Macromolecular structure visualization: a look at the applications that provide graphical interface to structure analysis. Part III PyMol(X11Hybrid).

You, dear reader, might be a crystallographer or just a scientist interested on the fruits of X-ray crystallography. Regardless, you will be interested on visualization software. In my experience a GUI will lower the entry barrier for need minds (eyes and hands) to venture into the realm of structure analysis.

The purpose of this blog entry is to bring an update to the reviews for free visualization software available. I will cover three main topics: ease of use, available features and overall strengths and weaknesses.

Now, up for my third installment PyMol.

N.B.  I am a Mac user (10.6) and in the case of PyMol (current version 1.3) I always run the X11 version the one so called PyMolX11Hybrid. The reason for this is to gain access to the Plugin menu.

PyMol ease of use.

It might be that my own history learning the use of structure visualization software but I originally found PyMol to be the least easy to use. It might also be that he late Dr. Warren L. DeLano did a wonderful job at improving it in a relative short time.

The default screen you’ll see when you run PyMol for the first time will be deceptively simple. You’ll have two windows, one will be the graphical portion and the other will be a sort of expanded menu bar. I am calling it expanded because it contains not only menus but also a simulated command line and a few function buttons. Similarly to the Benchmark menu in UCSF Chimera, there is a Wizard menu. This menu contains a handful set of wizards and demo of the graphical capabitities PyMol offers. I recommend you try it as soon as you start using PyMol.

I must admit that I haven’t used Build  or Movie that much but at least Movie is very powerful. From some tutorials I have seen you can use Movie in a fashion not to different to any key-frame assigning animation. And ray tracing in PyMol is gorgeous.

PyMol was thoughtfully designed to work with one, two or three-buttoned mice. You can move between this options with the Mouse menu.

I like the Scene menu a lot since it lets the user customize several “screens” out of the same structure, ie. You can save a front view with your macromolecule displayed as sticks and another viewed from above but displayed as surface. PyMol allows you to store both representations and navigate between them by using the F keys.

Available features.

Besides the features mentioned above the most interesting features lie in the Wizard and Plugin menus. The Wizard gives you the power to change the appearance of your macromolecule, make some measurements for distances between atoms, mutagenesis, pair fitting, density displayed (although I prefer this feature in Coot), model filtering, Sculpting (haven’t use this seriously), labeling and charge display.

The Plugin menu is a winner too. PyMol comes with a PDB loader (straight from the RCSB) and APBS. But, visit PyMolWiki and you’ll find a treasure trove of plugins (and scripts and general info to use PyMol). 

Overall strengths and weakness.

Now I recognize the way PyMol blends the graphical interface with the internal command line. Everything that can be done with the GUI and much more can be done from the command line. An independent developer community is also a plus although the contributions are plugins or scripts not actual features within PyMol.

As a weakness I see the somewhat atypical interface, at least when you first try to use it. Another might the that PyMol is User-Sponsored so to obtain a compile version you need to pay for it. However, it is possible to get the source code and compile it yourself.

Conclusion.

Overall PyMol is neat easy and to use. Something about the interface (both GUI and command line) gives the feeling of total control over the software.  A trend that should be apparent by this review is that there is no single perfect visualization program. PyMol is another one very good in certain areas but weak in others. The task for the reader is to use the good and overcome the bad with another option.