NAMOT2 allows the user to build non-standard units and keep them in the unit
library. This is done by reading in the bases as rigid bodies, manipulating
them, writing them out, then reading them back in with the right
There are two methods of manipulating the bases.
By known geometry
Create a pdb file for the bases you are interested in.
The base must already be defined in the base library. If it isn't,
you will need to add the base to the library.
Delete the current molecule.
Load the files as rigid bodies. Example:load pdb rigid gua.pdb
Change the mouse mode to "Base".
Use the mouse to rotate and position the
bases. Also use the mouse to set up distance
Write out the file in pdb format.
Example:write pdb ug.pdb
Edit the file to remove the "ENDMDL" records, except for the last