I am trying to convert a bunch of PDB files to silent files. Though I am successful in doing this with covert_silent and relax applications I still miss out Secondary structure information in the computed silent out file (every residue is defined as "L"). What I am actually looking for a way to obtain SS with its backbone dihedral angles of a given idealized pdb file. Is it even possible ? or I am missing any magical flag?
My understanding is that what you actually want is just a secondary structure assignment (DSSP?) for each structure in a large set?
If that's what you want, I wouldn't use Rosetta at all. Rosetta can certainly do it but it's like using a machete to trim your toenails. I would use DSSP (http://swift.cmbi.ru.nl/gv/dssp/) or any of the other lightweight solutions on the internet.
If you really want to use Rosetta let me know and we'll cook up a method. We can either add a quick hack in C++ to an existing executable, or do it in PyRosetta. If you're comfortable with Python this will be super-easy in PyRosetta.