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 modeller-care@salilab.org 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-care@salilab.org 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 nick.burton@bristol.ac.uk