Saturday, June 13, 2009

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.

Friday, June 12, 2009

Review of scientific manuscripts

While reading an editorial of Maddox [Nature. 1995 Dec 7; 378(6557):521-3], I found the following comment quite interesting:

It's a good joke (which I have often used) that Watson and Crick's paper on the structure of DNA could not be published now. If is only necessary to imagine what people would say if it reached them in the mail: "It's all model-building, just speculation, and such data they have are not theirs but Rosalind Franklin's!" Some would complain that the sentence beginning, "It has not escaped our attention..." is certainly unsubstantiated, and must be an attempt to claim credit for developments in genetics that lies years ahead.

Maddox continued to imagine what could have happened behind the scene that led to the publication of Watson and Crick's paper, together with Franklin's crucial experimental work illustrating the helical signature of crystalline DNA.

In some sense (to my understanding), Watson and Crick were lucky, not only in that they solved the puzzle of DNA structure elegantly by connecting the various experimental pieces together, but also they worked in the Cavendish Laboratory at Cambridge University and had the support from Sir Lawrence Bragg. One could easily imagine what would have happened if they did this work in a not so famous lab, without support from a leading, powerful figure.

In a scientific field (e.g. RNA), what appears to be a common sense, a decade old issue, could have something significant when view from a novel perspective. Such unconventional results, however, are often hard to get across the review process, especially for new comers to a field and without backing of big names. In principle, the reviewers should be fair to the author, being specific with his/her comments, especially in case of negative ones. That would be far more convincing to the authors than some vague, general remarks. As a general rule, I won't accept to review a manuscript for a journal unless I have time to read it thorough carefully, and the expertise to understand the details, in order to provide some concrete comments.

In this regard, it is worth reading the essay by Keith Manchester titled "Historical Opinion: Erwin Chargaff and his 'rules' for the base composition of DNA: why did he fail to see the possibility of complementarity?" [Trends Biochem Sci. 2008 Feb;33(2):65-70]. For completeness, the abstract is quoted below:
Erwin Chargaff was one of the more interesting and colourful figures of the historic decade that heralded the proposal of the double helical structure of DNA by Watson and Crick in 1953. In describing Chargaff's important contribution to the study of DNA, particularly its base composition, this article seeks to suggest why, despite his substantial achievements, he failed to anticipate some of the key features of the Watson-Crick model, particularly complementarity between bases--a failure that left him deeply embittered for the rest of his life.