Friday, June 11, 2010

3DNA citations from mainland Chinese researchers

Over the past couple of weeks, I have been quite surprised to notice the following four papers, by researchers from mainland China, that cite 3DNA:
For more ten years, this is the first time (to the best of my knowledge) that 3DNA has been cited by scientists from China, and it so happens that four come in a row. I am so happy to see that structural biology is shaping up in China. Surely, I would expect more 3DNA-citing papers from China to come in the following years.

block_atom, a little used 3DNA utility script

Following my previous post, "How is a base-pair rectangular block defined in 3DNA?", I feel it is in order to mention a tiny Perl script named block_atom that seems to have been little used by the 3DNA user community.

The basic idea of block_atom is to get an ALCHEMY data file which combines both atomic and block representations of nucleic-acid-containing structure in PDB format. The ALCHEMY file can then be displayed interactively using RasMol (v2.6.4, by its original author) (or Jmol).

Again, the point is best illustrated with an example. Here I am using 355d, the famous Drew-Dickerson B-DNA dodecamer solved at a high resolution by Williams and colleagues. Let the input PDB file be 355d.pdb, then the output file is automatically named 355d.alc, which can be displayed using RasMol with the options '-alchemy -noconnect'.
block_atom 355d.pdb
rasmol -alchemy -noconnect 355d.alc
One view of RasMol rendered image is as below, which shows more clearly the minor-groove (colored blue) of the DNA duplex and the various intra-base-pair deformations (e.g., propeller and buckle):
I initially wrote this utility script mostly for verification purpose, i.e., to make sure that the base reference frames are defined properly. For those who want to know more about 3DNA, having a look of the script (which is tiny) and understanding how it works could be a good exercise.