View source for Jmol-Application/C2/Structures-from-Database/English-timed

{| border=1
| '''Time'''
| '''Narration'''

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| 00:01
| Welcome to this tutorial on '''Structures from Database''' in '''Jmol'''.

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| 00:07
| In this tutorial, we will learn to:

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| 00:10
| * '''Load''' chemical structures from '''PubChem''' database and

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| 00:14
| * Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.

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| 00:21
| To follow this tutorial, you should be familiar with '''Jmol Application'''.

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| 00:27
| If not, watch the relevant tutorials available at our website. 

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| 00:33
| To record this tutorial, I am using: 

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| 00:35
| * '''Ubuntu Linux '''OS version. '''12.04'''

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| 00:40
| * '''Jmol''' version '''12.2.2'''

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|00:44 
| * '''Java''' version '''7'''.

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| 00:46
| * '''GChemPaint''' version '''0.12.10'''

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| 00:51
| * '''Mozilla Firefox''' browser '''22.0'''

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| 00:56
| I have opened a new '''Jmol Application''' window.

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| 01:00
| '''Jmol''' has a feature to '''load''' '''structure'''s of compounds listed in the database.

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| 01:07
| The ''''File'''' menu on the menu bar has an option ''''Get MOL'.'''

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| 01:12
| This loads molecules from chemical structure database ''''PubChem'.'''

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| 01:17
| It also has another option ''''Get PDB'''' to load '''protein''' structures from '''Protein Data Bank'''. 

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| 01:26
| This feature will be explained in detail in another tutorial.

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| 01:31
| To load a chemical structure on the panel, click on ''''Get Mol''''.

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| 01:36
| An ''''Input'''' dialog-box opens on the '''screen'''.

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| 01:40
| Any molecule listed in the database can be loaded by typing the following in the text box:

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| 01:48
| Common name or '''IUPAC''' name, 

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| 01:51
|  '''CAS '''number, 

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| 01:54
|  '''CID''' number, 

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|01:56
|   '''InChi identifier'''  or

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| 01:58
|'''SMILES identifier'''.

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| 02:01
| Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical.

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| 02:09
| Let us display '''phenol''' on screen.

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| 02:13
| So, type: ''''phenol'''' in the '''Input '''text box.

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| 02:16
| click on '''OK''' button.

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| 02:20
| A Model of '''phenol''' is displayed on the panel.

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| 02:24
|We can modify the display of '''phenol''' using various rendering options.

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|02:30 
| These options are listed in the '''Menu bar '''and '''Pop-up''' menu. 

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| 02:36
| We can add substituents to the '''benzene''' '''ring''' of '''phenol'''.

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| 02:41
| First, let us label the atoms in the '''model'''.

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| 02:45
| Click on the '''Display''' menu and select''' Label'''. Click on '''Number '''option. 

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| 02:52
| Now, let's replace a '''hydrogen number 10 '''attached to the '''carbon atom number 4 '''with an '''amino group'''.

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|03:00
| Open the '''modelkit''' menu,  select '''nitrogen''' from the options. 

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| 03:06
| Click on '''hydrogen number 10'''.

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| 03:09
| This is a molecule of '''Para-Amino Phenol''' on the '''panel'''.

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|03:14 
|We will change the display to '''Sticks display'''.

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| 03:18
| Exit the '''modelkit''' menu.

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| 03:21
| Open the Pop-up menu, scroll down to '''Style ''', select '''Scheme''' and click on '''Sticks''' options.

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| 03:30
| On the panel, we have a model of '''Para-Amino-phenol''' in '''sticks''' display.

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| 03:36
| Complex structures which are difficult to create, can easily be loaded on the '''panel'''.

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| 03:42
| For example '''cholesterol.''' 

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| 03:45
| Click on '''File''' menu.

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| 03:47
| Click on '''Get Mol''' option,   in the text box type: '''Cholesterol '''.

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| 03:54
| click on '''OK''' button.

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| 03:57
| A molecule of '''Cholesterol '''is displayed on the '''panel'''. 

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| 04:02
| We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule.

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| 04:08
| To highlight double-bond,  let us first change the color of '''carbon''' atoms of the double-bond. 

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| 04:15
| Click on ''''Select atoms'''' icon in the tool bar.

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| 04:19
| Then click on the '''carbon''' atoms involved in the double-bond.

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| 04:24
| A yellow halo appears around the atoms.

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| 04:28
| Open the Pop-up-menu.

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| 04:30
| Scroll down to '''Color''', select '''Atoms''' and click on '''Orange''' option. 

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| 04:37
| Now Click on ''' “Rotate molecule”''' option in the tool bar.

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| 04:42
| The double-bond in the '''cholesterol '''model is now in orange color.

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| 04:49
| Similarly, we can highlight the '''carbons '''in the side-chain.

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| 04:54
| Using '''Pop-up'''-menu change the color to violet.

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|04:59
| On the '''panel, '''we have a model of '''Cholesterol '''with important features highlighted. 

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| 05:06
| As an assignment-

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| 05:08
| * Load structure of caffeine from '''Pubchem''' database .

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| 05:11
| * Highlight the important features in the molecule.

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| 05:15
| * Modify the display to '''wireframe'''.

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| 05:19
| Now I will discuss another important feature of '''Jmol.'''

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| 05:24
| We can convert '''2D structure'''s of molecules drawn in another software into '''3D model'''s.

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| 05:31
| Here, I have a model of '''aminoacid Alanine''' on the panel.

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| 05:36
| 2D structure of this molecule was drawn in software called '''GChemPaint.'''

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| 05:42
| The structure was saved as a ''''.mol' '''file. 

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| 05:46
| '''GchemPaint '''is an Open source software for drawing 2D chemical structures.

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| 05:51
| Tutorials on '''GChemPaint '''are available at the following link.

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| 05:56
| To draw structures and save in '.mol' format, refer to '''Analysis of Compounds''' tutorial.

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| 06:05
| Shown on this Gchempaint display area are 2D drawings of- 

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| 06:10
| * '''Amino acid -Alanine'''

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| 06:12
| * '''Nuclioside -Adenosine'''

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| 06:14
| * '''Saccharide -Alpha-D glucopyranose'''.

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| 06:19
| I have saved them in ''''.mol'''' format on my '''Desktop.'''

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| 06:24
| First, let's view the 2D structure of '''Alanine '''as 3D model in '''Jmol Application'''.

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| 06:32
| So, I will open a new '''Jmol '''window.

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| 06:36
| Click on '''Open a file''' icon in the tool bar.

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| 06:40
| I will choose '''Desktop''' folder and click on open. Choose the file '''Alanine.mol '''and click on '''Open''' button.

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| 06:51
| A 3D model of ''''Alanine'''' opens on screen.

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| 06:55
| Open the '''modelkit''' menu and click on ''''fix hydrogens and minimize'''' option.

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|07:03
| '''Hydrogens''' are added to the structure and the energy minimized.

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| 07:08
| As with any '''.mol''' file, we can change the display using menu bar and also '''Pop-up '''menu. 

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| 07:15
| Here is the 3D model of '''Adenosine.mol '''in '''Jmol.'''

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| 07:19
|And this is a 3D model of '''Alpha-D-glucopyranose.mol '''in '''Jmol.'''

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| 07:25
| Let's summarize. 

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| 07:27
| In this tutorial, we have learnt to:

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| 07:32
| * Load chemical structures from '''Pubchem''' data base. 

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| 07:34
| * Modify the display of '''Phenol''' and '''Cholesterol'''. 

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| 07:38
| * Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.

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| 07:44
| * Convert 2D structures of '''Alanine, Adenosine''' and '''Alpha-D-glucopyranose '''to 3D models.

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| 07:53
| Here is another assignment for you.

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| 07:56
| # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint'''-

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| 08:01
| * '''Cysteine '''

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| 08:03
| * '''Histidine '''

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| 08:04
| * '''Phenylalanine'''

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| 08:06
| # Save as ''''.mol' '''files.

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| 08:09
| # Open the files in '''Jmol''' and modify the display. 

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| 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: 

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| 08:26
| Conducts workshops using spoken tutorials.

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| 08:29
| Gives certificates to those who pass an on-line test. 

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| 08:33
| For more details, please write to:  contact@spoken-tutorial.org 

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| 08:40
| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. 

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| 08:45
| It is supported by the National Mission on Education through ICT, MHRD, Government of India.

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| 08:52
| More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro   

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| 08:57
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining. 
|}