4.3.1. PYMOL

URL:

http://www.pymol.org/

This example below uses the external software called PyMOL. It can be installed via conda:

conda install -c schrodinger pymol-bundle

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.

import __main__

__main__.pymol_argv = ["pymol", "-qc"]  # Quiet and no GUI

import os

if os.path.isfile("bioservices_pdb.png"):
    os.remove("bioservices_pdb.png")

# BioServices 1: obtain the PDB ID from a given uniprot ID (P43403 i.e. ZAP70)
from bioservices import PDBe, UniProt

print("Retrieving PDB ID")
u = UniProt(verbose=False)
res = u.mapping(fr="UniProtKB_AC-ID", to="PDB", query="P43403")
pdb_id = res["results"][0]["to"]  # e.g, "1FBV"

# BioServices 2: Download the PDB file from the PDB Web Service
print("Fetching PDB file")
p = PDBe()
res = p.get_files(pdb_id)

# General: save the fetched file in a temporary file
import tempfile

fh = tempfile.NamedTemporaryFile()
fh.write(res)
sname = fh.name

# THIS IS NOT BIOSERVICES ANYMORE but PYMOL
import pymol

pymol.finish_launching()
pymol.cmd.load(sname)
pymol.cmd.png("bioservices_pdb.png", width="15cm", height="15cm", dpi=140)
# pymol.cmd.png("my_image.png")
# Get out!
pymol.cmd.quit()

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.