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LoopRemodel

Perturbs and/or refines a set of user-defined loops. Useful to sample a variety of loop conformations.

<LoopRemodel name="&string" auto_loops="(0 &bool)" loop_start_(pdb_num/res_num) loop_end_(pdb_num/res_num) hurry="(0 &bool)" cycles="(10 &Size)" protocol="(ccd &string)" perturb_score="(score4L &string)" refine_score="(score12 &string)" perturb="(0 &bool)" refine="(1 &bool)" design="(0 &bool)"/>
  • pdb_num/res_num: see the main RosettaScripts Documentation for more.
  • auto_loops: use loops defined by previous LoopFinder mover? (overrides loop_start/end)
  • loop_start_pdb_num: start of the loop
  • loop_end_pdb_num: end of the loop
  • hurry: 1 = fast sampling and minimization. 0 = Use full-blown loop remodeling.
  • cycles: if hurry=1, number of modeling cycles to perform. Each cycle is 50 steps of mc-accepted kinematic loop modeling, followed by a repack of the surrounding area. if hurry=0 and protocol=remodel, this controls the max number of times to attempt closure with the remodel protocol (low cycles might leave chain breaks!)
  • protocol: Only activated if hurry=0. Choose "kinematic", "ccd", or "remodel". ccd appears to work best at the moment.
  • perturb_score: scorefunction to use for loop perturbation
  • refine_score: scorefunction to use for loop refinement
  • perturb: perturb loops for greater diversity?
  • refine: refine loops?
  • design: perform design during loop modeling?

See Also