| -h, --help | show this help message and exit |
| -fasta t000_.fasta | the sequence to be modelled by ROSETTA |
| -frags FRAGS FRAGS | fragments to be used for denovo-sampling by ROSETTA |
| -native NATIVE | supply a native pdb for RMSD calculation |
| -native_restrict [NATIVE_RESTRICT [NATIVE_RESTRICT ...]] | supply a .rigid file to restrict evaluation of native rms. This wil be column rms_full |
| -rdc [ |
rdc-restraint files |
| -cyana_upl [final.upl [final.upl ...]] | cyana upper distance restraints |
| -restraints [ |
rosetta restraint file |
| -centroid_stage_restraints [*.cst.centroid [*.cst.centroid ...]] | rosetta restraint file with atoms C, CA, O, H, N, CB, HA only |
| -flexible_residues [FLEXIBLE_RESIDUES [FLEXIBLE_RESIDUES ...]] | residues that should be considered flexible, use e.g., cs2rigid |
| -cs |
add chemical shift score to final output |
| -fix_topol FIX_TOPOL | provide topology file (obtained with r_pdb2top from pdb-file |
| -peaks [ |
add peak files for automatic assignment |
| -shifts [ |
add 1 or N files with chemical shifts, N=number of peak-files |
| -silent SILENT | start assignment from the provided ensemble (silent file) |
| -no_auto_intensities | add intensity values for protons, override whats in shift files |
| -local_distances LOCAL_DISTANCES | provide a file of local distances, e.g., predicted with FragsToAtomDist from fragment library |
setup_target.py -target t000_ -method abrelax -frags frags9.dat frags3.dat -fasta t000_.fasta
prepare a basic abrelax run for target t000_ (use default target-library location $CS3_BENCH_TARGETLIB)
setup_target.py -target t000_ -method rasrec -transfer_method abrelax
copy settings from Setup (t000_, abrelax, standard) to Setup (t000_, rasrec, standard)
setup_target.py -target t000_ -method rasrec -transfer_label standard -label with_rdc -rdc med1.rdc med2.rdc
add rdc data to existing Setup (t000_, rasrec, standard) and call it Setup (t000_, rasrec, with_rdc)