[phenixbb] Simulated anneal

Ed Pozharski epozh001 at umaryland.edu
Tue Nov 13 17:50:38 PST 2012

Your R-values are already good enough (but make sure the density is 
traced correctly)

No, simulated annealing does not always reduce Rfree.  You just 
demonstrated that it does not.

And no, not only it is not necessary to use simulated annealing in the 
final stages, it is completely counterproductive. You are supposedly 
already near the global minimum.

On 11/13/2012 08:33 PM, Qiang Chen wrote:
> Hi all,
> I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use
> Molprobity to check the structure. The clash score is 100th and Molprobity
> score is 99th.  I was suggested to run simulated anneal to help reduce
> Rwork and Rfree. I tried Cartesian and Torsion and different seed. The
> best result I got is: torsion anneal, start_temp=2500,final_temp=300,
> random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model
> and found that some places in a domain were not correctly traced. The
> density for that domain is not good and have several flexible loops.  My
> question is: does simulated anneal always work and reduce Rwork/Rfree?  At
> the final stage of refinement, does it necessary to use simulated anneal
> again?
> Thanks!
> yamei
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