Brandon Mills wrote: > I have recently been toying with certain restraints in my .rsr files, > and I have a couple questions. Can someone elaborate on the effect of > restraints which contain eight atoms and a multiple of six parameters > (I've seen 6, 12, 18, 24, and 30), and the restraints which contain 4 > atoms and 28 parameters? What exactly are these parameters? Also, is > there an easy way to pick out the psi and phi restraints out of the > general dihedral restraints? Thanks in advance!

See http://salilab.org/modeller/9v1/manual/node382.html for a description of the restraints file format. The second column (restraint form) is the one you're probably interested in (it will be 9 for multi-binormal (phi/psi) restraints). There is a multiple of six parameters for each of these because there are six parameters for each well in the function (weight, 2 means, 2 stdevs, and a correlation; see http://salilab.org/modeller/9v1/manual/node91.html).

The other restraints you mention are almost certainly cubic spline restraints (form 10). These are used because it is more efficient to evaluate a cubic spline than a multiple Gaussian.

Ben Webb, Modeller Caretaker