Hi Fengyun, I won't comment about whether averaging these maps is a good thing to do since I've never done it myself and never heard about someone doing this. What that script does is it just reads in a bunch of MTZ files and averages the maps (map coefficients) taken with selected labels. So may be you just need to change the label name so it takes the right one.. Pavel. On 10/1/10 7:09 AM, [email protected] wrote:

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:

...

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 ：

...

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?