The document discusses molecular visualization techniques used to explore and understand macromolecules like proteins, DNA, and RNA through computer-generated models. It outlines various representations, such as ball and stick, wireframe, and ribbon models, along with tools like Rasmol for 3D visualization. The document also highlights methods for structural analysis and color schemes for macromolecules to help interpret their structures.

1. MOLECULAR
VISUALIZATION
ALEN SHAJI
P1914015

2. INTRODUCTION
 Looking at molecular models in order to explore and understand them.
 Does not necessarily involve molecular modeling (changing the existing
model).
 Macromolecules – Protein, DNA, RNA, or their complexes.
 3-D view of different molecules on the computer.

3. REPRESENTATIONS OF MOLECULAR MODELS
ATOMIC REPRESENTATION
 It includes ball and stick, stick (wireframe), and spacefilling.
 These representations show positions of atoms and covalent bonds.

4. SLABBING
 A usefull way to see atomic details of a small part of a large macromolecular
model is to centre the moiety of interest, and then cut away front and back
portions of the molecules.
 It is usefull to see buried structures and their environments, such as the
hydrophobic core of a protein domain.
 It can be done using FirstGlance in Jmol.

5. SIMPLIFIED SCHEMATIC REPRESENTATIONS
BACKBONES
 Simplified representations of the polypeptide backbone or main chain, are
very helpful in understanding structure when it comes to large molecules such
as Proteins, DNA, RNA, and their complexes.
 Using FirstGlance in Jmol.

6. DISULFIDE BONDS
 FirstGlance in Jmol highlights disulfide bonds in one click, and has several
options for rendinering and coloring them.

7. COLOUR SCHEMES FOR MACROMOLECULES
 A set of standard color schemes for macromolecules, called DRuMS, was
released in 2000.
 Colors for chemical elements.

8. STRUCTURAL ANALYSIS
 Molecular function.
 Prediction of function.
 Experimental design to test predictions.

9. TYPES OF MOLECULAR VISUALIZATION
 WIRE FRAME MODEL.
 BALL AND STICK MODEL.
 RIBBON SHAPED MODEL.
 SPACE FILLING.
 SIMPLE HARMONIC MODEL.
 BACKBONE.
 SURFACE.

10. WIRE FRAME MODEL
 Skeletal form of molecules – represent as wires.
 Network of wire.
 Line represents the bonds.
 Shows individual bonds and corresponding angles.

11. RIBBON SHAPED MODEL
 Spherical or cylindrical ribbons.
 Display the folding and structure of proteins.

12. BALL AND STICK MODEL
 Ball represents the atoms.
 Stick represents the bonds.
 Shows atomic positions and bonds and volume.

13. SIMPLE HARMONIC MODEL
 Only represents grooves and projections in the molecules.

14. SPACE FILLING
 Spheres represents the electro cloud around nuclei of atoms.
 Relative size of atoms and groups show up clearly.
 Merged spheres represents the sharing of electrons.

15. RasMol
 Most frequently available tool.
 Derived from Raster and molecules.
 Molecular graphics programe.
 For visualizing proteins, nucleic acid and small molecules for which 3-D
structures is available.
 In order to display molecules, RasMol requires atomic coordinate file that
specifies the position of every atom in the molecule through its 3-D Cartesian
coordinates.
 RasMol accept this coordinate file variety of formats including Protein Data
Bank format.

16.  It provides user a choice of colour schemes and molecular representation.
 Additional features including test labelling for slected atoms, different colour
schemes of different parts of the molecule, zoom, rotation etc.

17. REFERENCE
 Jin Xiong (2007) Essential Bioinformatics, Cambridge University, PressIndia,
Pvt LTD.
 Wikipedia - Molecular Visualization, Bioinformatics.

18. THANK YOU