MultiStructureFeaturesReporters

ProteinRMSDFeatures

Compute the atom-wise root mean squared deviation between the conformation being reported and a previously saved conformation. There are several ways of specifying the reference structure, which are considered in the following order

• Using the SavePoseMover :

    <ROSETTASCRIPTS>
        <MOVERS>
            <SavePoseMover name=spm_init_struct reference_name=init_struct/>
            <ReportToDB name=features_reporter database_name="features_SAMPLE_SOURCE_ID.db3" batch_description="SAMPLE_SOURCE_DESCRIPTION">
                <feature name=ProteinRMSDFeatures reference_name=init_struct/>
            </ReportToDB>
        </MOVERS>
        <PROTOCOLS>
            <Add mover_name=spm_init_struct/>
            <Add mover_name=features_reporter/>
        </PROTOCOLS>
    </ROSETTASCRIPTS>

• Using -in:file:native

• Using the resource manager (TODO)

• protein_rmsd :

  • reference_tag : The tag of the structure this structure is compared against
  • protein_CA : the C-alpha atoms of protein residues are considered
  • protein_CA_or_CB : the C-alpha and C-beta atoms of protein residues are considered
  • protein_backbone : the backbone atoms (N, C-alpha, C) of protein residues are considered
  • protein_backbone_including_O : the backbone atoms and the carbonyl oxygen atoms of protein residues are considered
  • protein_backbone_sidechain_heavy_atom : the non-hydrogen atoms of protein residues are considered
  • heavyatom : all non-hydrogen atoms are considered
  • nbr_atom : the neighbor atoms are considered (the C-beta atom for canonical proteins) see the NBR_ATOM tag in the residue topology files
  • all_atom : all atoms are considered

    CREATE TABLE IF NOT EXISTS protein_rmsd (
        struct_id INTEGER AUTOINCREMENT,
        reference_tag TEXT,
        protein_CA REAL,
        protein_CA_or_CB REAL,
        protein_backbone REAL,
        protein_backbone_including_O REAL,
        protein_backbone_sidechain_heavyatom REAL,
        heavyatom REAL,
        nbr_atom REAL,
        all_atom REAL,
        FOREIGN KEY (struct_id) REFERENCES structures (struct_id) DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY (struct_id, reference_tag));

ProteinRMSDNoSuperpositionFeatures

Same as above, but does not superimpose poses prior to calculating RMSD.

CREATE TABLE protein_rmsd_no_superposition(
        struct_id INTEGER,
        reference_tag TEXT,
        protein_CA REAL,
        protein_CA_or_CB REAL,
        protein_backbone REAL,
        protein_backbone_including_O REAL,
        protein_backbone_sidechain_heavyatom REAL,
        heavyatom REAL,
        nbr_atom REAL,
        all_atom REAL,
        FOREIGN KEY (struct_id) REFERENCES structures(struct_id) DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY (struct_id, reference_tag));

RotamerRecoveryFeatures

The RotamerRecoverFeatures is a wrapper for the rotamer_recovery scientific benchmark so it can be included as a feature.

    <feature name=RotamerRecovery scfxn=(&string) protocol=(&string) comparer=(&string) mover=(&string)/>

See the above link for explanations of the parameters.

• rotamer_recovery : The rotamer_recovery of a feature is how similar Rosetta's optimal conformation is compared to the input conformation when Rosetta's optimal conformation is biased to the input conformation.
  • struct_id , resNum : These are the primary keys for the residues table in the ResidueFeatures reporter
  • divergence : This is the score that the RRProtocol returns.

    CREATE TABLE IF NOT EXISTS nchi (
        name3 TEXT,  
        nchi INTEGER,
        PRIMARY KEY (name3));

    INSERT OR IGNORE INTO nchi VALUES('ARG', 4);
    INSERT OR IGNORE INTO nchi VALUES('LYS', 4);
    INSERT OR IGNORE INTO nchi VALUES('MET', 3);
    INSERT OR IGNORE INTO nchi VALUES('GLN', 3);
    INSERT OR IGNORE INTO nchi VALUES('GLU', 3);
    INSERT OR IGNORE INTO nchi VALUES('TYR', 2);
    INSERT OR IGNORE INTO nchi VALUES('ILE', 2);
    INSERT OR IGNORE INTO nchi VALUES('ASP', 2);
    INSERT OR IGNORE INTO nchi VALUES('TRP', 2);
    INSERT OR IGNORE INTO nchi VALUES('PHE', 2);
    INSERT OR IGNORE INTO nchi VALUES('HIS', 2);
    INSERT OR IGNORE INTO nchi VALUES('ASN', 2);
    INSERT OR IGNORE INTO nchi VALUES('THR', 1);
    INSERT OR IGNORE INTO nchi VALUES('SER', 1);
    INSERT OR IGNORE INTO nchi VALUES('PRO', 1);
    INSERT OR IGNORE INTO nchi VALUES('CYS', 1);
    INSERT OR IGNORE INTO nchi VALUES('VAL', 1);
    INSERT OR IGNORE INTO nchi VALUES('LEU', 1);
    INSERT OR IGNORE INTO nchi VALUES('ALA', 0);
    INSERT OR IGNORE INTO nchi VALUES('GLY', 0);

    CREATE TABLE IF NOT EXISTS rotamer_recovery (
        struct_id INTEGER AUTOINCREMENT,
        resNum INTEGER,
        divergence REAL,
        recovered INTEGER,
        PRIMARY KEY(struct_id, resNum));