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?