hi,
being a new user, I am facing many problems with modeller. now consider
a situation in which i want to model only one particular domain/protein
in a protein-protein complex, since the structure for the other
domain/protein is available, but then i want to optimize the binding
region of the modelled domain taking into context, the other domain as
well... is it possible that i use the optimization routine of modeller
for the same, only after putting both the proteins of the complex into
proper interacting/binding orientation, so that energy minimization can
be performed taking into context the entire complex and not just the
modelled part
thanks, for helping out...
sincerely.