Superimposing two PDB files with superpose_pdbs



superpose_pdbs is a command line tool for superimposing one PDB model on another and writing out the superimposed model.


How superpose_pdbs works:

superpose_pdbs performes a least-squares superposition of two selected parts from two pdb files. If no selections is provided for fixed and moving models the whole content of both input PDB files is used for superposition. If the number of atoms in fixed and moving models is different and the models contain amino-acid residues then the sequence alignment is performed and the matching residues (CA atoms by default, can be changed by the user) are used for superposition. Note that selected (and/or matching) atoms are the atoms used to find the superposition operators while these operators are applied to the whole moving structure.

Output files from superpose_pdbs

A PDB file with fitted model.


Standard run of superpose_pdbs:

Running the superpose_pdbs is easy. From the command-line you can type:

phenix.superpose_pdbs fixed.pdb moving.pdb

Parameters can be changed from the command line:

phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and name CA" selection_moving="chain B and name CA"

Possible Problems

Specific limitations and problems:


Additional information

List of all available keywords