Monday, August 20, 2012

PyMOL on the iPad

I just got an email (labeled as spam for who knows reason) from Schrödinger saying that they made PyMol available for the iPad, and most of all for free. Now, who am I to resist and not try it head on? In fact I downloaded it immediately.

First impression: very negative! It starts with a very condensed help panel, closing which one should see a demonstration molecule. The molecule did not show up because the app says that I have not enough free memory on my device! So, here we have me with big expectations staring at a black screen with just a couple of buttons on the top. So sad.

Never mind, I decided to try and load another protein structure from the pdb. Second impression: amazing! One can finally "touch" proteins, rotate and move and zoom them as one wishes. There are the familiar ways of displaying a structure (e.g. lines, cartoon etc., but not ball-and-sticks for non ligands) and many possibilities for performing a selection. It is only 10 minutes that I'm playing with it, so I haven't figured out all the available tools. One thing I tried is to ray trace (yes, ray tracing!) the actual scene I had. The app miserably crashed.
My guess is that the app could become a nice tools for both (self-)education and production of nice images.

Here is my good-bad list after 10 minutes of playing around:
good
- possibility to load structures from many different sources (pdb, dropbox and others)
- possibility for different rendering
- possibility to directly save screenshots
- multiple structures can be displayed
- but most of all you can rotate them with your finger tips!

bad
- it seems it requires a lot of memory
- no possibility (at least I haven't found out) to fade out parts of the structure other than that one is interested in

One more thing: it would be soooooo great if Schrödinger would distribute the code behind the structure visualizer. It would open up many possibilities for visualizing a structure inside another app. Think like BioFET-SIM 2.0 on the iPad...
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