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Time Narration
00:01 Welcome to this tutorial on Structures from Database in Jmol.
00:07 In this tutorial, we will learn to:
00:10 Load chemical structures from PubChem database and
00:14 Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
00:21 To follow this tutorial, you should be familiar with Jmol Application.
00:27 If not, watch the relevant tutorials available at our website.
00:33 To record this tutorial, I am using:
00:35 Ubuntu OS version 12.04
00:40 Jmol version 12.2.2
00:44 Java version 7
00:46 GChemPaint version 0.12.10
00:51 Mozilla Firefox browser 22.0.
00:56 I have opened a new Jmol Application window.
01:00 Jmol has a feature to load structures of compounds listed in the database.
01:07 The File' menu on the menu bar has an option Get MOL.
01:12 This loads molecules from chemical structure database PubChem.
01:17 It also has another option Get PDB to load protein structures from Protein Data Bank.
01:26 This feature will be explained in detail, in another tutorial.
01:31 To load a chemical structure on the panel, click on Get Mol.
01:36 An Input dialog-box opens on the screen.
01:40 Any molecule listed in the database can be loaded by typing the following, in the text box:
01:48 Common name or IUPAC name,
01:51 CAS number,
01:54 CID number,
01:56 InChi identifier or
01:58 SMILES identifier.
02:01 Please visit Pubchem database website for information on identification numbers, for a particular chemical.
02:09 Let us display phenol on screen.
02:13 So, type: "phenol" in the Input text-box.
02:16 click on OK button.
02:20 A model of phenol is displayed on the panel.
02:24 We can modify the display of phenol using various rendering options.
02:30 These options are listed in the Menu bar and Pop-up menu.
02:36 We can add substituents to the benzene ring of phenol.
02:41 First, let us label the atoms in the model.
02:45 Click on the Display menu and select Label. Click on Number option.
02:52 Now, let's replace a hydrogen- number 10, attached to the carbon atom -number 4, with an amino group.
03:00 Open the modelkit menu, select nitrogen from the options.
03:06 Click on hydrogen- number 10.
03:09 This is a molecule of Para-Amino Phenol on the panel.
03:14 We will change the display to Sticks display.
03:18 Exit the modelkit menu.
03:21 Open the Pop-up menu, scroll down to Style , select Scheme and click on Sticks options.
03:30 On the panel, we have a model of Para-Amino-phenol in sticks display.
03:36 Complex structures which are difficult to create, can easily be loaded on the panel.
03:42 For example: cholesterol.
03:45 Click on File menu.
03:47 Click on Get Mol option. In the text-box, type: Cholesterol .
03:54 click on OK button.
03:57 A molecule of Cholesterol is displayed on the panel.
04:02 We can highlight the features like double-bond and side-chain, in the molecule.
04:08 To highlight double-bond, let us first change the color of carbon atoms of the double-bond.
04:15 Click on Select atoms icon in the tool bar.
04:19 Then click on the carbon atoms involved in the double-bond.
04:24 A yellow halo appears around the atoms.
04:28 Open the Pop-up-menu.
04:30 Scroll down to Color, select Atoms and click on Orange option.
04:37 Now click on “Rotate molecule” option in the tool bar.
04:42 The double-bond in the cholesterol model is now in orange color.
04:49 Similarly, we can highlight the carbons in the side-chain.
04:54 Using Pop-up-menu, change the color to violet.
04:59 On the panel, we have a model of Cholesterol with important features highlighted.
05:06 As an assignment-
05:08 Load structure of caffeine from Pubchem database.
05:11 Highlight the important features in the molecule.
05:15 Modify the display to wireframe.
05:19 Now I will discuss another important feature of Jmol.
05:24 We can convert 2D structures of molecules, drawn in another software, into 3D models.
05:31 Here, I have a model of amino acid Alanine on the panel.
05:36 2D structure of this molecule was drawn in a software called GChemPaint.
05:42 The structure was saved as a ".mol" file.
05:46 GchemPaint is an Open source software for drawing 2D chemical structures.
05:51 Tutorials on GChemPaint are available at the following link.
05:56 To draw structures and save in ".mol" format, refer to Analysis of Compounds tutorial.
06:05 Shown on this Gchempaint display area are 2D drawings of-
06:10 Amino acid -Alanine
06:12 Nuclioside -Adenosine and
06:14 Saccharide -Alpha-D glucopyranose.
06:19 I have saved them in '.mol' format on my Desktop.
06:24 First let's view the 2D structure of Alanine as 3D model, in Jmol Application.
06:32 So, I will open a new Jmol window.
06:36 Click on Open a file icon in the tool bar.
06:40 I will choose Desktop folder and click on Open. Choose the file 'Alanine.mol' and click on Open button.
06:51 A 3D model of Alanine opens on screen.
06:55 Open the modelkit menu and click on fix hydrogens and minimize option.
07:03 Hydrogens are added to the structure and the energy minimized.
07:08 As with any ".mol" file, we can change the display using menu bar and also Pop-up menu.
07:15 Here is the 3D model of Adenosine.mol in Jmol.
07:19 And this is a 3D model of Alpha-D-glucopyranose.mol in Jmol.
07:25 Let's summarize.
07:27 In this tutorial, we have learnt to:
07:32 Load chemical structures from Pubchem data base.
07:34 Modify the display of Phenol and Cholesterol.
07:38 Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
07:44 Convert 2D structures of Alanine, Adenosine and Alpha-D-glucopyranose to 3D models.
07:53 Here is another assignment for you.
07:56 Draw 2D structures of the following Amino acids in GChemPaint-
08:01 Cysteine
08:03 Histidine Phenylalanine
08:06 Save as '.mol' files.
08:09 Open the files in Jmol and modify the display.
08:12 Watch the video available at this URL:
08:16 It summarizes the Spoken Tutorial project.
08:19 If you do not have good bandwidth, you can download and watch it.
08:23 The Spoken Tutorial Project team:
08:26 Conducts workshops using spoken tutorials.
08:29 Gives certificates to those who pass an on-line test.
08:33 For more details, please write
08:40 Spoken Tutorial project is a part of the Talk to a Teacher project.
08:45 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
08:52 More information on this mission is available at this link:
08:57 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14