[phenixbb] refinement in low resolution

Pavel Afonine PAfonine at lbl.gov
Tue Dec 15 09:14:51 PST 2009

> I am trying to refine the model in low resolution and there are 
> multimer in the asu.
> I did rigid body refinement after MR , molecule did not move much and 
> R/Rfree stays 45 %

Did you define multiple rigid groups for rigid body refinement? If not, 
then it's not too surprising that it didn't move much since the MR 
programs typically do a good job on rigid body refinement anyway.

So, use "sites.rigid_body" keyword for this.

> If I do simulated annealing or any type of refinement (group_adp), 
> Rfree is high and R goes down, but
> the if do the superposition of the monomer, rms is 1.5 to 1.8.

Try SA in torsion angle space (main.simulated_annealing_torsion=true). 
At this resolution you may need to refine one ADP per group (say per 
residues or any bigger selected group of atoms). Also, use TLS. Use NCS 
if available, and you can defined it's strictness by adjusting 
appropriate weights.


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