3DNA

Stacking diagrams: based on the file stacking.pdb generated with analyze, the above image can be produced directly with stack2img and rendered with Raster3D.
(Image from 3DNA website examples.)

3DNA is a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame. In its core, the software uses a simple, yet mathematically rigorous and geometrically sensible, scheme for calculating a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters. Unique features of 3DNA include automatic classification of a dinucleotide step as A-, B-, or TA-like based on the positioning of the phosphorus atoms, and the generation of "standardized" base stacking diagrams. The rebuilding routines give Calladine-Drew style schematic representations of DNA as well as full atomic models with the sugar-phosphate backbone.

To use 3DNA in the Core, type:

setup 3dna

and select the relevant 3DNA component program to run.

A brief user's manual (still for version 1.5) is available in PDF format to get you started.

Examples are available in /srv/local/3DNA/current/examples.

Additional information is available at the 3DNA website.

Please Note: If you publish results obtained with this program please cite one of the the following:

Xiang-Jun Lu & Wilma K. Olson (2008). "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.", Nat Protoc. 3(7), 1213-27.

Xiang-Jun Lu and Wilma K. Olson (2003). "3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures", Nucleic Acids. Res., 31(17), 5108-5121.