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

Pavel Afonine pafonine at lbl.gov
Thu Sep 9 17:38:13 PDT 2010

  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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