On 02/05/2014 10:57 AM, Manjula Mummadisetti wrote: > I would like to understand the link below. I am not quite sure what each > of those numbers mean, although the link does mention, can somebody > clearly explain what those numbers are in restraints panel? > > http://salilab.org/modeller/8v1/manual/node157.html#SECTION:atomid

That's a very old version of the docs. Here's the latest: http://salilab.org/modeller/9.12/manual/node480.html

All the numbers are explained at that link. However, we don't generally recommend you add restraints by hand-writing raw restraints files; you can do it from Python instead. There is an example at http://salilab.org/modeller/9.12/manual/node27.html

> Also, I would like to restrain N-N distance rather than C-alpha C-alpha. > How do I make those changes?

It's exactly the same - the atom type doesn't matter.

Ben Webb, Modeller Caretaker