Can anyone clarify the advantages and disadvantages of these two ways of generating fragment libraries? I note that the FAQ now strongly recommends the server. Two advantages of the server might be
- access to secondary structure prediction methods not otherwise distributed (only Psipred seems available in a form that can be plugged into rosetta_fragments/nnmake/make_fragments.pl)
- automatic updating of nr etc
In general, though, it would be handy to be independent of server load and obtain fragments locally. My general experience is that make_fragments.pl does a good job.
Am I missing something? What method to other people prefer and why?