GETTING STARTED WITH CHIME
In this exercise you will learn some basic manipulations using the Chemscape Chime
Plug-in. Most of this exercise will also be applicable to the Rasmol interactive
Molecular Visualisation program. You must be using a Netscape browser (v3.01 or
above), and have the Chime
Plug-in (v2.0) installed. You may also need to configure your browser to use
the Chime plug-in for displaying pdb files (instead of Rasmol).
You will have some questions to answer along the way! These will
be indicated by the Q/A icon 
.
When you see this icon, single click on it to go to the appropriate
questions.
To view answers to the questions, your web browser must be capable of
recognising JavaScript, Netscape3.01 or above is recommended.
If you have problems, check your browser configuration to ensure that JavaScript
is enabled (under Edit -> Preferences -> Advanced in Netscape 4.x browsers).
For further information on any of the commands used in this tutorial,
consult the online RasMol Manual
Most commands used with Chime are identical to Rasmol commands.
Step One
In the left frame you should see the Chime Plug-in's graphics display window (the empty black box).
Underneath the graphics window there is a text box to use as the 'command line'. You will be asked to type in instructions for the Chime program in this box.
Results from the Chime commands will be displayed in the text area just below the command line.
<-
Click on the button to load the Carboxypeptidase A protein into the Chime Graphics Window.
The coordinates for this enzyme are in the file '5cpa.pdb'
In the graphics window you should now see a wireframe image of
Carboxypeptidase A.
Step Two
Practice ways to manipulate the enzyme image :
Click and hold the mouse button anywhere within the image and move the
image around (Use the left button on Unix/Dos systems). You should have
a full range of motion within the xyz planes.
Now try rotating the image in only one plane using a command.
Click in the command line box and
type the following:
rotate y 45 (enter)
You should see the image rotate on the y axis 45 degrees in a leftwise
motion.
Then in the command window type:
rotate x 45 (enter)
What do you observe? Use the 'Again' button to bring up the
previous rotate command and press enter. Again, What do you observe? The
rotate command is convenient for manipulating the image without using the
mouse.
Now try manipulating the image in the z plane. On a Mac, hold down
the shift key, the command key and the mouse button simultaneously.
PC
and Unix users try the shift key plus the right mouse button. Move
the mouse around over the image and observe the effect. In the command
window type :
rotate z 45 (enter)
What do you observe?
Hold down the shift key and the mouse button simultaneously (Use the left
button on Unix/Dos systems). Move the mouse up and down over the image.
It should zoom in and out. You can accomplish this in the command window
with the zoom command:
zoom 150 (enter)
zoom 300 (enter)
zoom 100 (enter)
Mac
Hold down the option key and mouse button (simultaneously) over the image.
Move the mouse up, down, side to side in the graphics window. The image
should move around the window in the x and y planes.
PC Windows
Hold down the ctrl key and right mouse button over the image then move the mouse up,
down, and side to side. The image should move around the window in the
x and y planes.
All Systems
You can accomplish this image movement on the command line using the translate
command :
translate x 10 (enter)
translate x -10 (enter)
translate y 25 (enter)
translate y -25 (enter)
The translate command is another convenient way to move the image around
without the mouse.
Use the mouse button to "pick" a single atom within the molecule with a
single click. This may be easier if you can see the individual atoms - try
a 'spacefill' view.
select all (enter)
spacefill
Now you can see the individual atoms. Notice the numerous isolated red atoms.
These are the oxygen molecules of water. Click on one of these.
You should see information for that atom written out in the
message window. It may look something like :
Atom: O 2560 Hetero: HOH 397
This tells you the atom (Oxygen), The atom number (2560), that it is part of a 'hetero' group -
the HOH or water group, and that the number assigned to that group is 397. Notice that the hydrogen
atoms are not shown for the water molecules (or for the protein). This is because coordinates for individual
hydrogen atoms in large molecules are too difficult to resolve, and so are not included in the PDB file
that describes the molecular structure.
Now click on an atom that is clearly part of the Carboxypeptidase A protein. Try to find a yellow atom.
You might get:
Atom: SD 835 Group: MET 103
This is the sulphur atom (atom number 835) at the delta position in the amino acid residue methionine (MET) which
is at position 103 in the peptide chain to which it belongs.
You will notice that in the default colour scheme (called the CPK colour scheme) for molecules loaded into Chime (or Rasmol),
each atom (or sometimes group of similar atoms) is assigned a different colour.
Carbon - grey
Nitrogen - cyan (light blue)
Oxygen - red
etc.
Consult the RasMol Manual for more information on the various colour schemes.
Step Five
The command line is used to manually enter custom designed commands
of your own choosing.
For example, you may wish to restrict your view of
a molecule to its active site, or you may wish to custom colour parts of
the molecule under question. Results (if any) from the Chime commands are written into
the Chime message box (below the command line). You can access useful information via
the command line using certain commands, and see it displayed in the message box.
To get a better view of all the information available
to you in the message box, single click on the button below it ('Enlarge Message Box') and a new Navigator
Window will appear with a larger message area.
Type in the commands
show sequence (enter)
show information (enter)
Take note of the information displayed after each command.
You may be able to use the information in the command window to answer the questions.
The show information command provides additonal information about
the secondary structure of the molecules.
Step Six
Finally, check out the extensive set of Chime menu options by holding the mouse button down
over the graphics window. The menu should appear and you can use the mouse to navigate through it.
Let go of the mouse when you wish to select an option. Try out a few things, but
leave the 'Edit' and 'File' menus alone.
When you are ready to move on to the next exercse, click on the arrow below.
