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

fn1 at rice.edu fn1 at rice.edu
Thu Sep 9 17:56:16 PDT 2010

Thanks Pavel!

I am now running your script.

引用 Pavel Afonine <pafonine at lbl.gov>:

>  Hi Fengyun,
> my previous email actually doens't answer your question - I realized  
> this after I pushed Sent button -:)
> To really answer your question I just wrote a Python script that  
> does the following:
>   - run multi-start Simulated Annealing,
>   - combine all refined models into one multi-model PDB file (models  
> separated by MODEL-ENDMDL records), and
>   - compute averaged 2mFo-DFc map.
> The complete working example is here:
> http://cci.lbl.gov/~afonine/mssa/
> You have two options at this point:
> - take this example, slightly change inputs by editing the run.py  
> file (change input data and model file names, number of SA runs,  
> etc) and run it as following:
> phenix.python run.py
> (since I spent 15 minutes on writing this script it's obviously not  
> thoroughly tested or parameter-optimized, although I believe it  
> should do the job right)
> or
> - wait a few days for one of the next PHENIX nightly builds where  
> the above script will be available as a user-friendly either  
> phenix.multi_start_sa command or an option of phenix.maps (I haven't  
> decided yet what is better).
> Let me know if you have any questions.
> Pavel.
>> 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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