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2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

NAMOT (Nucleic Acids MOdelling Tool)

Namot is a graphical tool for the manipulation of nucleic acid structures. It was developed at Los Alamos National Laboratory.


  • PDB
  • Amber4,
  • Parameters
  • Output:

  • Amber4,
  • PDB
  • Parameters (PPM or encapsulated postscript)
  • General:

  • Can be used to manipulate standard or unusual nucleic acid structures(i.e. poly-stranded molecules) using reduced parameters that have intuitive meaning and also allow easy manipulation of the base/unit without bond breakage.
  • Auto-adjusts:

  • C5'-O5`-P and O3'-P-O5' to allow the phosphate to cross varying gaps.
  • Generation of structures:

  • Generates the molecules in A,B,& Z forms.
  • Online help:

  • There is an extensive online help system.
  • Libraries:

  • A set of external libraries allow users to customize their own bases,phosphates, sugars, units, and forms.
  • Graphics:

  • Color and monochrome
  • CPK and wireframe

  • HTML documentation is available as well as the on-line help in the Graphical NAMOT window.

    NAMOT also has a homepage.

    To get started in the CSB core, type:

    setup namot (or source /srv/local/setup/namot.set)

    Once the GUI is launched you can look at the examples by typing one of the following in the command window:

    execute /srv/local/namot/demos/6way/6way.his

    execute /srv/local/namot/demos/bending/bending.script

    execute /srv/local/namot/demos/cube/full.cube.script

    execute /srv/local/namot/demos/curve/curve.history

    Note: If results from Namot are included in a publication please cite the following:

    Soumpasis, D. M., and Tung, C.-S. (1994) J. Biomol. Str. Dyn. 11, 1327-1344

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    Last Modified: Thursday, 07-Jun-2007 11:05:25 EDT by P. Fleming