Friday, 24th February 2012

PyMOL visualising binding interfaces

Today I’ve been trying to come up with a nice way of visualising the binding interface between protein-protein or protein-DNA complexes. What follows is a quick little walk-through mostly for my own purposes so that I can remember what I’ve done in the future.

Download PDB file from pdb.org, here XXXX will be your PDB accession code.

Point a terminal window at the download directory

cd ~/Downloads

Run CCP4:

ncont XYZIN XXXX.pdb >> XXXX.ncont << eof
source A              [or whatever your protein chain is]
target E,F            [or whatever the DNA chains are]
eof

This will give us a file XXXX.ncont in the Downloads folder which contains all the information about the binding interface

Download the PyMOL script for converting CCP4 (*.cont) files: ccp4_ncont.py

Now in PyMOL, load the CCP4 interuptation script

run ~/Downloads/ccp4_ncont.py

Load the file using File -> or:

load ~/Downloads/XXXX.pdb

Manipulate the file to something presentable

 

In command line type:

ccp4_ncont ~/Downloads/XXXX.ncont, selName1=prot, selName2=DNA

This gives us all of the atoms and residues involved in binding as useful objects (right hand side of the Viewer Window)

Now we can visualise things a bit better.

select dsDNA, chain E+F

This selects chains E and F and creates an object called dsDNA. On this object, hide everything, they we can set about visualising the thing better:

show_as cartoon, dsDNA

set cartoon_ring_mode, 3

set cartoon_ring_finder, 1

color green, dsDNA and elem C

For other styles see the Pymol wiki

Now we can work on the protein and show the residues at the binding interface

show sticks, prot_res

color gray60, plot_res

Or select the object and click C (for Color) then “by element”

And then adjust the Carbon colour to the desired using

color gray60, elem C

Replacing gray60 with your chosen colour

Currently we have a pretty good stick diagram, but a delicate ball and stick model looks more professional

set stick_radius, 0.1

show spheres, prot_res

set sphere_scale, 0.15

So our balls of the ball and stick are now present, but to make these more presentable we need to improve their quality when we render

set sphere_quality, 4

set stick_quality, 16

As the figure grows in complexity it maybe required to turn ray shadows off

set ray_shadow, off

I’ve also recoloured the DNA bases using

color green, dsDNA+ elem C

Now we can add Van der Waal radii of the key atoms to emphasize the binding interface.

show dots, prot_atom

show dots, dna_atom

Optimise the viewing angle using:

orient dsDNA

And then use the mouse-wheel to move the transparency of the background, so that the emphasis is in what want to see and the background does not distort it

Finally, to show the co-factor (here it is Mg, in light green) I show it as a Sphere but as we’ve changed the spheres for the ball and stick model we need to:

alter elem mg, vdw=10.0

rebuild

And dont forget to “ray” for pretty pictures

About Morgan Bye

Scientist, programmer and all around techie

Category

Research