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Re: [modeller_usage] how to constrain automodel to remain closer to the template

Jake Gunn-Glanville wrote:
> I have been modeling a protein with a template I am quite confident in,
> and a loop that I would like to use a separate template for. When I
> generate 200 models, they all seem to show a great deal of structural
> diversity. Curious, I developed 20 models of a solved structure against
> itself, and found a bit of diversity in all of these resulting models as
> well. Is there a good way to constrain automodel so that it diverses
> less from the templates when thre are no obvious residue clashes forcing
> it to make adjustments?

The objective function optimized by Modeller does not encode all of the
information in the template (e.g. it also incorporates statistical
information such as Ramachandran-like maps) so you will always see some
divergence, even with 100% identical templates. Another thing you should
be aware of is that the starting structures are not exactly the
templates - the coordinates are randomized slightly. You can reduce this
randomization for the entire model with the deviation parameter when you
create your automodel object (see
http://salilab.org/modeller/manual/node42.html); you can dial this down
from the default 4A. If you only want to randomize part of the model,
you can write your own function to do that and assign it to
automodel.rand_method (see http://salilab.org/modeller/manual/node46.html)

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