On Tue, May 13, 2014 at 6:34 AM, Mark A Saper <saper@umich.edu> wrote:

Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet.

The same, or different? Atoms with identical altlocs will always interact with each other (and atoms with blank altlocs).

-Nat