series The two character code used to disambiguate Rosetta runs. For fragment libraries this is almost always aa. pdb The four character code of the PDB the fragments were generated for. chain The one character code of the protein chain the fragments were generated for. Usually "_" for all. size Fragment size, either a 3-mer or 9-mer. Acceptable values are 03 and 09. strategy Fragment selection strategy used in NNMake. Acceptable values are 04, 05 and 06. See below. depth Number of fragments of descending score which are kept in the library, usually 200. version Version of NNMake, usually v1_3.
tcsh% pfilt nr.fasta > filtnr tcsh% formatdb -t filtnr -i filtnr tcsh% cp filtnr.p?? $BLASTDB
$> make_fragments.pl -verbose 2ptl_.fasta
$> make_fragments.pl -verbose -nohoms -nojufo 2ptl_.fasta
$> make_fragments.pl -template 2ptl_ 2ptl_.fasta