Good morning
I have been generating models using the dopehr_loopmodel route, having
decided it would be more efficient to only generate loop models for the
lowest energy comparative model I switched to generating structures
using the automodel class and then defining the loop regions by
visualizing the lowest energy structure and plugging the values in to
the 'Loop refinement of an existing model' example script provided with
Modeller 9v1. The resulting loop models do not generate models of
nearly the same quality - as judged by Ramachandran plots - than the
automatically generated loop models. Is there a convenient way to
extract the loop sequence information that loop model uses to generate
it's models.
Regards
Mike Paterson