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side is a top level plop command used to optimize side chain positions. The possible sub-commands are:

sing[le]               - single side chain prediction
pred[ict]              - predict
   RESIDUESELECTION    - a valid residue selection (required)
   iter[ations] #      - number of iterations to start with
   rand[omize] yes/no  - randomize starting side chain positions
   relax_clash YES/no  - relax sidechain steric clashes
combi[inatorial]       - combinatorial sampling
mc                     - monte carlo sampling
titr                   - titration curve
init                   - just prepare atom list
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