Rosetta Movers XML Script for Protein Design and Optimization

<MOVERS>
  <MutateResidue name='mutres0' new_res='%%new_res0%%' target='%%target0%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres1' new_res='%%new_res1%%' target='%%target1%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres2' new_res='%%new_res2%%' target='%%target2%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres3' new_res='%%new_res3%%' target='%%target3%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres4' new_res='%%new_res4%%' target='%%target4%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres5' new_res='%%new_res5%%' target='%%target5%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres6' new_res='%%new_res6%%' target='%%target6%%' preserve_atom_coords='true'/>
  <MutateResidue name='mutres7' new_res='%%new_res7%%' target='%%target7%%' preserve_atom_coords='true'/>
  <ConstraintSetMover name='add_CA_cst' cst_file='%%cst_full_path%%'/>
  <AtomCoordinateCstMover name='fix_res_sc_cst' coord_dev='0.5' bounded='false' sidechain='true' task_operations='not_to_cst_sc'/>
  <PackRotamersMover name='prm' task_operations='init,include_curr,rtr,fix_not_neighbor,fix_res' scorefxn='scorefxn_full'/>
  <RotamerTrialsMinMover name='rtmin' task_operations='init,include_curr,rtr,fix_not_neighbor,fix_res' scorefxn='scorefxn_full'/>
  <MinMover name='min' bb='1' chi='1' jump='0' scorefxn='scorefxn_full'/>
  <PackRotamersMover name='soft_repack' scorefxn='soft_rep_full' task_operations='init,include_curr,rtr,fix_not_neighbor,fix_res'/>
</MOVERS>

This XML script defines a protocol for protein design and optimization using Rosetta Movers. Here's a breakdown of the script:

Residue Mutation:

• The script starts by defining eight MutateResidue movers. Each mover replaces a specific residue (defined by the target attribute) with a new residue (defined by the new_res attribute).
• The preserve_atom_coords attribute ensures that the backbone coordinates of the mutated residue are preserved.

Constraint Application:

• The ConstraintSetMover (add_CA_cst) applies constraints defined in the cst_file to guide the design process.

Sidechain Optimization:

• AtomCoordinateCstMover (fix_res_sc_cst) fixes the sidechain coordinates of specific residues.
• PackRotamersMover (prm and soft_repack) optimizes the sidechain conformations of the protein. It uses different score functions (scorefxn_full and soft_rep_full) for different stages of optimization.

Energy Minimization:

• RotamerTrialsMinMover (rtmin) performs a local minimization of the sidechain conformations.
• MinMover (min) performs a more extensive minimization of the protein structure, including backbone and sidechain movements.

Task Operations:

• Several movers use task_operations to specify which residues are affected by the mover. For example, fix_not_neighbor and fix_res limit the optimization to specific residues.

This script provides a flexible framework for protein design, allowing users to customize the target residues, mutations, constraints, and optimization parameters for their specific needs.