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_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.

DESCRIPTION

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.

foo_out.pdb

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.

PROGRAM OUTPUT

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.

EXAMPLES

Runnable example

superpose.exam

SEE ALSO

lsqkab
Gesamt

AUTHOR

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

REFERENCE