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

[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, fn1 at rice.edu 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 <pafonine at lbl.gov>：
>
>>  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?
>>
>>
>>
>
>
>