[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
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:
> 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)
> - 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.
>> 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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