Example 2-Making an intercalation site.

  1. Start NAMOT2
  2. Select "Generate..." from the "File..." menu
  3. Pick double from the Strand choices.
  4. Pick form "B"
  5. Pick "Deoxyribose"
  6. Enter the sequence "atgc"
  7. If you are using the Motif interface click on "Apply", XView users need to simply press return.
  8. Rotate the molecule on axis three by -90 degrees. (on the XView version this can be accomplished on the interface, on the motif version use the command rotate). See figure 1.
  9. Select the third base by clicking the left, then the middle mouse button over any atom in the unit. This sets the starting and the ending unit to that base.
  10. From the "Parameter" menu select "Dz".
  11. Leave the "Affect" setting on "Global".
  12. Input a change of 2.0, this will take affect when you press return. Notice that the phosphate angles(C5'-O5'-P and O5'-P-O3') will automatically adjust to compensate for the change in distance.See figure 2.
  13. Increase Dz by another 1.4 angstroms. This will break the backbone. See figure 3.
  14. To reconnect the back bone, reduce the twist angle by 10 degrees. See figure 4.
For clarity, a script is provided.