DESCRIPTION==In brief, the program reads a database file (nicknamed vall), input query sequence or sequence profile and other files and produces fragment files for modeling with Rosetta. 
ALGORITHM==Detail of the algorithm are described in Gront D. et al paper. 
REFERENCES==Gront D, Kulp DW, Vernon RM, Strauss CEM and Baker D, "Generalized fragment picking in Rosetta: design, protocols and applications", submitted to PLoS ONE
INPUTS==vall: protein structures database, your fragments come from there. http://www.bioshell.pl/rosetta-related/vall.apr24.2008.extended.gz - Mandatory\n.wghts: defines scoring system for fragment selection - Mandatory\n.fasta Amino Acid sequence - Mandatory unless .chk file given.\n.chk: sequence profile created with PSI-Blast with further modifications (pseudocounts added) use make_fragments.pl - any sequence profile - based score, e.g. ProfileScoreL1; mandatory file unless .fasta is given\n.ss2:secondary structure prediction in PsiPred format - The easiest way is to run make_fragments.pl script. You may also try to run a secondary prediction software on your own and then convert the resulst to the proper format. A script convert_ss_predictions.py can turn TALOS, Juffo, Porter and SAM into ss2.\n.cst:distance (or dihedral) constraints - Convert your data (distances or torsion angle values) into the proper format.\n.tab:NMR experiment; examples can be downloaded from BMRB database\n.pdb:Your structure
