[modeller_usage] Extend the helix

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