Christy, did you ever find this file? I sent you an email via the forums tool, but I’m not really sure it’s working.
I seem to have basically followed Christy’s steps in getting the make_fragments.pl tool, and I’m currently stuck on the missing overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net file used by predict-2nd. Has anyone actually put together a working make_fragments script?
Presumably Kevin Karplus has or knows how to generate this file, so I guess I’ll ask him next.