I am so far using a distance restraint, which is satisfy if the
particules are below the distance, down to 0, ie contact. Is that
correct? Then what is the point of the std_dev if it is anything below
distance that score lowest?
No, this is a harmonic distance restraint. It keeps the distance to 10
angstroms with a standard deviation of 1.
However, I would like to have a function with a minimal score if the
particules are at the give distance, with some stdev. I probably need to
use the DistancePairScore function. But how to do that in XML format?
Restrainer only supports a subset of IMP restraints, and it is designed
to work with experimental types (e.g. "pulldown" or "yeast 2-hybrid")
rather than mathematical forms (e.g. "harmonic"). If you want more
flexibility, you'll have to write Python scripts instead. That said,
restrainer's distance restraint should do exactly what you want here.