Re: [modeller_usage] Adjust weight of homology restraints

Nick Burton wrote: > OK, I didn't realise that restraints listed in those locations were a > break-down of the homology-derived restraints. Is there anywhere which > details which are homology-derived and which aren't (eg are the bond > length/angle potentials homology-derived, or based on dictionary values)?

The best source for this is the 1993 Modeller paper, but there is also a brief description at http://salilab.org/modeller/9v7/manual/node196.html

Bond lengths, angles and some dihedrals come directly from the CHARMM forcefield, so are not homology-derived. But phi/psi and sidechain dihedrals take the template residue type into account, and so are homology-derived.

Ben Webb, Modeller Caretaker