Difference between revisions of "Jmol-Application/C2/Structures-from-Database/English-timed"

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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 Linux '''OS version. '''12.04'''

| 00:40

| * '''Jmol''' version '''12.2.2'''

| * '''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''' '''structure'''s 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,  

|   '''InChi identifier'''  or

| 01:58

| 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

| 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'''.

| 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'''.

| 03:18

| 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.

| 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 structure'''s of molecules, drawn in another software, into '''3D model'''s.

| 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.

| '''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

| 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'''

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| # 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.

 

| 08:23

| 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.