Category Archives: Molecular Visualization

Making Protein-Protein Interfaces Look (decently) Good

This is a little PyMOL script that I’ve used to draw antibody-antigen interfaces. If you’d like a commented version on what each and every line does, contact me! This is a slight modification of what has been done in PyMOL Wiki.

load FILENAME
set_name FILENAME, complex	

set bg_rgb, [1,1,1]  	

color white 	     		

hide lines
show cartoon

select antibody, chain a
select antigen, chain b

select paratopeAtoms, antibody within 4.5 of antigen 
select epitopeAtoms, antigen within 4.5 of antibody

select paratopeRes, byres paratopeAtoms
select epitopeRes, byres epitopeAtoms

distance interactions, paratopeAtoms, epitopeAtoms, 4.5, 0

color red, interactions
hide labels, interactions

show sticks, paratopeRes
show sticks, epitopeRes

set cartoon_side_chain_helper, on

set sphere_quality, 2
set sphere_scale, 0.3
show spheres, paratopeAtoms
show spheres, epitopeAtoms
color tv_blue, paratopeAtoms
color tv_yellow, epitopeAtoms

set ray_trace_mode, 3
unset depth_cue
set specular, 0.5

Once you orient it to where you’d like it and ray it, you should get something like this.
contacts

Making small molecules look good in PyMOL

Another largely plagiarized post for my “personal notes” (thanks Justin Lorieau!) and following on from the post about pretty-fication of macromolecules.  For my slowly-progressing confirmation report I needed some beautiful small molecule representation.  Here is some PyMOL code:

show sticks
set ray_opaque_background, off
set stick_radius, 0.1
show spheres
set sphere_scale, 0.15, all
set sphere_scale, 0.12, elem H
color gray40, elem C
set sphere_quality, 30
set stick_quality, 30
set sphere_transparency, 0.0
set stick_transparency, 0.0
set ray_shadow, off
set orthoscopic, 1
set antialias, 2
ray 1024,768

And the result:

ligand

Beautiful, no?

Good looking proteins for your publication(s)

Just came across a wonderful PyMOL gallery while creating some images for my (long overdue) confirmation report.  A fantastic resource to draw sexy proteins – especially useful for posters, talks and papers (unless you are paying extra for coloured figures!).

It would be great if we had our own OPIG “pymol gallery”.

An example of one of my proteins (1tgm) with aspirin bound to it:

Good looking protein