Chapter 1

Getting Started

NAMOT2 will accept all molecules. If the molecule is a nucleic acid, the user has the option of viewing it as a rigid body or as a modifiable structure, for non-nucleic acids, NAMOT2 will automatically import them as rigid bodies once it is unable to locate a group name in its library. This means that if the user attempts to load in a nucleic acid structure with a base that does not appear in the library, the structure will automatically be considered as a rigid body.

NAMOT2 breaks down all molecules into the following format:

Molecule
Chain
Group
Atom

Nucleic acid structures are also broken down into the following format:

Helix-NAMOT2 defines helix as a consecutive stretch of units with the same number of bases in each unit.
Unit-One or more bases that are hydrogen bonded. The Unit is the fundamental module that comprises a helix.
Base- Both modified and unmodified purine or pyrimidine bases.

The Helix:Unit:Base format is generated in two ways. NAMOT2 automatically attempts to determine this information on its own. It can locate Watson-Crick pairing and uses this information to build the H:U:B structure. Because this WILL fail for non-Watson-Crick pairing, NAMOT2 also looks for a pairing file. The pairing file is user generated. This file is explained in the file format section.

These two ways of describing structure are used to specify portions of the molecule that will be acted on. A more detailed description of the specifiers can be found in appendix two.

Once the molecule is imported, the H:U:B and M:C:G structures will be listed in the data window.

Important commands(see chapter 5):

Important topics:

Specification-Appendix 2.
Mouse-Appendix 3.

Demo 1-loading a pdb file

Note: Members of the interface, such as menus, menu buttons, fields, and settings are enclosed in quotes.

Start NAMOT2
Select "Open..." from the "file" menu.
Click over "PDB"
Click in the "File:" field and enter the name. If using the XView version, pressing return will start the process. In the Motif interface, you will need to press the "Ok" button.
Use the mouse and side controls to manipulate the molecule.

Demo 2-Generating a B form helix and introducing an intercalation site.

Start NAMOT2
Select "Generate..." from the "File..." menu
Pick double from the Strand choices.
Pick form "B"
Pick "Deoxyribose"
Enter the sequence "atgc"
If you are using the Motif interface click on "Apply", XView users need to simply press return.
Rotate the molecule on axis one by -90 degrees. (on the XView version this can be accomplished on the interface, on the motif version use the command rotate)
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.
From the "Parameter" menu select "Dz".
Leave the "Affect" setting on "Global".
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.
Increase Dz by another 1.4 angstroms. This will break the backbone.
To reconnect the back bone, reduce the twist angle by 10 degrees.