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

fn1 at rice.edu fn1 at rice.edu
Fri Oct 1 07:09:33 PDT 2010


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 <pafonine at lbl.gov>:

>  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?
>>>
>>>
>>>
>>
>>
>>
>
>
>






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