I want to know the meaning of each score term. For example, what does fa_atr,fa_rep,fa_sol,fa_intra_rep,fa_pair,fa_plane,fa_dun,hbond_lr_bb,hbond_sr_bb,hbond_bb_sc ,hbond_sc,dslf_ss_dst dslf_cs_ang,dslf_ss_dih,dslf_ca_dih or pro_close in score12 measures, respectively? Where I can get that information.
Thank you very much!
fa_atr - van der Waals attraction
fa_rep - van der Waals repulsion
fa_sol - Lazaridis-Karplus solvation model
fa_intra_rep - van der Waals repulsion within a residue molecule (weakly weighted, only for distantly-bonded atoms, like a lysine NZ with its backbone),
fa_pair - statistics-derived potential for how frequently residue types are near one another; functionally an electrostatics term
fa_plane - does nothing
fa_dun - rotamericity
hbond_lr_bb, long range (beta or loop) backbone-backbone hydrogen bonds
hbond_sr_bb, helix backbone-backbone hbonds
hbond_bb_sc, sidechain to backbone hbonds
hbond_sc, sidechain to sidechain hbonds
dslf_ss_dst, dslf_cs_ang, dslf_ss_dih, dslf_ca_dih disulfide statistics based on SS distance, CS angle, SS and CA dihedrals
pro_close - keeps proline residues connected properly; they are internally represented with a broken bond due to the requirement for an acyclic graph AtomTree, so this term enforces that the prolines form proper pentamer rings
Thank you for your help and I find it at https://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/sco....
However, I have other score terms that I can't find its informations. They are "envsmooth" in score13 and "coordinate_constraint" in pack_no_hb_env_dep. Would you help me to introduce it or give some information about it?
coordinate_constraint is the score term for coordinate constraints. They're normally not present by default, but you can add these constraints to a pose to fix atoms at particular xyz coordinates.
envsmooth is a smoothed full atom version of the centroid "env" environment term. Basically, a statistical potential about how likely an amino acid identity is in a given environment (number of 10 angstrom neighbors.)