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SequenceRecoveryMetric

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A metric for measuring sequence recovery and adding it to the resulting score file.

There's several options for how the sequence recovery is calculated, depending on what parameters are set. Each metric is only calculated over the set of residues specified by the residue selector.

  • Standard - Used when PSSM isn't set but reference pose is This is a strict match/no-match fraction.
  • Pass/Fail PSSM - Used when PSSM is set and use_ave_pssm is not (does not use reference pose) This is the PSSM recovery metric from DeLuca, Dorr and Meiler 2011 Biochem 50(40):8521 Residue identities with positive (or zero) values in the PSSM count as a match, those with negative vales as no-match.
  • Ave PSSM - Used when PSSM is set, use_ave_pssm is true, and no reference PDB is given This value is the average of the values in the PSSM matrix for the residue identities.
  • Delta PSSM - Used when PSSM is set, use_ave_pssm is true, and a reference PDB is provided. This value is the average of the change in value of the PSSM matrix (mut - ref)

For PSSM metrics, it's assumed that the Pose numbering of both the main and reference structure matches the numbering of the PSSM.

<SequenceRecoveryMetric name="(&string;)" custom_type="(&string;)"
        use_native="(false &bool;)" pssm="(&string;)"
        use_ave_pssm="(false &bool;)" reference_name="(&string;)"
        residue_selector="(&string;)" residue_selector_ref="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" />
  • custom_type: Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.
  • use_native: Use the native if present on the cmd-line.
  • pssm: a filename of a blast formatted pssm file containing the sequence profile to use
  • use_ave_pssm: Use an average value metric for PSSM, rather than a pass/fail
  • reference_name: Name of reference pose to use (Use the SavePoseMover to create a reference pose)
  • residue_selector: Calculate the sequence recovery for these residues
  • residue_selector_ref: Selector for the reference pose. If not specified, assume there's a 1-to-1 correspondence between the active pose and the reference pose.
  • task_operations: As a convenience, instead of a residue_selector for selecting which residues to count, you can pass task operations and the design residues will be used. The use of the residue_selector attribute is prefered.
  • packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).

See Also