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?
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.