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Some people, like Imelda Marcos and our new Dr. Isis, have a thing for fancy shoes.

I go crazy for gadgets.

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For my birthday this year, my family bought me a new iPhone! Yeah!

So, I’ve been killing several hours today filling it with cute little iPhone apps. Who knew one little phone could be so much fun?

One app, I enjoy, is called Molecules.

Molecules lets you download structure files from the Protein Data Bank (PDB) and play with the structures on your phone!

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Spreading your fingers makes the molecule larger.

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Working with your fingers also lets you turn the molecule around.

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It’s also nice that the developer, Brad Larson, made the code available, ’cause I have all kinds of requests for improvements and new features.

Here’s my wish list:

  • Make the colors match the colors in Cn3D. Phosphorus should be green, not orange.
  • In Cn3D, I can add annotations, I would like to be able to view those annotations.
  • I would like to be able to see superimposed structures.
  • I would like to be able to limit the view to selected parts of the structure.
  • I would like to be able to change rendering and coloring styles.
  • Add support for mmdb formatted files. I would be fine with making annotated files in Cn3D on my desktop computer and then viewing them in Molecules.

This sort of thing must be why I hear stories about schools getting iPhones for students.

Comments

  1. #1 Invader Xan
    November 24, 2008

    That’s so wonderfully geeky. I love it! :)
    (Now all I need is an iPhone…)
    Do you have to download the structures for this, or can you import your own PDB files?

    Oh, and FYI, I think some colours are a discipline thing. In most branches of chemistry, phosphorus tends to be purple. Green is normally reserved for chlorine. ;)

  2. #2 Sandra Porter
    November 24, 2008

    I tried using both the PDB-formatted structures that I downloaded from the Protein Data Bank and PDB-formatted structures that I downloaded from the NCBI.

    Only the structures from the Protein Data Bank worked.

    I see your point about the colors, some of the viewers at the Protein Data Bank show phosphorus as orange, too.

  3. #3 Brad Larson
    November 24, 2008

    I’m glad that you find it useful. If you’re interested in my vision for the program, I was invited to write an article for the RCSB Protein Data Bank newsletter’s educational column: http://www.rcsb.org/pdb/general_information/news_publications/newsletters/2008q3/education_corner.html .

    I agree that there’s a lot left to be done before the full educational and scientific potential of the application can be realized. I’ll add mmdb as a file format for importing structures. I had hoped to get the ability to select NMR structures and overlay multiple structures in the latest update, but couldn’t fit it in. I didn’t spend as much time with metadata, so I’m not sure if the PDB format supports annotation, but I’ll look at adding support in a way that won’t clutter the limited display real estate of the portable device.

    As far as coloring goes, I’ve used Jmol in the past, so I relied on its color scheme: http://jmol.sourceforge.net/jscolors/ . If there’s a standard you could point me to, it would be simple to adjust the colors to match. Maybe a pop-up legend might help.

    In regards to changing rendering styles, you can access a couple of simple ones via double-tapping on the display. Cartoon or ribbon visualization modes are high on my list of things to work on, and others have volunteered to help with that.

    Unfortunately, I’m a little distracted right now with another educational / science application, so progress may be slow on this for the next couple of months.

  4. #4 Isis the Scientist
    November 24, 2008

    This may be one of the hottest things I have ever seen in my life. I wonder if I could get an anatomy atlas for my iPhone? That would make surgery a whole lot easier when I am suddenly like, “Now wait, where is the spleen supposed to be again?”

  5. #5 Sandra Porter
    November 24, 2008

    You’re in luck, Isis, check out this movie on YouTube.

  6. #6 Sandra Porter
    November 24, 2008

    Brad: Thanks for stopping by!

    I haven’t been able to find any documentation for the color scheme in Cn3D, but I will keep looking.

    I’ll definitely take a look at your article. I’m definitely interested. I don’t know if it’s helpful or not, but I do know that Cn3D is open source, so maybe that will be helpful.

  7. #7 Brad Larson
    November 24, 2008

    Hey, I’m just glad to hear from researchers / educators that like the application. It makes me feel like this was worth it (a reassurance I sometimes need after reading some of the iTunes reviews).

    You also mentioned that you were having trouble with non-RCSB PDB files. If you could point them out here or in the forums ( http://www.sunsetlakesoftware.com/forum ), it would help me to figure out what I’m doing wrong. I only tested the custom import functionality on a small number of non-RCSB files.

  8. #8 Sandra Porter
    November 24, 2008

    Thanks Brad,

    I will post some examples in the forum.

  9. #9 fery hossein
    December 22, 2008

    ANIMATION DNA

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