This is the Midas PDB file viewer generated (using the scripts show_chains.pl) graphical view of one of the successful cyclizing molecules. The B-form region of the DNA is colored white, the Atract region is colored red and the flexibility region is colored yellow. The second picture is simply the "wire view" of the first picture.

bass (lapham):> show_chains sequence.in chain_cyclized.dat 1
bass (lapham):> rotmat2pdb.pl chain_1.rotmat
bass (lapham):> midas chain_1.pdb

bass (lapham):> show_chains sequence.in chain_cyclized.dat 1
bass (lapham):> rotmat2pdb.pl wire chain_1.rotmat
bass (lapham):> midas chain_1.pdb