Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers
The stacking interactions are quantified in 3DNA by the shared overlap area, in Å2, of closely associated base rings, i.e. the nine‐membered ring of a purine R (A or G) and the six‐membered ring of a pyrimidine Y (C, T or U), projected in the mean base pair plane.So 3DNA, as is, may not provide a sensible value when a non-standard base ring is involved, such as your 3-ring linker. However, you can have a look of the corresponding step in the "stacking.pdb" file, and write a purpose-specific script to get your job done; after all, mathematically, it is all about getting the intersection of two polygons, and then calculating its area.
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.