Calculating Simple Superposition¶

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

Command Line Interface¶

This example takes in a reference and a fit protein, aligns them with either the method global, ddm, or weighted-DDM method (see OESuperpositionType for method descriptions).

prompt> simplesuperposition <reference protein> <fit protein> [global|ddm|weighted]

Code¶

Download code

simplesuperposition.py and both 1A29.pdb (the reference PDB file) and 1CLL.pdb (the fit PDB file)

Example¶

prompt> simplesuperposition.py 1A29.pdb 1CLL.pdb ddm

will generate the following output:

RMSD for the fit of 1CLL.pdb to 1A29.pdb is 0.596203 Angstroms.

Writing superimposed fit protein to 1CLL_sp.oeb.gz