[phenixbb] a question on starting temperature of Phenix refine simulated annealing

Pavel Afonine pafonine at lbl.gov
Mon Nov 21 17:28:56 PST 2011

Hi Dialing,

>> The default value of the starting temperature of Phenix refine 
>> simulated annealing is 5000. At this temperature all the protein 
>> structure will be destroyed.

it depends on parametrization. In phenix.refine you can use 10000-15000K 
and the model will not explode. Simply try it - that's the best way to 
find out.

>> Will you please explain why we start the simulated annealing at 5000?

As with ~500-600 parameters in phenix.refine, the defaults are set to 
the values that are "good in average, most of the time". If you want to 
do aggressive SA refinement (eg.: Korostelev et al, PNAS 2009), then 
5000K is too low, and 10000 may be way better. If you want to get 
multi-start SA averaged map for a 1A resolution model, then 5000 is too 
high, and 500-1000K is a better start.


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