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