How to pick fragments for Rosetta
Fragment libraries are a core part of ab initio and other protocols in Rosetta. They are used in the assembly of proteins whether for structure prediction or design, to cut down on the size of the protein-folding search space. A library of fragments that represent the range of accessible local structures for all short segments of the protein chain are selected from a database of known protein structures.
This file contains all necessary flags with parameters that are needed to make the fragments. You should use 2 flagfiles, because you need both: short (3-mers) and long (9-mers) fragments.
-in:file:fasta QUERY.fasta -in:path:database /PATH/Rosetta/database -in:file:vall ../vall.dat.apr24.combo.v2.mar10.bfactor.v2.gz -frags:n_candidates 1000 -frags:n_frags 200 -frags:frag_sizes 3 #or 9 -out:file:frag_prefix QUERY -frags:scoring:config ../score3 -in:file:checkpoint QUERY.checkpoint -frags:write_ca_coordinates -frags:describe_fragments QUERY-frags.3.scf -spine_x QUERY.fasta.spXout -frags:ss_pred QUERY.ss2 psipred
* QUERY.fasta - the amino acid sequence in fasta format of data
* QUERY.checkpoint - text file in .chk format of data (.chk is a prediction of ss2 from PSIBLAST)
* QUERY.fasta.spXout - the prediction of ss2 from SPINEX
* QUERY.ss2 - prediction of ss2 from PSIPRED
* QUERY.frag3.flagfile - file with flags for fragment_picker, which makes 3-mers
* or QUERY.frag9.flagfile - file with flags for fragment_picker, which makes 9-mers
* score3 - file with the definition of weights when calculating the score, the default unchanged
* or score9 - file with the definition of weights when calculating the score, the default unchanged
* QUERY.200.3mers - file with 3-mers (short fragments), really need them!
* QUERY.200.9mers - file with 9-mers (long fragments), really need them!
* QUERY-frags.3.scf - description of fragments