I am trying to replicate an old experiment and I'd need to generate fragments using old structures only. How can I do that?
at the moment I created a database of old structures and I downloaded the rosetta fragment picker tool so I am trying to find out what internal database of rosetta I should update, any suggestions?
Thanks a lot in advance
The fragment picker works off of the "Vall" database of filtered structure input. To limit the fragments to certain structures, you just need to generate (or obtain) a Vall which corresponds to the limited set of PDBs. In Rosetta/tools/fragment_tools/pdb2vall/ there is a script which should be able to generate a Vall database from a set of PDB files.