A review of protein/DNA visualization software on a iOS iPad

I know it has been quite while since I have posted my last review. So it is time do another review.

Last post in this blog was about Energy Minimization (I still owe you the Yasara review, I haven't done that because I am still biased against that visualizer. But I'll overcome that) and not long after I read this post from Bosco Ho (http://boscoh.com/protein/purity-in-the-atomic-force-fields-of-molecular-dynamics-simulations). Check that one out, I think his perspective is a good and relevant one.

Now, after reviewing visualization software for Mac OS X is a natural step to review visualization software for the iOS. By now, there are a few on the App Store, such as Molecules, iMolView and Ball & Stick. I guess there might be many more out there but I haven't tried any other yet.

This time I'll review Ball & Stick, from http://www.molysym.com/ (2.99 buckaroos at the iTunes Store http://itunes.apple.com/us/app/ball-stick/id434305371?mt=8).

The apps is a very nice attempt at having a visualizer on an iPhone or iPad. The App allows you to search the PDB for keywords or directly for PDB ID codes. The search feature is moderately successful and I have seen it hang when the search query grows beyond 3 or 4 words.

Once you load a protein you have the regular options to display it (wireframe, stick, ball and stick and space filling). Now, this is a bit counter-intuitive but the ribbons representation is an independent option. How does this works?
I am not sure but I have observed that if you load a protein without any heteroatom (except water) both settings (ribbons and the rest) affect the whole protein. If you have a protein with a ligand, the ribbons setting affects the whole protein while the other options only affect residues near ligands.

Let's skip this for a second and move on to other options. Ligands, water and ion atoms have independent settings with the same options. Ribbons (for protein) can only be turn on or off. At the bottom of the settings there is a slider to select the cut-off distance for displaying residues near ligands.

Now, when you load a protein with a ligand the ribbons setting affects the whole protein while the protein representation setting will only affect the residues close to the ligand. Kinda makes sense but I would prefer finer control over that.

Coordinate manipulation is easy: one finger to rotate, two fingers in a pinch-like fashion to zoom or two fingers fixed to translate the model. I haven't been able to find a way to center on an atom. Maybe that would be good improvement.

Image quality is good and you can save scenes to you photo library or send then it attached to a email.

A problem I ran into is that complex heteroatoms or residues with double occupancies are not displayed properly.

There is a collaboration tool that I haven't test but if that works as good as advertised that would be a good recommendation point. Other than that iMolview (review coming soonish) is a better choice.