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
OESuperposeMethod for methods and descriptions).
prompt> superpose <reference protein PDB> <fit protein PDB> [global|ddm|weighted|sse|site] [site-residue 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