RMSD API

The RMSD API allows users to calculate the RMSD between a set of PDBs. By default, the API calculates all-atom all-pair RMSD between all input PDBs. Users can specify a reference PDB for all inputs.

Alignment and calculation methods available include: all-atom (default), CA-only, CB-only, backbone atoms, and GDTHA. If using all-vs-all comparisons, the API will also attempt to cluster structures based on a cutoff (default 2 angstroms).

The API will return a CSV reporting the RMSD between the reference and all inputs, or if no reference is provided, a matrix of for all pairs of inputs, a heatmap for visualizing these scores, a CSV of cluster assignments, and a dendrogram for visualizing the clustering relationships.

Command Line Interface

Examples

Find RMSD-based clusters between all-atom structures.

lev engine submit rmsd *pdb \
    --chains A \
    --cutoff 3.0 \
    --mode all-atom

Calculate alpha carbon RMSD between a reference structure and other structures.

lev engine submit rmsd *pdb \
    --reference-structure reference.pdb \
    --mode ca-only

Flags

  • --chains (str)
    • Comma separated list of chains to use in alignments.
  • --cutoff (float) (Optional)
    • Cutoff for clustering (default 2 angstroms)
  • --mode (str)
    • Mode to use (all-atom, ca-only, cb-only, backbone, gdtha) (default “all-atom”)
  • --pdb-file (str)
    • Path to input pdb file(s).
  • --reference-structure (str)
    • Path to reference structure for all-vs-all RMSD calculations (default “null”)

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