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Autogenerated Tag Syntax Documentation:

This is XML that calls RosettaES (aka the loop grower)

References and author information for the FragmentExtension mover:

FragmentExtension Mover's citation(s): Frenz B, Walls AC, Egelman EH, Veesler D, and DiMaio F. (2017). RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nat Meth 14(8):797-800. doi: 10.1038/nmeth.4340.

<FragmentExtension name="(&string;)" fasta="(&string;)"
        beamwidth="(32 &non_negative_integer;)"
        fragtrials="(200 &non_negative_integer;)" debug="(false &bool;)"
        chainbreak="(1.5 &real;)" continuous_weight="(0.3 &real;)"
        rms_cutoff="(1.5 &real;)" fragcluster="(0 &real;)"
        masterbeamcutoff="(3.0 &real;)" sheetbonus="(0.5 &real;)"
        sheet_tolerance="(0.7 &real;)" sc_scale="(1 &real;)"
        windowdensweight="(30 &real;)"
        masterbeamwidth="(200 &non_negative_integer;)" rmswindow="(20 &real;)"
        rmscutoff="(1.5 &real;)" steps="(10000 &non_negative_integer;)"
        pcount="(0 &non_negative_integer;)"
        sheetcriteria="(2 &non_negative_integer;)"
        comparatorrounds="(100 &non_negative_integer;)"
        beamscorecutoff="(0.85 &real;)"
        pack_min_cycles="(2 &non_negative_integer;)" dumpbeam="(false &bool;)"
        dumperrors="(false &bool;)" dumpfinalbeam="(false &bool;)"
        dumprms="(false &bool;)" dumpfragments="(false &bool;)"
        direction="(1 &non_negative_integer;)" minimize="(true &bool;)"
        nativegrow="(false &bool;)" parametercheck="(false &bool;)"
        cenrot="(false &bool;)" writebeams="(true &bool;)"
        readbeams="(false &bool;)" clustercheck="(false &bool;)"
        rescorebeams="(false &bool;)" writelps="(true &bool;)"
        fafilter="(true &bool;)" famin="(false &bool;)"
        samplesheets="(true &bool;)" trackfragments="(false &bool;)"
        filterprevious="(false &bool;)" rephasemap="(false &bool;)"
        checksymm="(false &bool;)" asymmdump="(true &bool;)"
        continuous_sheets="(false &bool;)" auto_stop="(false &bool;)"
        greedy="(true &bool;)" read_from_file="(false &bool;)"
        assign_incomplete="(false &bool;)"
        looporder="(0 &non_negative_integer;)"
        maxloopsize="(8 &non_negative_integer;)"
        nfrags="(&nnegative_int_cslist;)" fraglens="(&nnegative_int_cslist;)"
        fragmelt="(2 &non_negative_integer;)"
        minmelt="(15 &non_negative_integer;)" storedbeams="(&string;)"
        filterbeams="(&string;)" coordfile="(&string;)"
        skeletonfile="(&string;)" scorefxn="(&string;)" censcorefxn="(&string;)"
        cenrotscorefxn="(&string;)" >
    <Fragments fragfile="(&string;)" />
</FragmentExtension>
  • fasta: The name of the fasta file
  • beamwidth: Controls the maximize size of the beam search
  • fragtrials: The maximum number of fragments to apply at each extension.
  • debug: Triggers all the debuging options
  • chainbreak: The weight on the chainbreak term when closing the loop
  • continuous_weight: The weight on the non-continuous density penalty
  • rms_cutoff: The rms cutoff for two structures to be considered different
  • fragcluster: The torsional RMS for two fragments to be considered different. Default doesn't filter
  • masterbeamcutoff: The RMS different for two structures to be considered in a different path
  • sheetbonus: The percentage of the score to add for the sampled sheets that fit the density
  • sheet_tolerance: How good do the sheets need to be in order to be accepted
  • sc_scale: Scales down the side chain density score
  • windowdensweight: Density weight on the windowdens
  • masterbeamwidth: Cap on the number of beams within a cluster
  • rmswindow: The number of residues to include in the
  • rmscutoff: How close two conformations must be to be considered identical
  • steps: The number of steps to take before exiting.
  • pcount: The tag for the parallelcount. Purely used for managing jobs through the python script
  • sheetcriteria: The strategy to use for deciding whether or not to grow sheets
  • comparatorrounds: The number of models to produce with the loop comparator
  • beamscorecutoff: The number of models to produce with the loop comparator
  • pack_min_cycles: The number of cycles of packing and minimization to use in full atom mode
  • dumpbeam: Dump the structures after filtering
  • dumperrors: Dump the poses when the beam deviates from the native
  • dumpfinalbeam: Dump the poses after the last step
  • dumprms: Dumps the rms of the beam for debugging purposes
  • dumpfragments: Writes the fragments as a fragfile after picking
  • direction: Which side of the missing segment to start growing from.
  • minimize: Whether or not to minimize the structures
  • nativegrow: Use the native structure as a fragment when growing
  • parametercheck: Uses the native structures to figure out what the settings would need to be to capture the native
  • cenrot: Use the cenrot representation
  • writebeams: Writes 'beamfiles' used in parallelization through python
  • readbeams: Reads the beams from the file
  • clustercheck: Dumps all the structures in the neighborhood of the native for debugging
  • rescorebeams: Rescores all the beams in the beamfile. Useful when testing score functions
  • writelps: Writes an lps file when the loop is finished that can be input for the monte carlo assembler
  • fafilter: Rescores the top 2N structures with the full atom representation before filtering down to N.
  • famin: Toggles minimization in full atom
  • samplesheets: Toggles the sheet sampler
  • trackfragments: Keep order of fragments instead of shuffling (useful only for debugging)
  • filterprevious: Filter against the beams in the filterbeams file. Used in taboo search
  • rephasemap: Triggers rephasing of the map when working with xray data, currently distabled
  • checksymm: Checks all the symmetric versions of the connecting segments to see if an alternative is a better match
  • asymmdump: If pose is symmetric, when filtering results dump only the asymmetric unit
  • continuous_sheets: Toggles a one time vs maintained bonus for the sheets
  • auto_stop: Toggles autostoping when running out of density. Currently unfinished
  • greedy: Only runs on the loop specificed by the loop order variable
  • read_from_file: Read the partial models directly from the file and run the monte carlo assembly
  • assign_incomplete: Have the option to assign no segment to a given peice in the structure when using Monte Carlo Assembly
  • looporder: Which loop to build. Labelted 1-N from N-C termini
  • maxloopsize: If loop order set to -1 all loops shorter than this will be skipped
  • nfrags: The number of fragments to pick
  • fraglens: Fragment Lengths To pick
  • fragmelt: How overlap of the old fragment to replace at every step. fraglen-fragmelt = # of new residues added
  • minmelt: How overlap of the old fragment to replace at every step
  • storedbeams: The name of the file containing the input beams
  • filterbeams: The name of the file containing the beams just used in filtering
  • coordfile: The name of the file with coordinates and score weights, currently not fully developed
  • skeletonfile: The name of the skeleton density map
  • scorefxn: Full Atom Scorefunction
  • censcorefxn: Centroid Scorefunction
  • cenrotscorefxn: Scorefunction for use with cenrot. This is typically not used

Subtag Fragments: Name of the fragment file

  • fragfile: The name of the fragment file