[phenixbb] Multistart simulated annealing refinement

Pavel Afonine pafonine at lbl.gov
Wed Dec 8 11:03:47 PST 2010

  Hi Joe,

to do this you can simply compose a script in whatever language you 
prefer, which prototype looks like this:

for random_seed in random_seeds:
    phenix.refine model.pdb data.mtz main.simulated_annealing=true 
main.random_seed=random_seed output.prefix=str(random_seed)

where random_seeds is the array of random seeds, containing ~100 elements.

If you have multiple CPUs then you can obviously split it among them.

I'm not sure we have GUI for this and I guess this kind of task is best 
run from the command line anyway.


On 12/8/10 10:47 AM, Joseph Noel wrote:
> Hi All,
> I'm sure this has already been addressed but is there a way through the PHENIX GUI to carry out multistart simulated annealing refinement either with different starting seeds (velocities) or temperatures automatically or does one have to start a fresh run each time?
> Thanks!
> Joe
> P.S. Similar procedure as described in the PNAS paper: "Multistart simulated annealing refinement
> of the crystal structure of the 70S ribosome"

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