I´m trying to model a 2 domain protein with a ~140 aa long semi-flexible linker. We have a general idea of relative orientation of the two domains.
1) Is there a way of inserting fragments in only the linker and allowing translational and/or rotational movements in both domains, keeping the internal “rigidity” of both domains (its structure is solved)? Using topology broker? Rosetta scripts?
2) I then want fit the centroid and/or full-atom structures in a open and closed conformation to a saxs map (i know were both domains are situated in that map). Is is possible? Using the EM-fold or density fitting tutorials could help me?