In order to use Chime effectively, you need to be familiar with the basic mouse commands available in Chime, and with invoking and using the Chime menu. This introduction to Chime is in three parts:

Chime mouse commands
the Chime menu
using Chime buttons

Using just the mouse you can rotate, translate and zoom in or out on any molecule in Chime. You also use the mouse to bring up the Chime menu. Using the menu, you can control many additional aspects of your molecule, such as the display style, the color, whether or not hydrogen atoms are shown, etc. In addition, you can apply these choices to the whole molecule or to selected portions.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Action	PC	Mac
pop-up the Chime menu	click right mouse button	hold mouse button down (while stationary)
Rotate X,Y	hold down left button and move mouse (in the region of the molecule)	hold down button and move mouse (in the region of the molecule)
Translate X,Y	hold down the Ctrl key, then hold down the right mouse button and move the mouse	hold down the Command key, then hold down the right mouse button and move the mouse (on some Macs, the Option (Alt) key has the same effect as the Command key)
Rotate Z	hold down the Shift key, then hold down the right mouse button and move the mouse	hold down the Shift and Command (or Alt) keys, then hold down the mouse button and move the mouse
Zoom	hold down the Shift key, then hold down the left mouse button and move the mouse	hold down the Shift key, then hold down the mouse button and move the mouse
Slab Plane	hold down the Ctrl key, then hold down the left mouse button and move the mouse (slab mode must be on for this to have any effect)	hold down the Ctrl key, then hold down the mouse button and move the mouse (slab mode must be on for this to have any effect)

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The Chime Menu

Clicking the right mouse button on a PC (or holding the mouse button down on a Mac) brings up the Chime menu. In the version of Chime available on our PC's, the menu looks like this:

You should try as many of the options on this menu as you wish, but please spend a little time with the display and color options. Some of the choices in Display are grayed out (as in the figure below) unless the molecule you are looking at is a large biological molecule.

If you were looking at a DNA fragment, for example, then the display menu would look like this:

You can further refine the display using the options menu. Although there is a command for turning hydrogens on and off, it will only work if the molecule structure file contains the appropriate information.

Many of the choices in the Color menu make sense only for large molecules. In most cases of small molecules you will want to use the CPK color scheme that assigns certain colors to specific elements. If your monitor is not displaying a sharp image try using the force palette option under Color.

The select menu, shown here, allows you to change the appearance of certain portions of the molecule, and to make a number of different types of measurements. The display list option allows you to view surfaces based on approximate calculations of electrostatic potential or lipophilicity.

Measurements of distance and angle are done using the Mouse Click Action submenu.

There are numerous other menu choices, and I urge you to try many or all of them. Here are two molecules that you can practice on. The first is a small molecule, a complex of chromium(III) with ethylenediamine.

Try various display modes on this molecule. See if you can turn the display of the hydrogen atoms on and off (it is frequently useful to not view the hydrogen atoms in a molecule and to focus on the structural framework - as molecules get larger, hydrogens also clutter up the display).

Whether or not a particular Chime command works as you expect depends to some extent on the information that is available to Chime in the molecule data file read by Chime. There is no need to go into the details of this now, but just be aware that not all commands will work on all molecules.

Here is a more complicated example, hemoglobin:

This is, to state the obvious, a mess. The hemoglobin molecule is surrounded by solvent molecules and a few stray perchlorate ions. There is no indication of where the heme groups are, and it is difficult to see that the molecule is made up of four subunits. Using various menu commands, including several from the Select menu, see if you can get the structure above to look like the picture below (this is just a picture, not an interactive molecule).

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Using Chime Buttons

Frequently you will encounter Chime pages where the author has automated some actions for you by the addition of some buttons. For example, there are several buttons on each page in the molecule collection on this website. Clicking one of these buttons will perform the indicated action. In the case of the measurement buttons, clicking an atom results in a pop-up box that identifies that atom. When such a box shows up, note what it says and then close it (Enter key or click on OK). If you are doing a distance measurement, click a second atom and the pop-up box will identify that atom and show the distance from the first atom. Clicking another atom starts a new measurement cycle. For angle measurements you need to click three atoms (closing the pop-up box after each one) and the third pop-up box will show the angle. To measure a torsion angle requires selecting four atoms.

Chime is a powerful tool for exploring molecular structures - enjoy!

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