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Re: [modeller_usage] Psi and Phi Dihedral Restraints



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
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