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

{| border=1

| '''Time'''

| '''Narration'''

| 00:01

| Welcome to this tutorial on '''Structures from Databases 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

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| * '''Jmol''' version 12.2.2

| * '''Java''' version 7

| 00:46

| * '''GChemPaint''' version 0.12.10

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| * '''Mozilla Firefox''' browser 22.0

| 00:56

| I have opened a new '''Jmol Application''' window.

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| '''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 data base ''''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:

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| Common name or '''IUPAC''' name  

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| '''CAS '''number  

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| '''CID''' number  

|   '''InChi identifier'''  or

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|'''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

| 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.'''  

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| Click on '''File''' menu

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| 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 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'''

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| 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.

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| 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

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| * 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.

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| # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''

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| * '''Cysteine '''

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| * '''Histidine '''

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| * '''Phenylalanine'''

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| # Save as '''.mol '''files.

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| # 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 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

 

 

| 08:57

| This is Snehalatha from IIT Bombay signing off. Thank you for joining.