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] | |
| [-traceback] |
| -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