Hello all!
I want to model a big fibrous protein using several templates. The templates do not overlap (gap is no longer then 1-3 residues) or overlap over few residues.
I found the following sentence in the FAQ: "If no additional information is available about the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains when the overlap between A and B is non-existing or short. To obtain satisfactory relative orientation of modeled domains in such cases, orient the two template structures appropriately before the modeling."
My questions are: how precisely the templates have to be oriented? Would be cursory placing enough?
How can I order the templates by using some simple constraints instead of orienting the templates?
Thanks for help, sdh