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