Jmol Application

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Jmol Application

Jmol is an open-source Java viewer for chemical structures and biomolecules in 3D. It does not require 3D acceleration plugins. 3D models created by using Jmol may be used as a teaching tool or for research in chemistry and biochemistry. It is free and open source software, written in Java, it runs on Windows, Mac OS X, Linux and Unix systems. There is a standalone application and a development tool kit that can be integrated into other Java applications, such as Bioclipse and Taverna.

The Spoken Tutorial Effort for Jmol Application has being contributed by Dr. Snehalatha Kaliappan with domain reviews done by faculty and research scholars from the Chem Engg Dept, IIT Bombay.

Learners: School students (9th standard upto Post Graduation level) as well as school teachers.

Basic Level

1. Overview of Jmol Application

  • Learn about Jmol Application
  • Important uses of Jmol
  • Official website to download Jmol
  • Information regarding Installation on various operating systems
  • Download, extract and run Jmol Application on Ubuntu Linux OS
  • Salient features of Jmol
  • Show Jmol Wiki main page
  • Advantages of Jmol
  • Various uses of Jmol
  • Play video clippings of Jmol Application tutorials available on ST website

2. Introduction to Jmol Application

  • Brief description about Jmol Application
  • Software requirements
  • Prerequisites
  • Open the Jmol Application on Ubuntu/ Linux system
  • Explain program interface (Menu Bar, Tool bar, Pop-up menu and display area)
  • Change the size of the display area
  • Create models of simple organic molecules (alkanes)
  • Energy Minimization
  • Save the image as .mol file

3. Create and Edit Molecular Models

  • Substitute the hydrogen in molecular model with a functional group
  • Add and delete bonds
  • Add and delete atoms
  • Pop-up-menu (Contextual menu)

4. Modify Display and View

  • Rotate, zoom, move and spin the model
  • Modify the view
  • Change the style of the display
  • Change the size and color of atoms and bonds
  • Axes and bound box
  • Save the image in various file formats

5. Measurements and Labelling

  • Create a model of Carboxylic acid. Example, Acetic acid
  • Create a model of Nitroalkane. Example, Nitroetane
  • Label atoms in a model with symbol of the element
  • Label atoms in a model with number
  • Label atoms in a model with both symbol and number
  • Measure bond lengths in a model
  • Examples : Carbon-Carbon single bond
  • Carbon-Oxygen single and double bonds
  • Measure bond angles in a model
  • Measure dihedral angles in a model

Intermediate Level

6. Script Console and Script Commands

  • About Script Commands
  • How to write Script commands
  • How to use Script console
  • Change display of propane by using script commands
  • Change the color of atoms and bonds
  • Change the size of bonds and atoms
  • Display lines of text on panel
  • Change color, font and sizeof font of the text

7. Surfaces and Orbitals

  • Create models of alicyclic molecules. Example: Cyclohexane
  • Create models of aromatic molecules. Example: Benzene
  • Display Surface topology of molecules. Example: Molecular surface and Dot surface
  • Create models of Atomic orbitals s, p, d and f
  • Create models of Molecular Orbitals sp3, sp2 and sp
  • Create molecular orbitals for methane molecule
  • Create molecular orbitals for ethene molecule

8. Structures from Database

  • Load chemical structures from chemical structure database (PubChem)
  • Load structure of Phenol and convert it to Para-amino Phenol
  • Load structure of cholesterol and highlight the double-bond and side-chain
  • Convert 2D structures drawn in GChemPaint to 3D models in Jmol
  • Convert 2D structures of Alanine, Adenosine, Alpha-d-glucopyranose to 3D models in Jmol

9. Crystal Structure and Unit Cell

  • Download CIF (Crystallographic Information File) from Crystallography Open Database (COD)
  • Open CIF files in Jmol
  • Display unit cell and unit cell parameters on Jmol panel
  • Display crystal structures of different crystal systems. For example Cubic (sodium chloride), Hexagonal (graphite) and Rhombohedral (calcite)

Advance Level

10. Proteins and Macromolecules

  • Load structures of proteins from Protein Data Bank (PDB)
  • Download .pdb files from the database
  • View the 3D structure of Insulin using PDB code (4EX1)
  • View the structure without water molecules
  • Modify the display of secondary structure
  • Highlight hydrogen bonds and disulfide bonds

11. 3D Models of Enzymes

  • Load structure of Hexokinase using PDB code
  • Modify the display of secondary structure
  • Highlight amino acid residues at the active site
  • Highlight the substrate
  • Highlight the co-factors
  • View Ramachandran plot for proteins

12. Symmetry and Point Groups

  • Draw lines (C2 and C3 rotational axes) through atoms in methane molecule
  • Spin and rotate the molecule along the axis
  • Draw reflection plane through atoms in methane molecule
  • Demonstration of point group classification using examples of methane and allene

13. Animation using Script Commands

  • Jmol animation using script commands.
  • Demonstration of animation using ethane and hemoglobin as examples.
  • Script commands with keywords, move, delay, slab, loop and capture.
  • Save the animation as GIF file.

Contributors and Content Editors

Nancyvarkey, PoojaMoolya, Snehalathak