Molecular visualization
- 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