[phenixbb] TLS + anisotropic ADP mixed refinement

Scott Classen sclassen at lbl.gov
Mon Feb 2 16:16:12 PST 2009

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.

So my strategy is:


adp.individual.isotropic = "not Chain A"
adp.individual.anisotropic = "Chain A"
adp.tls = "Chain B"
adp.tls = "Chain D"

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%

have I specified my refinement with bad syntax? or is this even  
possible with phenix.refine? I can submit more of the log file if  
you're interested.


Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Berkeley, CA 94720
C) 510.206.4418
O) 510.495.2697
Beamline) 510.495.2134

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