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## SequenceRecoveryMetric

Autogenerated Tag Syntax Documentation:

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;)"
packer_palette="(&named_packer_palette;)" />