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]
Code¶
Download code
superpose.py
and both
1A29.pdb
(the reference PDB file)
and
1CLL.pdb
(the fit PDB file)
Example¶
prompt> superpose.py 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
See also
OESuperpose class
OESuperposeOptions class
OESuperposeResults class
OESuperposeMethodnamespace