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

Thanks! With the multi-refined models, how can I make an average map for all the models? Can I do this in phenix? Fengyun 引用 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?