As far as I know, make_fragment will build fragment lib based on vall database. The local package make_fragment included a vall named vall.dat.2006-05-05. Does it mean that this vall was built on the basis of pdb data of 2006-05-05? Then how about Robetta fragment server? Does that online server use the same vall file with the released package?
Same question on nr database.
So the final question is: fragment lib built locally will definitely differ from that built online, is it right? (considering so many ss predictors involved.)