Friday, 3rd February 2012

pdbimport

pdbimport loads a PDB file into MATLAB, something which is very difficult to do yourself if you dont have the very expensive Mathwork’s Bioinformatics Toolbox. The difficulty largely arising due to the standards of the PDB format being so open.

pdbimport loads a PDB into a structure and from there you can view the sequence, any of the headers and remarks as well as breaking the individual atoms down into manageable fields

Syntax

PDBIMPORT ()

When run with no inputs a graphic user interface is launched that allows the user to navigate their system and select a file to load.

Alternatively, pdbimport can be called like so

PDBIMPORT('/path/to/file.pdb')
PDBIMPORT('http://example.com/file.pdb')
PDBIMPORT('XXXX')

The user can manually type the address to a local file or a web address as a string and the script will load it, but pdbimport also can fetch files directly from rcsb.org/pdb (pdb.org) if the PDB accession number is known

To save the fetched PDB as a structure pdbimport should always be run with an output, for example:

proteinA = pdbimport('1QTJ')

Available for direct download

About Morgan Bye

Scientist, programmer and all around techie

Category

EPR toolbox