Superimposes protein structures by matching ligand molecules.

All the given protein structures must contain the same ligand molecule, every time in the same conformation. The program calculates a transformation (rotation-translation) that superimposes that ligand from input structures on the same ligand molecule found in the native PDB. The transformation is then used to rototranslate whole protein structures. Results is written to “out.pdb” file

USAGE: ./ap_superimpose_pdb_by_ligand native_pdb ligand_name pdb_file_1 [pdb_file_2 …]

EXAMPLE: ./ap_superipose_pdb_by_ligand 4rm4A.pdb HEM 5ofqA.pd



  • core/calc/structural/transformations/PairwiseCrmsd