Re: [modeller_usage] Adjust weight of homology restraints
To: Nick Burton <>
Subject: Re: [modeller_usage] Adjust weight of homology restraints
From: Modeller Caretaker <>
Date: Thu, 09 Jul 2009 07:18:27 -0700
Cc:
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
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