[phenixbb] pseudo-translational symmetry refinement

Pavel Afonine PAfonine at lbl.gov
Tue Apr 29 17:25:52 PDT 2008

Hi Zhiyong Ren,

> The structure was solved by auto-sad at 2.7A. However, the r-factor can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any manipuliations we can do to deal with this situation?

At 2.7A I would use this strategy:

I would also try to use SA: "simulated_annealing=true"

If this will result in over-fitting or any sign of it, then I would play 
with target weights: wxc_scale (manually), or just let phenix.refine to 
find the optimal one using "optimize_wxc=true" keyword.

Next, I would let phenix.refine fill the water, but since the resolution 
is rather low I would tighten water picking criteria.

Try to run it through phenix.autobuild too.


More information about the phenixbb mailing list