File "stacking.pdb" is from the analysis of the 1.4 A resolution structure
(CGCGAATTCGCG)2 solved by Shui et al. (NDB code: bdl084). The eleven base
stacking diagrams in color PS format were generated using the following
command:
	     mstack2img '-tlcdo -s=25' stacking.pdb 1 11 bdl084_

"mstack2img" is a short Perl script which calls "stack2img" to do the job.
Option -c means color figure. By default, A is rendered red, T blue, G green
          and C yellow as in the NDB
       -d draws hydrogen bonds
       -t means "normal top view", with long base-pair axis horizontal
       -l label each base with chain ID and residue number
       -o means filled the base rings
           these one-letter options can be in either case, any order
           and/or combined
       -s=25 sets the scale factor so that all generated figures are 
           on the same scale

If you would like only a single structure, simply change "1 11" above to "n
n", where "n" is a integer between 1 and 11, say 5. Alternatively, run the
following:

ex_str -5 stacking.pdb step5.pdb
stack2img -cdo -s=25 step5.pdb step5.ps

That is, using utility program "ex_num" to extract the dinucleotide step to
a file, then run "stack2img" to get the PS file.
