This changes how the minimum and maximum segment sizes are specified. In the previous implementation, the smallest segment size was 2 residues, which corresponded to rotating the peptide bond (C and N atoms) between the two residues. In this implementation, that would correspond to a segment size of 4 atoms (CA, C, N, and CA). Because of the atom-centric implementation, the smallest possible size is now 3 atoms, which is the default. The previous default largest segment size, 12 residues, corresponds to the new default of 34 atoms. Because only CA atoms are enabled as pivots by default, the possible segments will be identical to those from the previous implementation.
Another difference is that this implementation uses continuous sampling of side chain chi angles instead of fixed rotamers. The angles are chosen according to the Dunbrack rotamer library probabilities. First, a rotamer well is chosen according to its probability of occurrence in the PDB. Second, the individual chi angles are chosen using gaussian distributed random angles with the means and standard deviations from the PDB.
Finally, backbone and side chain sampling are totally decoupled. They use different movers that are randomly chosen at each Monte Carlo step.
-database Database file input search paths
-s Name(s) of single PDB file(s) to process -l File(s) containing list(s) of PDB files to process -ignore_unrecognized_res Do not abort if unknown residues are found in PDB file; instead, ignore them.
If the PDB file contains a line beginning with FOLD_TREE, then the fold tree specified by that line will be used. The same fold tree will be appended to all resulting structures using the same format. See the documentation for fold trees for more information.
-nstruct Number of times to process each input PDB -backrub:ntrials number of Monte Carlo trials to run -mc_kt value of kT for Monte Carlo -mm_bend_weight weight of mm_bend bond angle energy term -cst_fa_weight weight of the fullatom constraint terms -cst_fa_file constraints filename(s) for fullatom. When multiple files are given a *random* one will be picked.
See the documentation about contraint files for more information.
-pivot_residues residues for which contiguous stretches can contain segments (internal residue numbers, defaults to all residues) -pivot_atoms main chain atoms usable as pivots -min_atoms minimum backrub segment size (atoms) -max_atoms maximum backrub segment size (atoms)
-resfile resfile filename(s). only the first is used. -sc_prob probability of making a side chain move -sc_prob_uniform probability of uniformly sampling chi angles -initial_pack force a repack at the beginning regardless of whether mutations are set in the resfile
-movemap MoveMap file specifying flexible torsions -sm_prob probability of making a small move
For more information about other application flags, please check the options list
cat << END_RESFILE > 2YPI.resfile NATRO start 3 A NATAA 7 A NATAA 95 A NATAA 96 A NATAA 129 A NATAA 131 A NATAA 134 A NATAA 139 A NATAA 164 A NATAA 165 A NATAA 167 A NATAA 168 A NATAA 170 A NATAA 172 A NATAA 174 A NATAA 177 A NATAA 179 A NATAA 180 A NATAA 183 A NATAA 208 A NATAA 211 A NATAA 216 A NATAA 219 A NATAA 220 A NATAA 223 A NATAA 230 A NATAA END_RESFILE backrub -database rosetta3_database -s 2YPI.pdb -ignore_unrecognized_res -resfile 2YPI.resfile -pivot_residues 127 128 129 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178