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Scans a protein and builds disulfides that join residues in one set of residues with those in another set. By default, non-protein, GLY, and PRO (or DPRO) residues are ignored. Residues to be joined must be min_loop residues apart in primary sequence. Potential disulfides are first identified by CB-CB distance, then by mutating the pair to CYS, forming a disulfide, and performing energy minimization. If the energy is less than the user-specified cutoff, it is compared with a set of rotations and translations for all known disulfides. If the "distance" resulting from this rotation and translation is less than the user-specified match_rt_limit, the pairing is considered a valid disulfide bond. Once valid disulfides are found, they are combinatorially added. For example, if disulfides are identified between residues 3 and 16 and also between residues 23 and 50, the following configurations will be found: 1. [3,16] 2. [23,50] 3. [3,16],[23,50] The mover is now able to place D-cysteine disulfides and mixed D/L disulfides.

<Disulfidize name="(&string;)" scorefxn="(&string;)" sort_scorefxn="(&string;)"
        match_rt_limit="(2.0 &real;)" min_disulfides="(&non_negative_integer;)"
        max_disulfides="(&non_negative_integer;)"
        keep_current_disulfides="(false &bool;)"
        keep_all_disulfides="(false &bool;)"
        include_current_disulfides="(false &bool;)"
        min_loop="(8 &non_negative_integer;)" max_disulf_score="(1.5 &real;)"
        mutate_gly="(false &bool;)" mutate_pro="(false &bool;)"
        max_cb_dist="(5 &real;)" score_or_matchrt="(false &bool;)"
        set1="(&string;)" set2="(&string;)" use_l_cys="(true &bool;)"
        use_d_cys="(false &bool;)" use_beta_cys="(false &bool;)" />
  • scorefxn: Name of score function to use
  • sort_scorefxn: Scorefunction to use for sorting results if more than one disulfide set found. If unset, will use a random shuffle of the results.
  • match_rt_limit: distance in 6D-space (rotation/translation) which is allowed from native disulfides. Lower values increase the stringency of the requirement that disulfides be similar to native disulfides.
  • min_disulfides: Smallest allowable number of disulfides.
  • max_disulfides: Largest allowable number of disulfides.
  • keep_current_disulfides: If true, all current disulfides are preserved. NOTE: THIS ONLY WORKS FOR DISULFIDES IN THE SELECTION. If false, existing disulfides containing a CYS residue within either set1 or set2 are mutated to alanine. Disulfides with both CYS residues outside of the union of the selected residue sets will not be affected. False by default.
  • keep_all_disulfides: If true, all current disulfides are preserved regardless of selection. This is the option you probably want.
  • include_current_disulfides: If true, current disulfides are included in the possible disulfide combinations to try. False by default (only new disulfide combinations tried).
  • min_loop: Minimum distance between disulfide residues in primary sequence space.
  • max_disulf_score: Highest allowable per-disulfide dslf_fa13 score. Reducing this requires that disulfide geometry be more ideal.
  • mutate_gly: Should the mover ignore glycine positions (false) or allow mutations to cysteine at these positions (true)? Default false (ignore gly positions).
  • mutate_pro: Should the mover ignore D/L-proline positions (false) or allow mutations to cysteine at these positions (true)? Default false (ignore pro/dpr positions).
  • max_cb_dist: Maximum Cb Cb disulfide distance.
  • score_or_matchrt: If true, disulfides are accepted if they pass the match_rt (rigid-body transform) criterion OR the full-atom disulfide score criterion. If false, disulfides must pass BOTH criteria. False by default (both criteria must pass).
  • set1: Name of a residue selector which identifies a pool of residues which can connect to residues in set2. (Default: all residues)
  • set2: Name of a residue selector which identifies a pool of residues which can connect to residues in set1. (Default: all residues)
  • use_l_cys: Should the mover consider placing L-cysteine? True by default.
  • use_d_cys: Should the mover consider placing D-cysteine? False by default. (Note that at least one of use_l_cys, use_d_cys, or use_beta_cys must be set to "true".)
  • use_beta_cys: Should the mover consider placing beta-3-cysteine at beta-amino acid positions? False by default. (Note that at least one of use_l_cys, use_d_cys, or use_beta_cys must be set to "true".)