[phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map - WORKING EXAMPLE
pafonine at lbl.gov
Thu Sep 9 17:38:13 PDT 2010
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
- 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:
(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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