Structure Alignment: align_binding_sites

This script performs a pairwise superposition of multiple structures using the C-alpha atoms of selected residues. The reference structure for the alignment is the first structure in the input file. The C-alpha atoms used for the alignment come from residues within the specified cutoff distance from the ligand in the reference structure. Alternatively, a list of residues may be given for the alignment, which must correspond to residues in the reference structure. C-alpha atoms in the structures that are aligned that are greater than the specified distance from any C-alpha in the reference are not considered in the alignment. The RMSD matrix for the alignment is written to the file jobname-matrix.csv in three columns: the indexes for the structures, then the RMSD value. The syntax is:

align_binding_sites [options] input-files

If you specify more than one input file, the reference structure is the first structure in the first file. For a description of the options, run the command with the -h option.