I hope this is the correct place to ask this. I am curious how the Rosettta Webserver (http://robetta.bakerlab.org/fragmentsubmit.jsp) actually generates fragments, particularly how the secondary structures are generated. Is the standard "make_fragments.pl" script used or is another wrapper script (with different secondary strcuture predictions and flags) used? If another script is used is there any documentation for that particular method (as in what weights/quotas/sspredictions/etc) are used in the fragment_picker binary?
The webserver generates fragments with a newer version of make_fragments.pl that has some improvements over the original. It is currently unpublished so it is not available yet for general use. There is no timeline for its release but it will happen when it is published.
(disclaimer - i am not involved in the development of the newer make_fragments.pl)