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]
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