On 04/12/2010 08:26 AM, Armin Meier wrote: > in a Modeller-generated .rsr file, I have lines like this one: > > R 9 3 4 25 8 18 2 5 4 4 7 9 10 12 9 > 10 12 14 0.1295 0.3250 0.5455 -1.0908 -0.7138 > -1.1903 2.5360 -2.3 3880 387 2.5656 0.0908 0.1065 > 0.2059 0.2164 0.5271 0.3072 -0.2541 3880 -0.4199 > -0.6670 > > I suppose it's a restraint on phi-psi angles, but I cant find a > description for Feature "4" (third number in first line) in the Modeller > documentation (http://salilab.org/modeller/manual/node447.html).
Yes, you are correct - it's a phi-psi restraint. Feature 4 is the same as feature 3 (it's a dihedral angle). (There are complicated historical reasons why there are two identical dihedral angle features.)
> Moreover, why are there two features for this restraint (numb_feat=2)
The two features are the two dihedral angles (phi and psi).
> and what does Modal2 = 5 stand for?
Actually for this mathematical form Modal2 is not used, so you can ignore it. Only Modality is used, which is the number of terms in the binormal.
> Are restraints of this type (i.e. Group=25, dihedral) always generated > by default (Modeller version>= 9.5)?
Yes, automodel generates these restraints for each residue that has both a phi and a psi angle (so the termini in each chain are excluded).
Ben Webb, Modeller Caretaker