Re: [modeller_usage] Adjust weight of homology restraints

[Nick Burton <>]

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.

Cheers,

Nick



--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
> --
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage



----------------------
Dr N M Burton
Department of Biochemistry
University of Bristol
BS8 1TD, UK
+44 117 3312149