OneScience-Group/flex_ddG_tutorial

1<ROSETTASCRIPTS>2  <!--3    Reprocess an EXISTING flex ddG run to recover per-chain intramolecular energies.4 5    No re-sampling is needed: struct.db3 already holds the coordinates of every backrub,6    wild type minimized, and mutant minimized pose. This protocol reads those poses back in,7    isolates one chain at a time, and reports the isolated chain's total score.8 9    Isolating the chain matters. A Chain residue selector alone is not enough, because10    struct.db3 stores the *bound* poses, so a selector-scoped metric still picks up cross-chain11    pair energies (roughly half the interface energy leaks into each chain). Deleting the other12    chains reproduces the separated, unrelaxed unbound state exactly, because intra-chain13    energy is invariant under the rigid-body translation InterfaceDdGMover uses to unbind.14 15    Chain selectors below are for a two chain A/B complex. Add one Chain selector, one16    DeleteRegionMover, one ReportToDB and one restore/delete/report triple per extra chain.17 18    Usage (run once per struct.db3, from the directory containing it):19 20      rosetta_scripts -inout:dbms:database_name struct.db3 -in:use_database \21                      -parser:protocol per_chain_rescore.xml \22                      -restore_talaris_behavior -in:file:fullatom -out:nooutput23 24    Then read per_chain.db3 with reprocess_per_chain.py.25  -->26  <SCOREFXNS>27    <ScoreFunction name="fa_talaris2014" weights="talaris2014"/>28  </SCOREFXNS>29 30  <RESIDUE_SELECTORS>31    <Chain name="chain_A" chains="A"/>32    <Chain name="chain_B" chains="B"/>33    <Not name="not_chain_A" selector="chain_A"/>34    <Not name="not_chain_B" selector="chain_B"/>35  </RESIDUE_SELECTORS>36 37  <MOVERS>38    <SavePoseMover name="save_full" reference_name="full_pose" restore_pose="0"/>39    <SavePoseMover name="restore_full" reference_name="full_pose" restore_pose="1"/>40 41    <DeleteRegionMover name="isolate_chain_A" residue_selector="not_chain_A"/>42    <DeleteRegionMover name="isolate_chain_B" residue_selector="not_chain_B"/>43 44    <ReportToDB name="chain_A_report" batch_description="per_chain" database_name="per_chain.db3">45      <ScoreTypeFeatures/>46      <ScoreFunctionFeatures scorefxn="fa_talaris2014"/>47      <StructureScoresFeatures scorefxn="fa_talaris2014"/>48    </ReportToDB>49    <ReportToDB name="chain_B_report" batch_description="per_chain" database_name="per_chain.db3">50      <ScoreTypeFeatures/>51      <ScoreFunctionFeatures scorefxn="fa_talaris2014"/>52      <StructureScoresFeatures scorefxn="fa_talaris2014"/>53    </ReportToDB>54  </MOVERS>55 56  <PROTOCOLS>57    <Add mover_name="save_full"/>58    <Add mover_name="isolate_chain_A"/>59    <Add mover_name="chain_A_report"/>60 61    <Add mover_name="restore_full"/>62    <Add mover_name="isolate_chain_B"/>63    <Add mover_name="chain_B_report"/>64  </PROTOCOLS>65  <OUTPUT />66</ROSETTASCRIPTS>67