Autogenerated Tag Syntax Documentation:


A special mover used to replicate the state of ab initio in early 2014

<AbscriptMover name="(&string;)" cycles="(&real;)"
        skip_stages="(&positive_integer_cslist;)" >
    <Stage ids="(&string;)" >
        <Mover name="(&string;)" weight="(1.0 &real;)" />
        <Preparer name="(&string;)" />
    </Stage>
    <Fragments selector="(&string;)" small_frags="(&string;)"
            large_frags="(&string;)" initialize="(true &bool;)" />
</AbscriptMover>
  • cycles: Equivalent to the -run:increase_cycles in standard ab initio; increases the number of ab initio cycles by that factor.
  • skip_stages: Comma-separated list of ab initio stages (1, 2, 3, or 4) that you wish to skip

Subtag Stage: Tag specifying behavior for a specific stage of the ab initio protocol

  • ids: (REQUIRED) Stage of ab intio to which this subtag refers.

Subtag Mover:

  • weight: How heavily should this mover be weighted relative to other movers in this stage, i.e. how frequently should it be used relative to others?

Subtag Fragments:

  • selector: Name of previously defined residue selector specifying where fragments should be inserted
  • small_frags: Fragments file containing small fragments (i.e. 3mers)
  • large_frags: Fragments file containing large fragments (i.e. 9mers)
  • initialize: Use small fragments insert a fragment at all positions before starting