Extracting Biounits by Aligning to a Reference Protein

Biounit (BU) extraction is one of the more basic functionalities offered through the Spruce TK. This example shows how to extract BUs using a sequence alignment to a reference protein.

Command Line Interface

This example takes in an extraction PDB file, a reference PDB file, and optionally the mininum score for the alignment to the reference as well as a boolean flag to instruct the code to superimpose the output BU to the input reference protein (see OEExtractBioUnits for details on the API).

prompt> extract_biounits_ref <extract protein PDB> <reference protein PDB> [min score] [superpose]

Code

Download code

extract_biounits_ref.py and both 4OBD.pdb (the extraction PDB file) and 2UPJ.pdb (the reference PDB file)

Example

prompt> extract_biounits_ref.py 4OBD.pdb 2UPJ.pdb

will generate the following output:

Writing biounit 0 to 4OBD_BU_0.oeb.gz
Writing biounit 1 to 4OBD_BU_1.oeb.gz

See also