Tag Archives: Molecular Graphics

Viewing 3D molecules interactively in Jupyter iPython notebooks

Greg Landrum, curator of the invaluable open source cheminformatics API, RDKit, recently blogged about viewing molecules in a 3D window within a Jupyter-hosted iPython notebook (as long as your browser supports WebGL, that is).

The trick is to use py3Dmol. It’s easy to install:

pip install py3Dmol

This is built on the object-oriented, webGL based JavaScript library for online molecular visualization 3Dmol.js (Rego & Koes, 2015); here's a nice summary of the capabilities of 3Dmol.js. It's features include:

  • support for pdb, sdf, mol2, xyz, and cube formats
  • parallelized molecular surface computation
  • sphere, stick, line, cross, cartoon, and surface styles
  • atom property based selection and styling
  • labels
  • clickable interactivity with molecular data
  • geometric shapes including spheres and arrows

I tried a simple example and it worked beautifully:

import py3Dmol
view = py3Dmol.view(query='pdb:1hvr')


The 3Dmol.js website summarizes how to view molecules, along with how to choose representations, how to embed it, and even how to develop with it.


Nicholas Rego & David Koes (2015). “3Dmol.js: molecular visualization with WebGL”.
Bioinformatics, 31 (8): 1322-1324. doi:10.1093/bioinformatics/btu829

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:


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