Jmol-Application/C2/Structures-from-Database/English-timed

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 Linux 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 aminoacid Alanine on the panel.
05:36	2D structure of this molecule was drawn in 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
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
08:04	* 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. http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial
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 to: contact@spoken-tutorial.org
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: http://spoken-tutorial.org/NMEICT-Intro
08:57	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14