Macromolecular structure visualization: a look at the applications that provide graphical interface to structure analysis. Part II UCSF Chimera.

One of the many products of a (successful) macromolecule crystallization experiment is the publication of a Cartesian coordinate file that represents a 3D structure (proteins, DNA, RNA, etc.). These files, faithfully deposited at the RCSB protein databank are usually referred as “3d structures”. Many tools for structure analysis have been produced but not all of them offer a GUI (graphical user interface). Although experience 3d structure users may scoff at the need of a GUI 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 second review UCSF Chimera.

N.B.  I am a Mac user (10.6) and in the case of UCSF Chimera (current version 1.5) I always run the X11 version. I do so since that way it is better integrated with 2dx.

UCSF Chimera ease of use.

I didn’t realized the power of UCSF Chimera until I started doing some serious structure validation and electron microscopy (no, I am not citing the Wikipedia). But Chimera can do far more than I can possible review properly. However, I can say that Chimera’s Main window might be daunting. The main menu shows seven menus: File, Select, Actions, Presets, Tools, Favorites and Help. I’ll skip help since USCF Chimera has a large, rich and complex website to help/guide you on its use.

I’ll jump to Presets. This menu contains several presets (doh!) that modify the way the 3D structure will be displayed. These are divided in three interactive and four publication presets. This is probably the first and easiest way to get some very nice images from your structure. The division might be arbitrary but publication presets are more CPU intensive that the interactive ones. But this takes us to the File menu. This menu is subdivided but presents you several options at once. It lets you know that you can open local files or actually connect to the Internet and download data from ten different databases!

Available features.

I missed this feature on DeepView and Chimera shares it: You can save and restore sessions of Chimera use. You can recover display, tools, processes, pretty much anything you can do within Chimera.

Other options include save image, PDB, mol2 or Export Scene (check this last link!).

The Selection  menu is no different form any other. Actions  contains several useful but common things such as display modifications (ribbons, backbone, etc.).  A few interesting options in this menu are the Inspect, Write List and Write PDB. They are handy for saving modifications to the displayed coordinates. Focus and Set pivot  are pretty much standard.

The true gold in UCSF Chimera lies on the Tools menu, it is so complex and rich that I will mention my ten favorite features:

Model panel, side view, FindHBond, Find Clashes/Contacts, Render by Attribute, Surface Capping, Minimize Structure, Scale bar, Volume Viewer and Fit in Map.

Favorites is a menu where you can store your favorite tools.

Rounding up the ease of use I’ll say that if you now what you need and where to find it, Chimera will be your best friend. If you don’t know either, visit the website and go through Tutorials and Feature Highlights.  

UCSF Chimera will also perform docking analysis, molecular dynamics, sequence and structure alignment and analysis, animation, etc. Between the internet database access and these features, you can handle electron microscopy 3d models, x-ray crystallography models and small molecules. If I had to work with only one 3d structure visualization suite I guess I’ll pick UCSF Chimera. Lucky me, I don’t have to pick there are other programs that are very useful too.

NB. I know that a new feature on v 1.5 is the addition of an interface to Modeller. I haven't tried it and I am a fan of running Modeller through the usual python scripts. 

Overall strengths and weakness.

Its strengths are many and they increase each development cycle. Cannot go wrong here. It has great documentation as well as tutorials and it is been developed and distributed for the three main platforms in 32 and 64 bit flavors.

As a weakness I can only mention that is complex and requires some time to master. If you are in a hurry this is probably not the tool for you.

Conclusion.

I’ll say it again, you cannot go wrong with UCSF Chimera. It will not save you if you are in a hurry but once you master it you won’t let go.