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MapHotspot

Map out the residues that might serve as a hotspot region on a target. This requires massive user guidance. Each hot-spot residue should be roughly placed by the user (at least as backbone) against the target. Each hot-spot residue should have a different chain ID. The method iterates over all allowed residue identities and all allowed rotamers for each residue. Tests its filters and for the subset that pass selects the lowest-energy residue by score12. Once the first hot-spot residue is identified it iterates over the next and so on until all hot-spot residues are placed. The output contains one file per residue identity combination.

Autogenerated Tag Syntax Documentation:

Map out the residues that might serve as a hotspot region on a target. This requires massive user guidance. Each hot-spot residue should be roughly placed by the user (at least as backbone) against the target. Each hot-spot residue should have a different chain ID. The method iterates over all allowed residue identities and all allowed rotamers for each residue. Tests its filters and for the subset that pass selects the lowest-energy residue by score12. Once the first hot-spot residue is identified it iterates over the next and so on until all hot-spot residues are placed. The output contains one file per residue identity combination.

<MapHotspot name="(&string;)" clash_check="(0 &bool;)"
        file_name_prefix="(map_hs &string;)" >
    <Jumps jump="(&non_negative_integer;)" explosion="(0 &non_negative_integer;)"
            filter_name="(true_filter &string;)" mover_name="(null &string;)"
            allowed_aas="(ADEFIKLMNQRSTVWY &string;)" scorefxn_minimize="(&string;)" />
</MapHotspot>
  • clash_check: Perform a clash check
  • file_name_prefix: Prefix for filenames

Subtag Jumps:

  • jump: Jump in question
  • explosion: Degree of extensive sampling at this jump
  • filter_name: filter with which to eliminate bad solutions
  • mover_name: mover for additional sampling
  • allowed_aas: amino acids allowed in design
  • scorefxn_minimize: Name of score function to use
<MapHotspot name="&string" clash_check="(0 &bool)" file_name_prefix="(map_hs &string)">
   <Jumps>
     <Jump jump="(&integer)" explosion="(0 &integer)" filter_name="(true_filter & string)" allowed_aas="('ADEFIKLMNQRSTVWY' &string)" scorefxn_minimize="(score12 &string)" mover_name="(null &string)"/>
     ....
   </Jumps>
</MapHotspot>
  • clash_check: whether the rotamer set is prescreened by the packer for clashes. Advised to be off always.
  • file_name_prefix: Prefix for the output file names.
  • explosion: How many chi angles to explode (giving more rotamers.
  • allowed_aas: 1-letter codes for the allowed residues.
  • scorefxn_minimize: which scorefxn to use during rb/sc minimization.
  • mover_name: a mover (no restrictions) to run just before hot-spot residue minimization.

See Also