GETTING STARTED WITH RASMOL

NB. It may be worth your while to obtain a hard copy of this tutorial exercise to avoid having to switch back and forth between the web browser and Rasmol windows. Choose 'print' from the file menu if you have access to a printer. Students working through the exercise in a tutorial session should have a copy with their tutorial handout.

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, eg. Netscape 2.0 or above. An alternative version of the tutorial is available for other web browsers.

For further information on any of the commands used in this tutorial, consult the online RasMol Manual

Step One

Click on the Rasmol icon (above) when you are ready to start the program. Two Rasmol windows will appear on the screen, the graphics window and the command window. In the graphics window you will see a wireframe image of Carboxypeptidase A.

Step Two

Manipulate your windows so that you can see the RasMol graphics window and the RasMol command window. Help is available to show you how to manipulate Macintosh and Unix windows.

Try resizing the command window so that it is just large enough to show the RasMol prompt with a bit of space left for typing in text. Leave as much room as possible for the graphics window.

Step Three

Practice manipulating the Rasmol window to get a feel for it. Try the following:

1. Use the mouse button to pick up the window in the title bar and move it to a new position on the screen.
2. Resize the window and observe the effects on the Carboxypeptidase image.
3. Zoom the window out to maximum size by clicking in the 'Maximise' button at the top right corner of the window.
4. Readjust the size by pulling in the corners with the mouse or clicking again in the same button.
5. Unix Systems Only
   Iconify the window by clicking in the 'Minimise' button to the left of the 'Maximise' button(Unix systems only!). Bring the window back up with a single mouse click in the icon.

Step Four

Now Check out ways to manipulate the enzyme image :

1. Grab the button in the slider bar at the bottom of the window with the mouse (point, click, and hold with the left mouse button). Move it back and forth. You should see a horizontal rotation about the y axis. Now try the same thing using the command window. Select the command window and enter the following at the Rasmol> prompt:
   rotate y 45 (enter)
   You should see the image rotate on the y axis 45 degrees in a leftwise motion.

   Try the slider bar on the right-hand side. This should rotate the image about the x axis. Then in the command window type:

   rotate x 45 (enter)

   What do you observe? Use the up-arrow key 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?

   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.

   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.

   Unix

   Move the mouse over the image, hold down the middle mouse button, then move up and down, side to side. What happens? How about the right mouse button? The image should move around the window in the x and y planes.

   PC Windows

   Hold down the 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. You should see information for that atom written out in the command window.

Step Five

The command line window 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. You may also access useful information via the command line. To get a better view of all the information available to you in the command line window, single click on the top right hand sizing button to maximise the view of the command line window. Then type in commands at the Rasmol> prompt as indicated.

show sequence (enter)

show information (enter)

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.

To minimise the command line window as before, single click on the sizing button.

Step Six

Finally, check out the Rasmol menu across the top of the Rasmol graphics window. To access a menu item, click the mouse button on the menu heading, then pull down to the menu item and release. Try out a few things, but leave the 'Export' and 'File' menus alone.

When you are ready to move on to the next exercse, select the RasMol command window and enter the quit command.