Rectangular block representation of base-pairs in 3DNA

One of 3DNA’s unique features is the simplified rectangular block representation of bases and base-pairs, as shown in the figure below. This type of schematic depiction was first made popular by Calladine and Drew (see their book titled Understanding DNA — The Molecule & How It Works), thus I usually call it the Calladine-Drew style representation.

rectangular blocks used in 3DNA

By default, a base-pair [BP, (a)] has dimensions of 10×4.5×0.5 (Å); a purine [R, (b) left] 4.5×4.5×0.5 (Å); a pyrimidine [Y, (b) right] 3×4.5×0.5 (Å); and a mean base [M, (c)], which is exactly half of the base-pair, 5×4.5×0.5 (Å).

The blocks are stored into separate files: Block_BP.alc, Block_R.alc, and Block_Y.alc for BP, R and Y respectively. To use M for R and Y (i.e., set R and Y to be of equal size), simple copy file Block_M.alc to overwrite Block_R.alc and Block_Y.alc in the current working directory for local effect, or the 3DNA installation directory ($X3DNA/config/) for global impact. These blocks are used in the rebuilding and visualization components of 3DNA.

Following SCHNArP, 3DNA uses alchemy, a simple chemical file format, to specify explicitly the nodes (atoms) and edges (bonds) of a rectangular block. Three file formats (alchemy, MDL molfile, and Tripos mol2), supported by RasMol v2.6 (the most popular molecular graphics visualization program in the 1990s), serve the purpose of specifying the rectangular block. I cannot recall exactly why I picked up -alchemy instead of -mdl and -mol2, perhaps because of its simplicity: I played around with sample alchemy files and came up with the alchemy rectangular block files used by SCHNArP, without much difficulty.

As an example, Block_BP.alc has the following content:

   12 ATOMS,    12 BONDS
    1 N      -2.2500   5.0000   0.2500
    2 N      -2.2500  -5.0000   0.2500
    3 N      -2.2500  -5.0000  -0.2500
    4 N      -2.2500   5.0000  -0.2500
    5 C       2.2500   5.0000   0.2500
    6 C       2.2500  -5.0000   0.2500
    7 C       2.2500  -5.0000  -0.2500
    8 C       2.2500   5.0000  -0.2500
    9 C      -2.2500   5.0000   0.2500
   10 C      -2.2500  -5.0000   0.2500
   11 C      -2.2500  -5.0000  -0.2500
   12 C      -2.2500   5.0000  -0.2500
    1     1     2
    2     2     3
    3     3     4
    4     4     1
    5     5     6
    6     6     7
    7     7     8
    8     5     8
    9     9     5
   10    10     6
   11    11     7
   12    12     8

Observant viewers may notice that nodes 1-4 are specified as nitrogens (N) which have exactly the same coordinates as 9-12 (carbons, C). This is a little trick to make RasMol display the minor groove edge in a different color (blue for N) than the other five sides of the rectangular (gray for C), as shown in the following figure:

base-pair rectangular block

Note that the rectangular is preset in the standard base reference frame. Thus the nodes have y-coordinates of +5 Å and -5 Å along the long edge of the base pair, and x-coordinates of +2.25 Å and -2.25 Å along the short edge.

As an extra bonus of storing the rectangular blocks in external alchemy text files, the dimensions of the blocks can be readily changed. For example, the thickness of a block (z-coordinates) can be easily increased from 0.5 to 1.0 Å to make it thicker. Moreover, the blocks do not need to be rectangular either — they can appear to be triangular blocks.

It’s worth noting that while extensively used in 3DNA for schematic representations, the alchemy format has largely become a legacy in cheminformatics/bioinformatics nowadays. Searching the internet, I cannot find the specification of the format. Moreover, the support of alchemy is quite limited and buggy in molecular graphics visualization programs most widely used today: PyMOL does not understand this format at all; RasMol v2.7 has a bug in interpreting it; only Jmol can properly read 3DNA base-pair rectangular block files in alchemy [see initial discussion and follow-up]. To resolve the issues associated with alchemy format, and thus to make 3DNA base-pair block schematics more widely available, I have recently added a converter in v2.1 to readily transform alchemy to MDL molfile, a format consistently supported by PyMOL, Jmol and RasMol. I’ll talk about this feature in another post.

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