blocview: a simple, effective visualization tool for nucleic acid structures

The 'blocview' Perl script in 3DNA was designed as a simple tool that nevertheless illustrates key features of nucleic acid structures effectively. Specifically, the 'bloc' part of the name means 'block', i.e., the base rectangular block in the Calladine-Drew style to show clearly the size (larger purine vs. smaller pyrimidine), identity (by color: red for A, yellow for C, green for G, and blue for T), and the groove (with minor groove edge filled in black); and the 'view' part means the most extended view (as defined by the principal axes of inertia). 'blocview' calls several utility programs of 3DNA and MolScript (for protein ribbons and nucleic acid backbone rods) to prepare the scenes, and then uses Raster3D (more specifically 'render') or PyMol (as of 3DNA v2.0) to generate a PNG image.

It has been my pleasure to notice that 'blocview' generated images are used in the NDB for each and every structure. See for example, an arbitrarily picked link on X-ray Drug-DNA Complexes. A nice thing about these images is that they can be generated automatically: using PDB id 1z8v as an example, the following command

blocview -i=1z8v.png 1z8v.pdb

would produce the image (named 1z8v.png above) shown in the right. In this representation, one can see clearly that there are two unpaired Gs (green) at each of the 5' end of the two DNA chains (red and yellow rods), and a drug molecule (ball-and-stick) binds in the minor groove (black edge of the rectangular blocks). Moreover, the first C-G pair has pronounced negative propeller twist.

It was a nice surprise when I found (several years ago) that such simple images have also be adopted by the PDB, prominently at the summary page, for every nucleic acid containing structure. There are so many sophisticated molecular graphics tools out there, why 'blocview'? After all, it is just a small utility tool in the 3DNA suite of programs, and I have never written a paper on it. Clearly, 'blocview' fills a niche.

On the other hand, given the effectiveness of this simple representation and its adoption by the NDB and PDB, I am surprised to found that 'blocview' images are not used that much in the literature. Maybe the situation will change as 3DNA gets more widely used, and when people pay more attention to its versatile functionalities: certainly, there are more handy features in 3DNA!

More blocview command-line options are available to suit some other common needs: just type 'blocview -h' for details. Furthermore, many aspects of the images can be fine-tuned by configuration files. Astute viewers could have noticed subtle differences of the 1z8v images shown here (above right), and in the NDB and PDB websites. Since 'blocview' is written in Perl script, users can easily check the implementation details to figure out exactly how it works.