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RepackMinimize

RepackMinimize does the design/repack and minimization steps using different score functions as defined by the protocol. For most purposes, the combination of PackRotamersMover with MinMover provide more flexibility and transparency than RepackMinimize, and are advised.

repack_partner1 (and 2) defines which of the partners to design. If no particular residues are defined, the interface is repacked/designs. If specific residues are defined, then a shell of residues around those target residues are repacked/designed and minimized. repack_non_ala decides whether or not to change positions that are not ala. Useful for designing an ala_pose so that positions that have been changed in previous steps are not redesigned. min_rigid_body minimize rigid body orientation. (as in docking)

<RepackMinimize name="&string" scorefxn_repack="(score12 &string)" scorefxn_minimize="(score12 &string)" repack_partner1="(1 &bool)" repack_partner2="(1 &bool)" design_partner1="(0 &bool)" design_partner2="(1 &bool)" interface_cutoff_distance="(8.0 &Real)" repack_non_ala="(1 &bool)" minimize_bb="(1 &bool * see below for more details)" minimize_rb="(1 &bool)" minimize_sc="(1 &bool)" optimize_fold_tree="(1 & bool)" task_operations="('' &string)">
    <residue pdb_num/res_num="(&string)" />
</RepackMinimize>
  • scorefxn_repack
  • scorefxn_minimize
  • interface_cutoff_distance: Residues farther away from the interface than this cutoff will not be designed or minimized.
  • repack_non_ala: if true, change positions that are not ala. if false, leave non-ala positions alone. Useful for designing an ala_pose so that positions that have been changed in previous steps are not redesigned.
  • minimize_bb*: minimize back bone conformation? (*see line below)
  • minimize_bb_ch1 and/or minimize_bb_ch2: allows to specify which chain(s)' backbone will be minimized
  • minimize_rb: minimize rigid body orientation? (as in docking)
  • optimize_fold_tree: see above
  • task_operations: comma-separated list of task operations. This is a safer way of working with user-defined restrictions than automatic_repacking=false.
  • pdb_num/res_num: see the main RosettaScripts Documentation for more.

If no repack_partner1/2 options are set, you can specify repack=0/1 to control both. Similarly with design_partner1/2 and design=0/1

See Also