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...
6 comments:
Thanks for the review. You're right -- PyMOL on the iPad requires more memory than most other apps. So, you need to close other apps to free up memory. We show you how to do this on our Mobile Support page (http://pymol.org/mobile-support) directly linked from the App Store. Once you close apps you're not using you should be fine -- even on the iPad1. Having said that, yes, memory issues are annoying and we're working on improving it.
The major challenge here was figuring out how to expose all that PyMOL can do via the touch interface. For example, because typing is inefficient on the iPad we chose not to provide a command line. And, because screen real estate is valuable we couldn't provide the typical PyMOL menus: it just doesn't make sense on this device.
We provided what we considered the most valuable features of PyMOL given the limitations of the device. It's really fun to "touch" the molecules, view them in lots of various representations, center, select, ray trace, use our special anaglyph 3D mode, copy screen shots, etc. All of this is now possible on a device the size of a paperback book.
Last, we're taking comments/ideas for improvements on the PyMOLWiki page, http://pymolwiki.org/index.php/Mobile.
Cheers,
-- Jason
I Jason! I have been playing around a bit more by now, and I have to say I like the general appearance of the app. As you say, it would have been foolish to clutter the screen with the usual PyMOL menus: it is good because you can use nearly all of it to show one's structure.
I have to say I cannot see any clipping while dragging three fingers.
I will try and write some comments on the wiki page, thanks for pointing it out.
Cheers!
/Luca
Hi Luca,
Clipping works but sometimes the iPad gets confused and rotates the scene instead. So, try this to get used to it. Load a structure. Double-tap an atom to focus on it (this places the atom at the center of the screen and the center of the clipping slab). Then using your left hand, place two fingers on the left side of the screen. Then, with your right hand on the right side of the screen, slowly drag one finger up/down. You should see the clipping slab become thinner/thicker. Once you get used to the timings try using three fingers up/down from one hand.
Cheers,
-- Jason
Yippie! That works like a charm!
Hi,
I just have a quick question - is there an easy way to select multiple atoms? (for example, all atoms within a structure in order to change their colour?) I'm looking at some pretty large nucleic acid structures and it would be impossible to select each individual atom.
Great app by the way!
Thanks in advance for your help
Hi Kathryn,
I'm no expert on it, I'm just playing around with the app. Anyway I can tell you that you can change what you select in the settings menu, which you can access by tapping in the gear icon on the top right corner. There in the selection pane you can decide to select atoms, residues, chains etc. Once you got your selection you can then color it by tapping and holding onto it. I hope it was helpful.
Cheers!
/Luca
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