[phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map
fn1 at rice.edu
fn1 at rice.edu
Thu Sep 9 17:32:50 PDT 2010
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?
>
>
>
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