Reads an alignment between two proteins (PIR format) and the two respective protein structures (PDB format)

and writes the aligned parts of the two structures.

The program concerns only the first two sequences found in the PIR file; they must be given in the same order as the input PDB files. Only the first chain will be used from either structure; if you need to superimpose chain ‘B’, use strc command to extract it prior using ap_aligned_pdb.

The program writes ‘query’ and ‘tmplt’ files which contain the respective structure fragments, already superimposed (the template on the query). One of the two structures may be missing (either the query or the template), dash ‘-‘ should be used instead of the respective file name, as in the examples below.

USAGE: ap_aligned_pdb example.pir prot1.pdb prot2.pdb ap_aligned_pdb example.pir - prot2.pdb ap_aligned_pdb example.pir prot1.pdb -



  • core/data/io/pir_io