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Places hotspot residues simultaneously on a scaffold, rather than iteratively as in PlaceStub. It is faster therefore allowing more backbone sampling, and should be useful in placing more than 2 hotspots.
<PlaceSimultaneously name="(&string)" chain_to_design="(2 &Integer)" repack_non_ala="(1 &bool)" optimize_fold_tree="(1 &bool)" after_placement_filter="(true_filter &string)" auction="(&string)" stub_score_filter="(&string)" stubscorefxn="backbone_stub_constraint &string" coor_cst_cutoff="100 &Real"/>
<DesignMovers>
<Add mover_name="(null_mover &string)" use_constraints="(1 &bool)" coord_cst_std="(0.5 &Real)"/>
</DesignMovers>
<StubSets explosion="(0 &integer)" stub_energy_threshold="(1.0 &Real)" max_cb_dist="(3.0 &Real)" cb_force="(0.5 &Real)">
<Add stubfile="(& string)" filter_name="(&string)"/>
</StubSets>
<StubMinimize min_repeats_before_placement="(0&Integer)" min_repeats_after_placement="(1&Integer)">
<Add mover_name="(null_mover &string)" bb_cst_weight="(10.0 &Real)"/>
</StubMinimize>
<NotifyMovers>
<Add mover_name="(&string)"/>
</NotifyMovers>
</PlaceSimultaneously>
Most of the options are similar to PlaceStub above. Differences are mentioned below:
rb_stub_minimization, auction and stub_score_filter allow the user to specify the first moves and filtering steps of PlaceSimultaneously before PlaceSimultaneously is called proper. In this way, a configuration can be quickly triaged if it isn't compatible with placement (through Auction's filtering). If the configuration passes these filters and movers then PlaceSimultaneously can be run within loops of docking and placement, until a design is identified that produces reasonable ddg and sasa.