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The AddHelixSequenceConstraints mover sets up sequence constraints for each helix in a pose or in a selection. It can require negative and positive charges at the N- and C-termini, respectively, can limit the number of helix-disfavouring residues in each helix, can require that the helix be a user-specified fraction alanine, and can require a minimum fractional hydrophobic content in each helix. Note that these constraints remain attached to the pose, and are intended to be used during design with the aa_composition score term. Helices are detected using DSSP when this mover is applied, so if the secondary structure changes between application of this mover and design, the constraints will applied to out-of-date residue indices. (In such a case, the sequence constraints can be re-applied with this mover after first clearing the old constraints with either the ClearCompositionConstraintsMover, or by setting "reset=true" in this mover's options.)

Note that this mover's defaults have been set so that it can be applied without manually setting anything, and still produce reasonable behaviour. For advanced users, all settings can be tweaked manually, but this shouldn't be necessary in many cases.

<AddHelixSequenceConstraints name="(&string;)" residue_selector="(&string;)"
        reset="(false &bool;)" min_helix_length="(8 &non_negative_integer;)"
        add_n_terminal_constraints="(true &bool;)"
        min_n_terminal_charges="(2 &non_negative_integer;)"
        n_terminal_residues="(3 &non_negative_integer;)"
        n_terminal_constraint_strength="(15.0 &real;)"
        add_c_terminal_constraints="(true &bool;)"
        min_c_terminal_charges="(2 &non_negative_integer;)"
        c_terminal_residues="(3 &non_negative_integer;)"
        c_terminal_constraint_strength="(15.0 &real;)"
        add_overall_constraints="(true &bool;)"
        types_to_avoid="(ASN ASP SER GLY THR VAL &string;)"
        overall_max_count="(0 &non_negative_integer;)"
        overall_constraints_strength="(5.0 &real;)"
        add_alanine_constraints="(true &bool;)"
        desired_alanine_fraction="(0.1 &real;)"
        ala_constraint_under_strength="(0.2 &real;)"
        ala_constraint_over_strength="(0.2 &real;)"
        add_hydrophobic_constraints="(true &bool;)"
        desired_min_hydrophobic_fraction="(0.25 &real;)"
        hydrophobic_constraint_strength="(0.2 &real;)" />
  • residue_selector: An optional, previously-defined ResidueSelector. If provided, only helices that contain at least one residue that is selected by the residue selector will have constraints applied. If not used, constraints are applied to all helices in the pose. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • reset: If true, all sequence constraints in the pose will be cleared (deleted) before this mover is applied. If false, the mover will append to existing sequence constraints. False by default.
  • min_helix_length: The minimum number of residues that a helix must have for this mover to act on it. By default, helices smaller than 8 residues are ignored since they have negligible helix macrodipoles.
  • add_n_terminal_constraints: If true, this mover will add sequence constraints requiring a user-specified minimum number of negatively-charged residues at the N-terminus of each helix. True by default.
  • min_n_terminal_charges: The minimum number of negatively-charged residues required at the N-terminus of helices. Defaults to 2 residues.
  • n_terminal_residues: The length of the stretch of residues that must contain negative charges at the N-terminus of a helix. Defaults to 3 residues.
  • n_terminal_constraint_strength: The strength of the sequence constraint requiring negative charges at the N-termini of helices. If set to be too weak, Rosetta's packer may sometimes put in too few negative charges. 15.0 by default. (For advanced users, this is the energetic penalty applied when there is one fewer than the desired number of negatively-charged residues. The penalty ramps quadratically for two fewer, three fewer, etc.)
  • add_c_terminal_constraints: If true, this mover will add sequence constraints requiring a user-specified minimum number of positively-charged residues at the C-terminus of each helix. True by default.
  • min_c_terminal_charges: The minimum number of positively-charged residues required at the C-terminus of helices. Defaults to 2 residues.
  • c_terminal_residues: The length of the stretch of residues that must contain positive charges at the C-terminus of a helix. Defaults to 3 residues.
  • c_terminal_constraint_strength: The strength of the sequence constraint requiring positive charges at the N-termini of helices. If set to be too weak, Rosetta's packer may sometimes put in too few positive charges. 15.0 by default. (For advanced users, this is the energetic penalty applied when there is one fewer than the desired number of positively-charged residues. The penalty ramps quadratically for two fewer, three fewer, etc.)
  • add_overall_constraints: If true, this mover will add sequence constraints penalizing more than a user-specified maximum number of helix-disfavouring residues in each helix. True by default.
  • types_to_avoid: The list of helix-disfavouring residue types that should be penalized at all helix positions by the "overall" constraints. This must be a whitespace-separated list of three-letter residue type codes, with no commas.
  • overall_max_count: The maximum allowed number of helix-disfavouring residue types. Default zero (though the penalty for having one is small by default).
  • overall_constraints_strength: The strength of the sequence constraint penalizing helix-disfavouring residue types. If set to be too weak, Rosetta's packer may sometimes put in too few helix-disfavouring residues. 5.0 by default. (For advanced users, this is the energetic penalty applied when there is one more than the maximum allowed number of helix-disfavouring residues. The penalty ramps quadratically for two more, three more, etc.)
  • add_alanine_constraints: If true, this mover will add sequence constraints penalizing too many or too few alanine residues in each helix. The user can set a user-defined desired fractional alanine content. Note that this constraint is usually set to be weak, so that some deviation from the desired fractional alanine content is tolerated. True by default.
  • desired_alanine_fraction: The desired fractional alanine content in each helix. Defaults to 0.1 (10 percent alanine). Note that deviation from this fraction is possible, if the alanine constraints are weak (and they are weak by default).
  • ala_constraint_under_strength: The alanine constraint penalty that is imposed if the fractional alanine content is 1 percent less than the desired fractional content. The penalty ramps quadratically as the alanine content falls below desired. Note that this penalty is weak, by default, to allow some deviation from the desired fractional alanine content on a case-by-case basis.
  • ala_constraint_over_strength: The alanine constraint penalty that is imposed if the fractional alanine content is 1 percent more than the desired fractional content. The penalty ramps quadratically as the alanine content rises above desired. Note that this penalty is weak, by default, to allow some deviation from the desired fractional alanine content on a case-by-case basis.
  • add_hydrophobic_constraints: If true, this mover will add sequence constraints penalizing too few hydrophobic residues in each helix. The user can set a user-defined minimum desired fractional hydrophobic content. Note that this constraint is usually set to be weak, so that some designs with fewer than the minimum hydrophobic count will be returned. Note that alanine is NOT considered hydrophobic. True by default.
  • desired_min_hydrophobic_fraction: The desired minimum fractional hydrophobic content in each helix. Defaults to 0.25 (25 percent hydrophobic). There is no penalty for more hydrophobic residues; only for fewer than desired. Note that helices slightly below this fraction are possible, if the hydrophobic constraints are weak (and they are weak by default).
  • hydrophobic_constraint_strength: The hydrophobic constraint penalty that is imposed if the fractional hydrophobic content is 1 percent less than the desired fractional content. The penalty ramps quadratically as the hydrophobic content falls below desired. Note that this penalty is weak, by default, to allow some deviation from the desired fractional hydrophobic content on a case-by-case basis.