SUPERPOSE (CCP4: Supported Program)
- structural alignment based on secondary structure matching
superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2]
... foo_Nth.pdb [-s CIDN] [-o foo_out.pdb]
where [-s CID1/2/.../N] are optional selection strings in
MMDB convention, and [foo_out.pdb] is
an optional output file.
superpose aligns and superposes two or more protein structures by matching
graphs built on the protein's secondary-structure elements, followed by an iterative
three-dimensional alignment of protein backbone C-alpha atoms.
For this method to work, aligned structures should always include at least three
secondary structural elements.
INPUT AND OUTPUT FILES
foo_1st.pdb / foo_2nd.pdb / ... / foo_Nth.pdb
Input coordinate files; at least two files must be given. Although typically a PDB file,
an input file can also be in mmCIF or MMDB binary formats. The input format is detected
automatically and independently for each input file. In case of pairwise aligbment,
foo_1st.pdb is considered to be the Query structure to which the transformation matrix
will be applied. In case of multiple (N>2) structure alignment, transformation matrices
will be calculated and output separately for each structure.
If specified, this file will contain a sequence of input structures with the
calculated transformation matrices applied.
Command line options
The optional selection strings [-s CID1/2] are in the
format described in the pdbcur
documentation. For example, -s A/23-55 means use only
residues 23 to 55 of chain A in calculating the alignment.
The program reports the Transformation Matrix calculated for
superimposing the input structures and the RMSD from the superposition.
The program then gives a residue-by-residue listing of the
alignment(a). Strands and helices in the aligned structures are identified
in the listing. The quality of the match for each residue is also given.
Eugene Krissinel, CCP4 (formerly at European Bioinformatics Institute, Cambridge, UK).
- E.Krissinel and K.Henrick (2004), Acta Cryst. D60, 2256-2268
Secondary-structure matching (SSM), a new tool for fast protein structure
alignment in three dimensions