[phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map - WORKING EXAMPLE
pafonine at lbl.gov
Thu Sep 9 23:31:32 PDT 2010
no problems, here is the updated script and inputs files to illustrate
how it works:
All it needs is a bunch of PDB files and corresponding map coefficients.
Let me know if you have any questions.
On 9/9/10 7:48 PM, fn1 at rice.edu wrote:
> Hi Pavel,
> The script works fine. I hope you could slightly revise the script for
> Since right now, I could run the multi-sa on different nodes at the
> same time. So I could get the refined models in the name of sa-#.pdb
> within a short time.
> So I could begin with the different models and combine them to
> "all.pdb" and calculate the average map after that. But I don't know
> how to revise the run.py to do that.
> Wait for your help.
> 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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