Viewing 1 reply thread
  • Author
    • #1636

        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!

      • #8994

          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

        • #8998

            Thank you for your help and I find it at
            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?
            Thanks again.

          • #9002

              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.)

          Viewing 1 reply thread
          • You must be logged in to reply to this topic.