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

[fn1 at rice.edu]

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 <pafonine at lbl.gov>：

>  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?
>
>
>