Re: [modeller_usage] (no subject)

[Modeller Caretaker <modeller-care@ucsf.edu>]

Mensur Dlakic wrote:
> Can someone provide an explanation about converting Modeller's dihedral 
> restraints into plain psi/phi/omega angles? I have read through the 
> manual and have an intuitive feel for the way Modeller calculates these 
> values, but there are so many columns in the output file that I still am 
> not able to decipher it. So my question is is what columns in the 
> restraint file correspond to dihedral angles and their deviations, and 
> how do I convert them back to numbers in the -180 to 180 range.

The angles are in radians, so the conversion should be straightforward. 
The deviations are calculated when the energy is calculated, so you 
can't read them out of the restraints file.

An example (see http://salilab.org/modeller/manual/node100.html)
R    7   1   3   3   4   2   0     5     4     2     3       3.1416 
1.4000

This creates a restraint with (in order) form 7 (cosine potential), 
periodicity 1, feature 3 (dihedral angle), group 3 (cosine dihedral 
potential), acting on 4 atoms, with 2 parameters. The indices of the 4 
atoms are 5, 4, 2 and 3, and the parameters (as in CHARMM, the phase and 
force constant) are 3.1416 (i.e. pi) and 1.4000.

	Ben Webb, Modeller Caretaker
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