On 10/09/2013 04:23 AM, Lalith Kumar wrote: > I want to build a complete structure for a protein that has partial > crystal structure available but with out any deviations for the side > chains of residues that are copied from template (crystal structure). > Please let me know if there is any script available for restraining side > chains of these residues.

Just remove those residues from the selection - then they won't be moved at all: http://salilab.org/modeller/9.12/manual/node23.html

Ben Webb, Modeller Caretaker