Macromolecular Modeling Blog ™

Hi folks, with all of these smartphones and touch tablets showing up, it’s very possible you could be carrying one around in a lab, at a conference, or at even some agonizing situation where you are bored and away from a real computer. In that case your structural needs can now be satisfied by mobile apps! I’ve personally made a demo to show just how easy this can be: https://play.google.com/store/search?q=andmol

Expect to see the development of more fully-featured mobile apps that allow you to consume and perform science from anywhere at your fingertips. You may even end up developing your own mobile Rosetta plugins soon. In the meantime, your general structural needs can be satisfied by the fully-featured JMol Android port: https://play.google.com/store/search?q=jmol The JMol folks were able to port the mature JMol Java suite to Android. Way to go! I consider that a success story for Android’s choice of platform.

By Justin Ashworth

About Justin: Justin is a postdoctoral fellow at the Institute for Systems Biology in Seattle, WA. He earned his PhD with David Baker at the University of Washington. He has been involved in the development and application of the Rosetta software suite for macromolecular design.

One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a “non-native” viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!)

We want to hear what is YOUR molecular viewer of choice. Each viewer is optimized for a different set of tasks. E.g. VMD is designed for molecular dynamics, UCSF Chimera integrates many molecular analysis tools, Rasmol is a quick and dirty command line operated little fellow, not producing the nicest figures though, PyMOL creates good looking figures and is highly scriptable (as we demonstrated before in PyMOL scripts), while Jmol is web oriented and easy to embed in web pages.

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There are other software available, please tell us in the comments what’s your favorite viewer advantages and what are the disadvantages of the other “lesser” viewers.