PERFORMANCE ASSIGNMENT

Using RasMol to Model Compounds

 

Opening the RasMol Menu

 

1. Click on My Computer and select the CDROM drive.  From the CDROM drive select rasmol.exe.
2. The Using RasMol menu will open, move the mouse over the RasMol logo and click once.
3. RasMol will open in a separate window.  You have now opened RasMol.

 

Using RasMol

 

1. Click on the File dropdown menu and select Open.  Navigate to the molecules folder and then to the carbon folder within it.
2. Open the diamond pdb file.  The pdb extension stands for protein databank.  These are files that are used to display molecular models.  The wire frame image will appear (figure 1).
3. Click on the Display dropdown menu and select Ball&Stick.  The Ball & Stick display shows the atoms and their bonds (figure 2).
4. This file is a portion of diamond.  Click on the File dropdown menu and select Information.  What is the version of Rasmol  ______________________,  how many atoms are in this sample  ______________________,  how many bonds are in this sample  ______________________.
5. Click on the Settings dropdown menu and select Pick Label.  Then use the mouse and navigate to the atom in the upper left hand corner of the sample.  What kind of atom is this and what number is it  ______________________.  Navigate to the lower right hand corner, click on this atom what kind and what number is this one  _____________.
6. Use the left mouse button, hold it down and move it around, what happens to the sample?  ___________________

____________________________________________ .

7. Click on the Settings dropdown menu and select Pick Distance.  Using the mouse click on C1 and then move the mouse to C95.  What is the distance displayed in Angstroms?  ______________________ .
8. If you have trouble reading the information, click on the Display dropdown menu and select Cartoons.  Only the information you have worked on is displayed (figure 3).  To return to the ball & stick image,  click on the Display dropdown menu and select Ball&Stick.
9. To save a model, click on Export and select GIF.  A popup menu appears and type in the name and location in which you would like to save the file.
10. To print you model, click on File and select Print.

 

Figure 1	Figure 2	Figure 3
Wire frame	Ball&Stick	Cartoon

 

 

Synthesis:

 

Open RasMol twice and load diamond.pdb into one and graphite.pdb into the other.  Rotate each and examine the bonds and structure.  Diamonds and graphite are allotropes of carbon since each only contains atoms of carbon.  Diamonds are however, the hardest of minerals and graphite is one of the softest.  Explain this difference.