plmallip@mail.uh.edu wrote: > I want to build a model using two templates. One of the templates > have >70% sequence homology while the other has <35% sequence homology. > To the extent of my knowledge, automodel gives more weight to the > template with more sequence homology. Is there any way I can manually > assign more weight to the template with less sequence homology, at some > of the regions? If there is, where can I get the details, as to how to > do it?

There is good news and bad news:

The good news is that Modeller does not weight the templates simply by their overall sequence identity. Instead, they are weighted by their *local* sequence similarity, over a sliding window of 5 residues. So for example, even if a template has a lower sequence identity to your target, Modeller will still "pick" it in regions where it is locally more similar to the target than the other template. The weighting is also not a simple "take 40% of template 1 and 60% of template 2" - Modeller uses its internal database of triple alignments to build reasonable restraints when two templates suggest different feature values. See the 1993 Modeller publication for more details.

The bad news is that since the weighting algorithm is not a simple one, you can't adjust it, at least not without a good understanding of the internals.

See also http://salilab.org/modeller/FAQ.html#2 for the extreme case where one template should not be used at all.

Ben Webb, Modeller Caretaker