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