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

Hi Pavel, I have a further question on combining the map coefficients. Since I did the density modification for the multi-start coordinates, I have three columns FDM, PHIDM, FOM to be combined. What shall I add to the following script? http://cci.lbl.gov/~afonine/mssa2/run.py Thanks! Fengyun Quoting Pavel Afonine :

Hi Fengyun,

no problems, here is the updated script and inputs files to illustrate how it works:

http://cci.lbl.gov/~afonine/mssa2/

All it needs is a bunch of PDB files and corresponding map coefficients.

Let me know if you have any questions.

Pavel.

On 9/9/10 7:48 PM, [email protected] wrote:

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Hi Pavel,

The script works fine. I hope you could slightly revise the script for me.

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. Thanks! Fengyun

引用 Pavel Afonine ：

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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.

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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?