Basic Applied Bioinformatics

CHAPTER 4Visualizing Protein Structure

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

4.1 INTRODUCTION

RasMol, developed by Roger Sayle, is freely downloadable interactive software that is used for visualizing molecular graphics. The name “RasMol” is an abbreviation of “Raster of a Molecule”, which means a computer display (Raster) of the solid surface molecule. RasMol displays the 3D format of the atom coordinates of a molecule, written in PDB file format.

4.2 OBJECTIVE

To visualize the structure of a peptide (we will use “bovine beta‐lactoglobulin (isoform A) in complex with dodecyl trimethyl ammonium chloride (DTAC)”) using RasMol software.

4.3 PROCEDURE

1. Download Rasmol: http://rasmol.org/ and run the executive file. Please get registered when you use RasMol for the first time.
2. Open RasMol by double clicking the “RasWin” icon on the desktop. This simultaneously opens two windows:
   1. The 3D visualization window(the GUI with black appearance). RasMol can be operated through the menu bar drop‐down options.
   2. The RasMol command line prompt. This window is used to write the commands (instead of operating RasMol through keyboard and GUI) to visualize the structure.
3. Go to “File > Open” and select the particular PDB file. We need to download the file 4IB7.pdb (i.e., Bovine beta‐lactoglobulin (isoform A)), as stated above, from PDB or UniProtKB (Figure 4.1). Presently, the following display patterns are available in the Display menu: “Wireframe” ...