3D Protein Imager a PyMOL/Qutemol web alternative


3d protein imaging web interface

Molecule of the Month

In the year 2000 David Goodsell started to provide stories on the The Protein Data Bank web site as the “molecule of the month” with his unique style that was later made available by the Qutemol software, unfortunately not updated since 2007 and therefore no longer working on many systems, most of them based on macOS.

This very recognizable style is again available in a web-based interface at the  3dproteinimaging.com site founded by Italian authors Gianluca Tomasello, Ilaria Armenia, and Gianluca Molla.

The interface is (mostly) self explanatory (sic) but there is a 10 pages PDF manual available. The one thing that I found difficult to understand was the selection mechanism, even though I was able to color the viral coat proteins vp 1, 2, 3  of rhinovirus B14 (PDB structure 4rhv) shown below in full screen.

3d protein imaging full screen web interface
rhinovirus B14 (4RHV) capsid proteins vp 1, 2, 3 are shown in bleue, green and red respectively.

Registration and services

Registration is free and provides the additional service to be able to “render” an image with better quality graphics through their server which uses the PyMOL rendering engine.

To produce the final high-quality rendered images, we exploited the internal ray tracer engine of the open source PyMol package. (Reference 1)

When the image is ready to download a link is provided in the user’s space (hence the need to register) as shown below:

3d protein imaging download image link example

Molecular graphics representations

Other representations as available in e.g. sicks, cartoons, and surfaces as well as the possibility to add membrane regions.


1. Gianluca Tomasello, Ilaria Armenia, Gianluca Molla, The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities, Bioinformatics, Volume 36, Issue 9, May 2020, Pages 2909–2911, https://doi.org/10.1093/bioinformatics/btaa009