[phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map

[Pavel Afonine]

  Hi Fengyun,

- to run many SA with different random seeds:

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

To create even broader variety, I would slightly shake the starting model:

for random_seed in random_seeds:
   phenix.refine model.pdb data.mtz simulated_annealing=true 
main.random_seed=random_seed output.prefix=random_seed 
modify_start_model.sites.shake=0.3

Note, you will need to filter the outliers - refined models that have 
significantly higher R-factors compared to the rest.

> I read on the paper that they use CNS (model_map.inp) to calculate the 
> avarage sigmaA-weighted 2fofc map. Right now I have set up the 
> simulated annealing with different random seeds. I wonder whether 
> phenix could calculate the average map with the multiple coordinates 
> from different starts?