Pick fragments based on chemical shifts and sequence information. This
application is a wrapper that integrates several steps required to obtain
fragments. First, BLAST is used to obtain a sequence profile from multiple
sequence alignment. This step also provides the names of homologous proteins
that can be excluded from fragment picking in benchmark mode using the -nohom
flag. Second, TALOS+ is executed to obtain secondary structure predictions
based on the chemical shift data. Finally, the ROSETTA application
fragment_picker is started to assemble the fragment libraries using the VALL.
Obviously, this wrapper has a great many dependencies. These dependencies are
configured in csrosetta3/frag_picker/setup_paths.pl. Run install.py if
dependencies have changed or to update the BLAST sequence database.


pick_fragments.py [-h] -cs cs.tab [-sizes [SIZES [SIZES ...]]]
[-nfrags NFRAGS] [-hom] [-nohom] [-outlier OUTLIER]
[-trim] [-fasta FASTA] [-nocheck] [-xray]

Detailed Help:

-h, --help show this help message and exit
-cs cs.tab chemical shifts in TALOS format
-sizes [SIZES [SIZES ...]] which sizes of fragments shall be build
-nfrags NFRAGS how many frags per size-class and sequence position to collect
-hom pick fragments also from homologous proteins [default]
-nohom do not pick fragments from homologous proteins
-outlier OUTLIER report chemical shift outliers that are x*limit (no effect on fragments)
-trim trim the sequence according to TALOS+ output and pred2rigid
-fasta FASTA a target sequence
-nocheck don't run TALOS to check for chemical shift offsets or trimmin
-xray Use a pdb file to fake TALOS-predicted secondary structure and phi/psi angles.
-traceback print full traceback in case of error


pick_fragments.py -cs 2jrm_trim.tab -nohom

pick fragments from non-homologous proteins (for benchmarking)

pick_fragments.py -cs exp.tab

pick fragments for chemical shifts in exp.tab

pick_fragments.py -cs 1yyv.pdb -xray

pick fragments using fake TALOS prediction drawn from 1yyv.pdb