I'm looking at a group of templates where only one of them has an
"extended" beta sheet / loop region. This single template is closer to
the model sequence (in this region only) than the other templates. Is
there a way to bias the construction of this particular "loop" towards
only one template! I don't want to just build a model based on this
structure alone however.
Modeller should do this automatically, since the template information is
weighted by the local sequence similarity. Of course, if you want to
bias the construction more, you can always deliberately misalign the
other templates in that region, so that you use only the one template
(although all templates would be used for the rest of the protein). An
alternative is to manually extract some key distances from the 'best'
template, and use these to add your own restraints to the modeling
procedure.