Molecules On Your iPod Or iPhone

For the benefit of the gadget geeks among C&ENtral Science's readership, I've created a video walkthrough of Molecules 1.0, a new application for the iPhone and the iPod Touch. (Apple officially unlocked access to 3rd-party applications last week). Molecules is a visualization tool for 3-D structures. I used to work with programs like this during college, when I was an intern in an x-ray crystallography group. This version of the software isn't super-powerful, and doesn't have all the features of a standard visualization program. I agree with the commenter here who thinks it would be neat to confer inertia on the molecules when rotating, so that they would keep spinning after you flick them (the iPod Touch does something like this when you scroll). But that aside, it's still amazing to me that programs like Molecules, which I worked with on advanced computers, are now available for handheld devices. The software is free and the developer's website says that the source code will become available soon, for those who are interested in tinkering with the program themselves. For brief reviews, see Wired Science and MacResearch. **My video walkthrough may not be 100% comprehensive, so please let me know if I've left anything out.**

Author: Carmen Drahl

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4 Comments

  1. Wow, thanks for the video walkthrough. I’d planned something similar once I got back home (I’m on the road right now).

    I apologize for the limited visualization and molecule download options right now. I wanted to get something out in the hands of users on day one so that they could see the possibilities of the iPhone / iPod Touch platform. I hope to have many of the suggested improvements incorporated soon and will make the source code available as soon as Apple’s NDA lets me.

  2. Brad, thanks for popping in! I’d love to know how much functionality you think a program like this should have in the long term (probably not all the functions of a standard program, which might be too hard on the processor). You mentioned in your blog that X-ray crystallographers might want to use Molecules to “show off” their new structures to others. I think chemists working with other types of molecules would love it, too. The best way to do that might be to arrange for downloads from the Cambridge Structural Database.
    http://www.ccdc.cam.ac.uk/products/csd/

  3. I’m getting raked over the coals in iTunes reviews for lack of an easy way to load new molecules, so that is a primary concern. In the near term, I’m working on integrating keyword searching for molecules in the PDB, as well as other data sources. In particular, I’d like to add support for sources of small molecule structures. If an organic chemistry student could enter in a molecule’s name and quickly view its structure, this could become an excellent educational tool. However, I couldn’t find a freely available API for users to download molecules from the CSD like they can from the PDB. Without that, I won’t be able to use it for a program like this. Finally, I’m working on a longer-term solution for users to import their own custom molecules onto the device.

    Next in the list of priorities would be additional visualization options. Spacefilling and cylindrical representations should be reasonably easy to implement, so I’d expect those soon. Ribbon visualization for secondary structure of proteins will take a little longer to put in place, but I have received offers of help on that front.

    Finally, I don’t think that I’m making full use of the iPhone’s computing power, so I’d expect optimizations in processing of files and the 3-D rendering to greatly improve performance.

  4. Brad, Please feel free to contact me at antonyDOTwilliamsATchemspiderDOTcom. We have over 21 million molecules online at ChemSpider and can provide you an API to download a molecule based on chemical name. It’s already built and we just need to help you with the visualization etc. I can point you to 3D optimization tools etc.

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