[modeller_usage] Restricting to Strand

[John Penniston <>]

I've been trying to restrict portions of my molecule to be alpha helix 
and other portions beta strand. I did it using the following addition to 
my special_restraints subroutine:
#This one is to put helices & sheets in the PMCA insert
  SET ADD_RESTRAINTS = on
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '254' '274'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '293' '302'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '275' '285'

The alpha restraints work fine, but the strand restraint seems to have 
no effect at all. When I look at a Ramachandran plot of the region which 
was supposed to be beta strand, the angles are all over the plot. I 
noticed on looking over the history of this forum that a French group 
had this same problem in 2002, but I can't find any solution to it.

This difficulty has happened in a number of different circumstances.

John T. Penniston, Ph.D.
Lab of Membrane Biology
Massachusetts General Hospital
Boston, MA, USA