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[modeller_usage] modelling multiple loops



Dear modellers,

I have searched the archives of the discussion forum for this and found a
few questions, but no answers.  I wish to impart the template structure to
a sequence exactly, and select only the loops for refinement. I am using
modeller 7v7, and have not switched to 8 yet.  I would be interested in
ways to do this for both versions, but most interested in 7v7. Currently,
I use a snippet of top script taken from one of the examples that looks
like this:

SUBROUTINE ROUTINE = 'select_atoms'
 PICK_ATOMS SELECTION_SEGMENT='100:' '105:', SELECTION_SEARCH='segment', ;
             PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ;
             SELECTION_FROM='all', SELECTION_STATUS='initialize'
  RETURN
END_SUBROUTINE

but I have no idea how to extend this to do multiple loop modelling all at
the same time... i.e. segment 100-105, 158-164, 200-206, etc...  all at
once.  I've tried lots of things, but I have not been able to figure out
the syntax of top too well. I saw an email in the archive by Obdulia
Rabal, who used something like


SUBROUTINE ROUTINE = 'select_loop_atoms'
  READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE,
ADD_SEQUENCE = off
  SET SELECTION_STATUS = 'INITIALIZE'
  SET SELECTION_MODE = 'ATOM'
  SET SELECTION_SEARCH = 'SEGMENT'
  SET SELECTION_FROM = 'ALL'
  SET GAP_EXTENSION = 2 2 # gaps are extended for two residues in both
                          # directions to get loops (insertions &
deletions)
  PICK_ATOMS SELECTION_SEGMENT = 'LOOPS'
  RETURN
END_SUBROUTINE

but he complained that the program still selected all the atoms for
refinement, instead of only the loop portions.  I've finally resorted to
modelling every single loop separately, but this is no fun at all, and is
time consuming. Can someone help please?

Thanks,
David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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