Computer Modeling of Biomolecules

Presented by Kam Bo Wong
Department of Biochemistry & Molecular Biotechnology Programme
email: kbwong@cuhk.edu.hk
http://smart.bch.cuhk.edu.hk/kbwong/index.htm

2. Using RasMol to look at a small organic molecule.

2.1 Starting up RasMol

Double click the icon RasWin.exe (RasMol for Windows) and the RasMol window should look like this:

2.2 loading a pdb file to RasMol

We will first look at a small molecule: urea. The 3D structural information of a molecule is stored in a so-called 'PDB' format. The 3D structure file for urea is named 'urea.pdb'. Load the structure of urea by selecting the command "Open" from "File" menu.

·  You will see the structure of urea shown in the RasMol window:

2.3 Spacefill model

The default display mode is 'wireframe' where only bond between atoms are shown. You can change the display mode to 'Spacefill':

In 'Spacefill' model, atoms are represented by spheres with sizes dependent on their atom types (e.g. hydrogen atoms are smaller than the nitrogen atoms.) In the default color setting, hydrogen atoms are white, nitrogen atoms are blue and oxygen atoms are red.

2.4 Ball & Stick

You can change the display mode to 'Ball-and-stick' by:

In 'Ball-and-stick' model, atoms are represented by spheres and bonds are represented by thicker lines.
 

·  Can you write down the chemical formula of urea?
 

2.5 Mouse Control in RasMol.


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