Which interface are you interested in using? It sounds like you’re using the backrub commandline application.
From what I can tell, the facilities to set pivot residues from a movemap are not actually invoked from any command line options. (Though they’re accessible from the C++ and PyRosetta level.)
The -backrub:minimize_movemap option doesn’t appear to be used in setting the pivot residues at all, instead being used just for the minimization portion of BackrubProtocol. The -in:file:movemap option is also not used for the pivot residue setting of the backrub portion, instead it’s used for the “small moves” part of the BackrubProtocol.
Regarding the difference between the backrub protocol and the relax protocol, backrub proper doesn’t really apply on a sub-residue level, like the minimization portion of relax does. Indeed, backrub doesn’t really operate on single residues, but over continuous segments of backbone atoms. While you can theoretically back out the backbone stretches from a MoveMap, for normal usage it’s not normally the way people think of it.
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