How to Use NAIL

NAIL Homepage


Base Pairs
Base Triples
Base Quartets
Amino Acid--Bases
Amino Acid--Base Pairs

How to Use NAIL

General Layout of Base Libraries

There are five nucleic acid interaction libraries listed on the left-hand control menu. Clicking on a library will allow you to browse through individual models. The control menu appears on all pages, but is displayed in the top of the browser window when viewing molecular models. Each library is sub-grouped by base composition, allowing, for example, all AGU base triples to be displayed on one page. When viewing a composition group, clicking on either the GIF image or the name of an interaction will display it in the main frame as a Chime image. For convenience, buttons are provided on the right that control some of the Chime display features. The top three groups of buttons are simple push buttons, and the last set are toggles--clicking on them a second time will reverse the change of the first click.

Amino Acid-Base Interactions

For amino acid interactions, the libraries are first sub-divided by the interacting amino acid. The first page of the amino acid-base and amino acid-base pair pages show all the functional groups that were used in the calculations. Clicking on one of them will take you to a page where you can choose the interacting base or base pair via a pull-down menu.

Chime

These pages use the plugin Chime 2.0 from MDLI. The Chime plug-in takes atomic coordinates and generates a 3-dimensional representation of the molecule. This representation can be manipulated with the mouse by clicking and draging in the window. The following is a table of mouse functions:


Chime Mouse Control Summary

Action Windows Macintosh
MENU Right Hold Down
Rotate X,Y Left Unmodified
Translate X,Y Ctrl-Right# Command*
Rotate Z Shift-Right Shift-Command*
Zoom Shift-Left Shift
Slab Plane Ctrl-Left Ctrl

*On some Macs, the Option (Alt) key has the same effect on RasMol as the Command key.

From the RasMol homepage maintained by Eric Martz.


From the Chime Menu you can change the display of the molecule, as well as save the PDB file to your hard drive. Many of the menu commands allow you to manipulate the display much like the RasMol command line. For more information, please see the RasMol and Chime web sites.

It is possible to measure the distance between any two atoms in a molecule by clicking on the two atoms. Clicking on the first atom identifies the atom with the information appearing at the bottom of the browser window. Clicking on the second atom will show the distance in Angstroms.