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
This page previously appeared on morganbye.net[^1][^2][^3]
[^1:] http://morganbye.net/pymol-visualising-binding-interfaces [^2:] http://morganbye.net/2012/02/pymol-visualising-binding-interfaces) [^3:] http://morganbye.net/uncategorized/2012/02/pymol-visualising-binding-interfaces/
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