10. RASMOL and Molecular visualization



The amino acid sequence in a given protein molecule determines the structure or the conformation of that particular protein. Protein conformation in turn determines the function of that particular protein. So, with the conformation or structure predicted, the function of any unknown protein can also be predicted with similarity search techniques. The relationship between sequence and function is primarily concerned with understanding the 3-D folding of proteins and inferring protein function from these 3-D structures.

Predicting the structure and thus the function shall eventually help in designing a target molecule. This is an effective approach that’s to revolutionize the medicine, pharmacology, chemistry, molecular biology and ecology. Molecular visualization helps the scientists to bioengineer the protein molecules just like that. User-friendly graphic interface makes this area of Bioinformatics a fun filled, scientific thrill to the bioscientists. 


Number of software’s both free and commercial are available to visualize the biomolecules. The most commonly used free software are the RASMOL, CHIME, MOLMOL and PROTEIN EXPLORER. 


RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. This wonderful software was developed by Roger Sayle and donated to the public domain by the author (Roger) and his employer Glaxo Wellcome. The standalone software can be downloaded from the RasMol homepage…


RasMol can read  files in the following formats:

pdb (Brookhaven Protein Databank),

-mdl (MDL's MOL File Format),

mol2 (Tripos' Sybyl MOL2 Format),

xyz (MSC's XYZ format),

alchemy (Alchemy File Format)

and charmm (CHARMm File Format).

It takes  input as a file containing the 3-dimensional coordinates of the atoms in a molecular structure. Atomic coordinate file or the PDB file for a particular protein is obtained as a result of  x-ray crystallography.

One can search and retrieve a particular protein PDB file in the Brookheaven protein data bank (PDB), located at… www.rcsb.org/pdb/

The PDB file downloaded from a structure database, is by default shown in the wire frame model, when opened through RasMol. The program also draws a representation of various types of model (a list is found in the display menu).

The most realistic model represents each atom as a solid sphere (hydrogen atoms are usually omitted, and the size of non-hydrogen atoms is therefore exaggerated a little so that the space-filling properties of groups and molecules are roughly correct).

'Ball-and-stick' models allow you to see through the structure; atoms are represented as small spheres, and the bonds joining them as rods.

In the 'wireframe' model the atoms are shrunk to the points where the bonds (represented as wires) meet.

In the 'backbone' model all the side-chains are removed, and straight rods joining the positions of the centres of the a-carbon or phosphate atoms show the folding of the polypeptide or nucleic acid chain.

The simplest model is a smooth ribbon drawn through the peptide units; this may be either solid ('Ribbons') or made of parallel thin wires ('Strands').

The model can be rotated about the x, y and z axes interactively so that all parts of the molecule can be studied. The molecule can be made smaller or larger and in addition it is possible to expand the viewing window up to the full size of the screen - but the larger the picture, and the more elaborate the model, the longer it takes the computer to calculate the appearance of the drawing.

Several colouring schemes are available (a list is found in the colours menu next to display menu); the four most useful are 'CPK' (carbon atoms pale grey; oxygen red, nitrogen blue and sulphur yellow), 'group' colouring (the chain is coloured with the colour of the rainbow, from blue a the N-terminus to red at the C- terminus; this is useful for following the fold from one end of the chain to the other), and 'shapely' and 'amino' colours. In the former scheme, the backbone is pale grey, and the side-chain atoms are all given a colour which depends on the size and the polarity of the side-chain. Oxygen-containing side-chains (acids, amides, and the hydroxy-aminoacids Ser and Thr) are various shades of red, and basic side chains (Arg, Lys, His) blue. Hydrophobic aminoacids are mostly grey, but Ile is dark green and Val a pale magenta. The sulphur-containing amino-acids (Cys, Met) have muddy yellow colours, Trp is yellow and Gly, white.

The 'amino' scheme is similar but simpler: E and D are red; K and R blue; C and M yellow; H unfaded blue jeans; Q and N a bright green/blue; S and T orange; P flesh; I,L and V dark green; W dark purple; Y and F a lighter purple; G and A are off-white and light gray respectively.

The properties of the drawing are changed either by picking items from menus with the mouse, or by typing commands into a second window. Clicking with the mouse on any atom will cause the atom to be identified in the second window. Drawings can be made using selected parts of the molecule only; and it is often useful, for example, to draw some atoms or groups with the space-filling representation and others as wireframe or backbone. H-bonds (involving the backbone of proteins or the bases of nucleic acids) and disulphide bonds can also be drawn, to help show secondary structure. The program

knows how to identify secondary structure, and so these too can be isolated and drawn differently.

Command-line window:

Starting the RasMol will open two windows. One with the black background  (ofcourse we can change the background colour, but the default is black) and the other which is a Command-Line window (white).

In the windows, once RasMol is started, the Command-Line window goes minimized and sits in the bottom of the screen (task bar).

Move or resize the two windows, so as to see both of them at the same time.

Now, place the mouse point on any one of the atoms in the 3-D molecule, immediately the Command-Line window will show the details corresponding to that particular atom (like, whats the amino acid there, which chain it belongs to, whats the amino acid residue number and atom number etc.,).

Lots of commands can be executed through the Command-Line window. For example, typing color red and pressing enter will change the background to red.

The groups other than protein, like water can be visualized, if the Command-Line argument is select water An online version of the RasMol Manual  which describes how all these features can be used, and all this information is also available using the on-screen 'Help' facility.