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Re: [modeller_usage] Adjust weight of homology restraints

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)?

Thanks also for the advice on electrostatics.



--On 08 July 2009 11:00 -0700 Modeller Caretaker <> wrote:

On 07/08/2009 02:35 AM, Nick Burton wrote:
Is it possible to alter the weight of homology-derived restraints, in
the same way you can scale other contributions to the energy function
(with 'environ.schedule_scale')? I would like to globally down-weight
homology-derived restraints to place more emphasis on
geometry/electrostatics etc.

Yes, certainly. The homology-derived restraints are not all placed in the
same restraint group though, so you'll have to down-weight multiple
groups (on the other hand, this gives you a little more flexibility, if
you only wanted to down-weight the distances or dihedrals for example).
Look in the log file from a comparative modeling run for the "Summary of
the restraint violations", particularly the RESTRAINT_GROUP, NUM and S_i
columns, and http://salilab.org/modeller/9v7/manual/node245.html for a
list of all the restraint groups.

Since there are many homology-derived restraints, it may make more sense
to simply up-weight the restraints you want to put more emphasis on - the
weights can be greater than 1.

BTW, by default Modeller does not consider electrostatics, since the
assumption is made that any electrostatic interactions are already
represented by the template conformation, and without solvation the
interactions are unlikely to be correct even if you do turn them on.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

Dr N M Burton
Department of Biochemistry
University of Bristol
+44 117 3312149