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.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle