Re: [modeller_usage] Psi and Phi Dihedral Restraints

[Modeller Caretaker <>]

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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