pavel Afonine PAfonine at lbl.gov
Mon Feb 2 16:29:51 PST 2009

Hi Scott,

> I am trying to perform refinement on a model with three chains (two  
> protein and one DNA... plus water, Cl, and a few other solventy  
> things). The B factors for chain A are generally better than for the  
> other two and I am thinking that the resolution (1.8Å) warrants  
> attempting anisotropic individual adp refinement for at least chain A,  
> and then using TLS for the other two.

You can do it in phenix.refine.

> So my strategy is:
> *individual_sites
> *individual_adp
> *tls
> *occupancies
> adp.individual.isotropic = "not Chain A"
> adp.individual.anisotropic = "Chain A"
> adp.tls = "Chain B"
> adp.tls = "Chain D"

This looks good too.

> Previously the model had only been refined with individual isotropic  
> adp (no TLS). The starting model has an r_work=0.2079 and  
> r_free=0.2427. With this new aniso/TLS strategy in the first  
> macrocycle when it gets to the initial TLS refinement it completely  
> blows up with r_work and r_free both going up to 60%

I have no idea why this happens. The only way I can answer is to 
reproduce this problem myself. Could you please send me the data, model 
and the exact command you used (including parameter files, if any).


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