Biocurious is a weblog about biology, quantified.

Publication quality molecules

by PhilipJ on 23 August 2007

A couple of months ago André asked about making and sharing scientific figures, and there was some great reader feedback. I’ve got another, similar question, but this time specifically relating to molecular structures. What does everyone use to create high resolution, publication quality structural images of proteins?

Freelancing science partially answers the question. Pawel suggests


Are there any others? (I’ve just noticed that even Mathematica 6 can now display protein structures!) What is your favorite, and why?

  1. Andre    4015 days ago    #

    From the list, I’ve only ever used VMD, which I find pretty good. Based on those screen shots though I’m going to give Qutemol a try. Those renderings look fantastic!

    I’ve also upgraded to Mathematica 6, so maybe I’ll load some pdbs just for fun. That could turn out to be a useful feature for combining molecular graphics with different plots, should the need arise.

  2. janet    4011 days ago    #

    I’m a big fan of UCSF Chimera. It offers several features that I find really useful (though I use them more for illustration/animation purposes rather than figures for publications).

    One great feature is called ‘multiscale model’ which is mainly meant for larger macromolecular structures (viruses, ribosome, etc) — see Chimera’s gallery especially the clathrin model. I’ve also used this feature to make some illustrations for my lab’s website.

    Another great feature is the ability to export surfaces as VRML (a couple other export options are available too). This allows for easy import of molecules into other 3D applications.

    Lastly, the folks who make Chimera are wonderful — really helpful and supportive.

    I’m a fan of occlusion too, which Qutemol appears to do really nicely. It’s a great way of visualizing molecules!

  Textile help