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