Using CHIME Molecular
Models
The left and right mouse buttons control the molecule on the
screen,
the antibiotic Penicillin G. Position the mouse arrow in the frame
surrounding
the molecule.
To rotate the
molecule
(a) around the x-, or
y-axes:
Hold down the left
button
and drag the arrow across the screen in
whichever
direction you wish the molecule to rotate (vertical
rotates around x-axis, horizontal
around y-axis);
Depressing the right
mouse
button while holding down the keyboard shift
key and moving the arrow horizontally
causes
rotation around the z-axis.
These combinations will give a 3-D view of the molecule from any
angle
you wish.
To zoom in on the
molecule:
depress the left button while holding the
keyboard SHIFT key down; then drag the
mouse
arrow downwards. Moving the mouse in the opposite direction zooms out.
To reposition the
molecule
in the frame:
depress the right button while holding
the
keyboard CONTROL key down and drag with
the
mouse to move the molecule within the frame.
To edit the
molecule:
click on the molecule with the right
button
to reveal a menu with a number of available options:
the File and Edit
sub-menus should be straight-forward for Windows users;
the Rotation
sub-menu has
2 options: 'start' and 'stop';
clicking on 'start' results in automatic rotation of the molecule from
left to right;
the Display
sub-menu has
5 available options:
Wireframe -
shows the bonds
and basic skeleton of the molecule.
Stick - makes
the bonds
thicker and more visible.
Ball & Stick
- shows
the atoms as balls joined by stick bonds.
Dot surface -
used to superimpose
a semitransparent image of the surface of the molecule over its
skeleton.
Spacefill -
represent the
atoms as solid spheres.
The Options
sub-menu has
9 options. The first five are self-explanatory. The other four are as
follows:
Slab mode -
shows those
parts of the molecule which are to the rear of a plane through it.
Specular -
adjusts the 'shininess'
of the atoms.
Shadows - adds
shadows to
give better definition.
Labels - adds
labels to
certain atoms and groups.
The Color
sub-menu changes
the colours of the molecule.
Monochrome -
shows the molecule
in one colour
CPK - shows each
type of
atom in a different colour:
Using CHIME to visualise and interact with
molecular
models is highly instructive and helps considerably in developing an
understanding
and appreciation of the 3-dimensional nature of molecules and the
stereochemical
consequences.
This CHIME tutorial was developed by
Stephen Hynes
DCU CHIME Pages