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Re: [modeller_usage] Distance Restraints: are they working?

> I've described each restraint like this:
> rsr.make_distance(at['SG:1'],at['SG:4'],aln,spline_on_site=False,restraint_group=physical.xy_distance,maximal_distance=5)
> I just want both atoms to be, in a maximal distance of 5A.

OK, but that's not what make_distance() does. It builds a set of
distance restraints to constrain the model to look like the template(s),
and thus is primarily used for building homology derived restraints.
This particular example will constrain the SG:1 to SG:4 distance to its
value from the template (if residues 1 and 4 in the model are both
aligned with a template). To avoid creating too many restraints, if the
distance in the template is greater than maximal_distance (5A in this
case) the restraint is not created.

What you want is something like that at

For this particular example, the following should do what you want,
assuming you want to constrain the atom-atom distance to be 5A +/- 0.1A
with a Gaussian distribution (harmonic restraint):

                       mean=5.0, stdev=0.1))

If you instead want the atom-atom distance to be no greater than 5.0A,
you can use forms.upper_bound rather than forms.gaussian. See

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage