[phenixbb] a question on starting temperature of Phenix refine simulated annealing
pafonine at lbl.gov
Mon Nov 21 17:28:56 PST 2011
>> 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
>> 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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