3.3.1. PYMOL

URL

http://www.pymol.org/

This example below uses the external software called PyMOL. We have installed it without trouble by downloading the source file from their website. Then, we typed those commands in a shell:

bunzip pymol-v1.6alpha1.tar.bz2
tar xvf pymol-v1.6alpha1.tar
cd pymol
python setup.py install

You may need to install library if requested. Tested under Fedora 15.

The following code uses BioServices to get the PDB Identifier of a protein called ZAP70. To do so, we use bioservices.uniprot.UniProt to get its accession number (P43403) and its PDB identifer. Then, we use bioservices.pdb.PDB to get the 3D structure in PDB format.

The script above uses PyMOL in a script manner to save the 3D graphical representation of the protein (here below) but you could also use PyMOL in an interactive mode.

bioservices_pdb.png