The AtomTree reflects the chemical and kinematic structure of the Pose and stores internal degrees of freedom on its edges.
An iterative protocol building on RASREC that uses the low-energy pool of structures to improve NOE peak assignments
A chainbreak is between consecutive residues (in the protein sequence) that are not connected in the AtomTree/FoldTree.
Penalty energy term computed for non-physical chainbreaks.
A low-resolution abstraction of the AtomTree with peptide- and jump-edges.
is a particular conformation of short pieces of protein, RNA or DNA backbone
A file that contains many possible conformations (fragments) for a given set of degrees of freedom.
sampling with non-trivial FoldTree
A choice of a structure calculation protocol (abrelax, rasrec, autoNOE) in the automated setup tools.
The Pose is the container of the molecular system including its chemical-, kinematic- and conformational structure.
A recipe for structure calculation.
An iterative protocol that recombines structural features found in the (genetic) pool of low-energy structures
A bias energy contribution usually based on experimental data
place for storage of common ROSETTA data files
An energy computed for a given Pose using the ScoreFunction.
A patch file to change individual weights of the ScoreFunction.
Weight-set for centroid scoring used during stage I of abrelax protocol.
score0 uses only vdw forces: ( env 0.0, pair 0.0, cbeta 0.0, cenpack 0.0, vdw 0.1, rg 0.0, hs_pair 0.0, ss_pair 0.0, rsigma 0.0, sheet 0.0 )
used during abrelax protocol.
( env 1.0, pair 1.0, cbeta 0.0, vdw 1.0, rg 0.0, cenpack 0.0, hs_pair 1.0, ss_pair 0.3, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 11
The weight-set used for full-atom scoring in Rosetta
A deprecated weight-set for full-atom scoring. Although using different weights its performance in discrimination of structures is not significant altered vs. score12.
Weight-set for centroid scoring used during stage III of abrelax protocol.
( env 1.0, pair 1.0, cbeta 0.25, cenpack 0.5, vdw 1.0, rg 0.0, hs_pair 1.0, ss_pair 1.0, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 6
Weight-set for centroid scoring used during stage IV of abrelax protocol.
( env 1.0, pair 1.0, cbeta 1.0, cenpack 1.0, vdw 1.0, rg 3.0, hs_pair 1.0, ss_pair 1.0, rsigma 1.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 0 6
Weight-set for centroid scoring used during stage III of abrelax protocol.
( env 1.0, pair 1.0, cbeta 0.25, cenpack 0.5, vdw 1.0, rg 0.0, hs_pair 1.0, ss_pair 1.0, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 11
Scoring is an application of a ScoreFunction to a pose.
Rosetta specific trajectory format.
Structure IO using a ROSETTA specific trajectory format
a beta-sheet forming contact between two residues in extended conformation.