Reply To: make_fragments

[Anonymous]

No clue, but this older thread describes running make_fragments in kind of a bare-bones mode. By turning off most of the SS predictors you can get results immediately instead of hammering on all the weird secondary libraries the perl script wants:

http://www.rosettacommons.org/node/1565

Messing with make_fragments.pl is fine for some fragment purposes. If you are doing abinitio, running the full make_fragments.pl might be important because of the intensive SS prediction. If you just need fragments for loop modeling, it doesn’t really matter (they’re used for sampling and get overwritten as the loop closes). (I don’t do abinitio so I’m not sure, but I do loops all the time and I’ve never cared how good the fragments were, it’s all loop anyway!)