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Re: Regarding modeller usage



Dear Senthil,

This routine selects  a  4 residue long loop, and builds it  in an  'ab initio
' style: initially the loop segment is completely removed, than it is built
from scratch.

I would suggest to build more loops (e.g. ENDING MODEL= 50 ) and select the one
with the lowest Modeller energy score (you can find it in the header of the
coordinate files).

best
Andras

R Senthil Kumar wrote:
> 
>  Dear modeller users,
> 
>    After i am getting the initial model using modeller if any bad regions
> are there(loop regions) i am using the following module for refinement.
> 
> INCLUDE
> SET SEQUENCE = 'topmodel'
> SET MODEL = 'topmodel.pdb'
> SET STARTING_MODEL = 1
> SET ENDING_MODEL = 2
> CALL ROUTINE = 'loop'
> 
> SUBROUTINE ROUTINE = 'select_atoms'
>     PICK_ATOMS SELECTION_SEGMENT = '0:' '3:', SELECTION_STATUS ='initialize'
>     RETURN
> END_SUBROUTINE
> 
> Actually i want to know whether the following module does the refinement
> of the loop or the loop building with some other loop.Please tell what is
> the exact use of this module.Expecting for your reply.
> 
>                                                Yours friendly,
>                                            Senthil kumar.R

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras