Calculating superposition

The superposition calculation is a functionality offered through the Spruce TK. This example shows how to calculate structural superposition using either the global, DDM, weighted-DDM, site sequence, or SSE methods.

Command Line Interface

This example takes in a reference and a fit protein (from either a PDB or OEDU file) and aligns them with one of the supported methods (see OESuperposeMethod for methods and descriptions).

prompt> superpose <reference protein PDB> <fit protein PDB> [global|ddm|weighted|sse|site] [site-residue file]


Download code

superpose.cpp and both 1A29.pdb (the reference PDB file) and 1CLL.pdb (the fit PDB file)


prompt> superpose 1A29.pdb 1CLL.pdb ddm

will generate the following output:

Superposing 1CLL.pdb to 1A29.pdb using ddm
Writing superimposed fit protein to 1CLL_sp.oeb.gz
RMSD: 0.596203 Angstroms
SeqScore: 642