Thanks Pavel!
I am now running your script.
引用 Pavel Afonine
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?