[modeller_usage] Extend the helix

["Narasimhamurthy." <>]

dear all,

i am modeling a hepta-helical membrane protein.
I want to elongate couple of my helices one-two loop more. 
Say for example, I have already modelled a helix  1-35
 and extend it up 
45 residue. I am using 

 SUBROUTINE ROUTINE = 'special_restraints'
   MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '35:' '45:'
   RETURN
 END_SUBROUTINE


It works but in that process, it always disturbs the helical conformation 
at the boundary, in this example, for 34-36 residues. 

There ia a trivial way to use special restriant, to model alpha 
helix for whole 1-45 
residue, but I dont want to do that since, this way,  
all the conserved kinks and helical bent would be lost.

Is there any way to extend the helix appropriately. 

Thanks,

T. Narasimhamurthy
Bioinformatics Center
IISc Bangalore