On 3/30/10 7:19 AM, abdullah ahmed wrote: > Is there a way to give preference to (or up-weight) one set of > restraints over another? > I have made distance restraints (group=physical.xy_distance) as well as > "restraint_type = stereo" and would like for the distance restraints to > be satisfied even if they cause violations of the "stereo" restraints.

Certainly - all of the commands that calculate or optimize the total energy/score of the system take a schedule_scale argument. This is a physical.values object, which can scale different groups of restraints. For example, to more strongly weight the xy_distance restraints you could say

sel.energy(schedule_scale=physical.values(default=1.0, xy_distance=10.0))

See also http://salilab.org/modeller/9v7/manual/node241.html for an example.

Ben Webb, Modeller Caretaker