Re: [modeller_usage] Restraining Secondary Structure

On 10/17/2011 01:27 AM, bharat lal wrote: > I am modelling a sequence in which I am restraining some portions of the > sequence to be helix as I have copied that sequence from a known > structure. But I want to ask whether the same restrained sequence would > also be same in real or not. What is the basis of restraining the > structure to be helix or sheets ??

Modeller's secondary structure restraints are derived from "ideal" helix or strand structures, so they will simply try to make your structure look like these, regardless of whether the "real" structure is a helix or beta strand.

See http://salilab.org/modeller/9.10/manual/node219.html

Ben Webb, Modeller Caretaker