SUPERPOSE (CCP4: Supported Program)

NAME

superpose - structural alignment based on secondary structure matching

SYNOPSIS

superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ]

where [-s CID1/2] are optional selection strings in MMDB convention, and [foo_out.pdb] is an optional output file.

DESCRIPTION

superpose aligns two 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, structures should always include at least three secondary structural elements.

INPUT AND OUTPUT FILES

foo_1st.pdb

First input coordinate file. Although typically a PDB file, it can also be in mmCIF or MMDB binary formats. The input format is detected automatically. This is considered the Query structure to which the transformation matrix will be applied.

foo_2nd.pdb

Second input coordinate file. Although typically a PDB file, it can also be in mmCIF or MMDB binary formats. The input format is detected automatically. This is considered the Target structure.

foo_out.pdb

If specified, the result of applying the transformation matrix to foo_1st.pdb is written to foo_out.pdb.

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.

PROGRAM OUTPUT

The program reports the Transformation Matrix calculated for superimposing foo_1st.pdb onto foo_2nd.pdb and the RMSD from the superposition.

The program then gives a residue-by-residue listing of the alignment. Strands and helices in the two structures are identified. The quality of the match for each residue is given.

EXAMPLES

Runnable example

superpose.exam

SEE ALSO

lsqkab

AUTHOR

Eugene Krissinel, CCP4 (formerly at European Bioinformatics Institute, Cambridge, UK).

REFERENCE