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