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

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{| border=1
+
{|border=1
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| '''Time'''
+
|'''Time'''
−
| '''Narration'''
+
|'''Narration'''
  
 
|-
 
|-
−
| 00:01
+
|00:01
−
| Welcome to this tutorial on '''Structures from Database''' in '''Jmol'''.
+
|Welcome to this tutorial on '''Structures from Database''' in '''Jmol'''.
  
 
|-
 
|-
−
| 00:07
+
|00:07
−
| In this tutorial, we will learn to:
+
|In this tutorial, we will learn to:
  
 
|-
 
|-
−
| 00:10
+
|00:10
 
|'''Load''' chemical structures from '''PubChem''' database and
 
|'''Load''' chemical structures from '''PubChem''' database and
  
 
|-
 
|-
−
| 00:14
+
|00:14
 
|Convert '''2D structure'''s drawn in '''GChemPaint''' to '''3D model'''s in '''Jmol'''.
 
|Convert '''2D structure'''s drawn in '''GChemPaint''' to '''3D model'''s in '''Jmol'''.
  
 
|-
 
|-
−
| 00:21
+
|00:21
−
| To follow this tutorial, you should be familiar with '''Jmol Application'''.
+
|To follow this tutorial, you should be familiar with '''Jmol Application'''.
  
 
|-
 
|-
−
| 00:27
+
|00:27
−
| If not, watch the relevant tutorials available at our website.  
+
|If not, watch the relevant tutorials available at our website.  
  
 
|-
 
|-
−
| 00:33
+
|00:33
−
| To record this tutorial, I am using:  
+
|To record this tutorial, I am using:  
  
 
|-
 
|-
−
| 00:35
+
|00:35
 
|'''Ubuntu '''OS version '''12.04'''
 
|'''Ubuntu '''OS version '''12.04'''
  
 
|-
 
|-
−
| 00:40
+
|00:40
 
|'''Jmol''' version '''12.2.2'''
 
|'''Jmol''' version '''12.2.2'''
  
Line 44: Line 44:
  
 
|-
 
|-
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| 00:46
+
|00:46
 
|'''GChemPaint''' version '''0.12.10'''
 
|'''GChemPaint''' version '''0.12.10'''
  
 
|-
 
|-
−
| 00:51
+
|00:51
 
|'''Mozilla Firefox browser''' '''22.0'''.
 
|'''Mozilla Firefox browser''' '''22.0'''.
  
 
|-
 
|-
−
| 00:56
+
|00:56
−
| I have opened a new '''Jmol Application''' window.
+
|I have opened a new '''Jmol Application''' window.
  
 
|-
 
|-
−
| 01:00
+
|01:00
−
| '''Jmol''' has a feature to '''load''' '''structure'''s of compounds listed in the database.
+
|'''Jmol''' has a feature to '''load''' '''structure'''s of compounds listed in the database.
  
 
|-
 
|-
−
| 01:07
+
|01:07
−
| The '''File'''' menu on the menu bar has an option '''Get MOL.'''
+
|The '''File'''' menu on the menu bar has an option '''Get MOL.'''
  
 
|-
 
|-
−
| 01:12
+
|01:12
−
| This loads molecules from chemical structure database '''PubChem.'''
+
|This loads molecules from chemical structure database '''PubChem.'''
  
 
|-
 
|-
−
| 01:17
+
|01:17
−
| It also has another option '''Get PDB''' to load '''protein''' structures from '''Protein Data Bank'''.  
+
|It also has another option '''Get PDB''' to load '''protein''' structures from '''Protein Data Bank'''.  
  
 
|-
 
|-
−
| 01:26
+
|01:26
−
| This feature will be explained in detail, in another tutorial.
+
|This feature will be explained in detail, in another tutorial.
  
 
|-
 
|-
−
| 01:31
+
|01:31
−
| To '''load''' a chemical structure on the panel, click on '''Get Mol'''.
+
|To '''load''' a chemical structure on the panel, click on '''Get Mol'''.
  
 
|-
 
|-
−
| 01:36
+
|01:36
−
| An '''Input''' dialog-box opens on the '''screen'''.
+
|An '''Input''' dialog-box opens on the '''screen'''.
  
 
|-
 
|-
−
| 01:40
+
|01:40
−
| Any molecule listed in the database can be loaded by typing the following, in the text box:
+
|Any molecule listed in the database can be loaded by typing the following, in the text box:
  
 
|-
 
|-
−
| 01:48
+
|01:48
−
| Common name or '''IUPAC''' name,  
+
|Common name or '''IUPAC''' name,  
  
 
|-
 
|-
−
| 01:51
+
|01:51
−
| '''CAS '''number,  
+
|'''CAS '''number,  
  
 
|-
 
|-
−
| 01:54
+
|01:54
−
| '''CID''' number,  
+
|'''CID''' number,  
  
 
|-
 
|-
 
|01:56
 
|01:56
−
|   '''InChi identifier'''  or
+
|'''InChi identifier'''  or
  
 
|-
 
|-
−
| 01:58
+
|01:58
 
|'''SMILES identifier'''.
 
|'''SMILES identifier'''.
  
 
|-
 
|-
−
| 02:01
+
|02:01
−
| Please visit '''Pubchem''' database website for information on identification numbers, for a particular chemical.
+
|Please visit '''Pubchem''' database website for information on identification numbers, for a particular chemical.
  
 
|-
 
|-
−
| 02:09
+
|02:09
−
| Let us display '''phenol''' on screen.
+
|Let us display '''phenol''' on screen.
  
 
|-
 
|-
−
| 02:13
+
|02:13
−
| So, type: "phenol" in the '''Input '''text-box.
+
|So, type: "phenol" in the '''Input '''text-box.
  
 
|-
 
|-
−
| 02:16
+
|02:16
−
| click on '''OK''' button.
+
|click on '''OK''' button.
  
 
|-
 
|-
−
| 02:20
+
|02:20
−
| A model of phenol is displayed on the panel.
+
|A model of phenol is displayed on the panel.
  
 
|-
 
|-
−
| 02:24
+
|02:24
 
|We can modify the display of '''phenol''' using various rendering options.
 
|We can modify the display of '''phenol''' using various rendering options.
  
 
|-
 
|-
 
|02:30  
 
|02:30  
−
| These options are listed in the '''Menu bar '''and '''Pop-up''' menu.  
+
|These options are listed in the '''Menu bar '''and '''Pop-up''' menu.  
  
 
|-
 
|-
−
| 02:36
+
|02:36
−
| We can add substituents to the '''benzene ring''' of phenol.
+
|We can add substituents to the '''benzene ring''' of phenol.
  
 
|-
 
|-
−
| 02:41
+
|02:41
−
| First, let us label the atoms in the '''model'''.
+
|First, let us label the atoms in the '''model'''.
  
 
|-
 
|-
−
| 02:45
+
|02:45
−
| Click on the '''Display''' menu and select''' Label'''. Click on '''Number '''option.  
+
|Click on the '''Display''' menu and select''' Label'''. Click on '''Number '''option.  
  
 
|-
 
|-
−
| 02:52
+
|02:52
−
| Now, let's replace a '''hydrogen'''- number 10, attached to the '''carbon''' atom -number 4,  with an '''amino group'''.
+
|Now, let's replace a '''hydrogen'''- number 10, attached to the '''carbon''' atom -number 4,  with an '''amino group'''.
  
 
|-
 
|-
 
|03:00
 
|03:00
−
| Open the '''modelkit''' menu,  select '''nitrogen''' from the options.  
+
|Open the '''modelkit''' menu,  select '''nitrogen''' from the options.  
  
 
|-
 
|-
−
| 03:06
+
|03:06
−
| Click on '''hydrogen'''- number 10.
+
|Click on '''hydrogen'''- number 10.
  
 
|-
 
|-
−
| 03:09
+
|03:09
−
| This is a molecule of '''Para-Amino Phenol''' on the '''panel'''.
+
|This is a molecule of '''Para-Amino Phenol''' on the '''panel'''.
  
 
|-
 
|-
Line 168: Line 168:
  
 
|-
 
|-
−
| 03:18
+
|03:18
−
| Exit the '''modelkit''' menu.
+
|Exit the '''modelkit''' menu.
  
 
|-
 
|-
−
| 03:21
+
|03:21
−
| Open the Pop-up menu, scroll down to '''Style ''', select '''Scheme''' and click on '''Sticks''' options.
+
|Open the Pop-up menu, scroll down to '''Style ''', select '''Scheme''' and click on '''Sticks''' options.
  
 
|-
 
|-
−
| 03:30
+
|03:30
−
| On the panel, we have a model of '''Para-Amino-phenol''' in '''sticks''' display.
+
|On the panel, we have a model of '''Para-Amino-phenol''' in '''sticks''' display.
  
 
|-
 
|-
−
| 03:36
+
|03:36
−
| Complex structures which are difficult to create, can easily be loaded on the panel.
+
|Complex structures which are difficult to create, can easily be loaded on the panel.
  
 
|-
 
|-
−
| 03:42
+
|03:42
−
| For example: '''cholesterol.'''  
+
|For example: '''cholesterol.'''  
  
 
|-
 
|-
−
| 03:45
+
|03:45
−
| Click on '''File''' menu.
+
|Click on '''File''' menu.
  
 
|-
 
|-
−
| 03:47
+
|03:47
−
| Click on '''Get Mol''' option. In the text-box, type: '''Cholesterol '''.
+
|Click on '''Get Mol''' option. In the text-box, type: '''Cholesterol '''.
  
 
|-
 
|-
−
| 03:54
+
|03:54
−
| click on '''OK''' button.
+
|click on '''OK''' button.
  
 
|-
 
|-
−
| 03:57
+
|03:57
−
| A molecule of '''Cholesterol '''is displayed on the panel.  
+
|A molecule of '''Cholesterol '''is displayed on the panel.  
  
 
|-
 
|-
−
| 04:02
+
|04:02
−
| We can highlight the features like '''double-bond''' and '''side-chain''', in the molecule.
+
|We can highlight the features like '''double-bond''' and '''side-chain''', in the molecule.
  
 
|-
 
|-
−
| 04:08
+
|04:08
−
| To highlight double-bond, let us first change the color of '''carbon''' atoms of the double-bond.  
+
|To highlight double-bond, let us first change the color of '''carbon''' atoms of the double-bond.  
  
 
|-
 
|-
−
| 04:15
+
|04:15
−
| Click on '''Select atoms''' icon in the tool bar.
+
|Click on '''Select atoms''' icon in the tool bar.
  
 
|-
 
|-
−
| 04:19
+
|04:19
−
| Then click on the '''carbon''' atoms involved in the double-bond.
+
|Then click on the '''carbon''' atoms involved in the double-bond.
  
 
|-
 
|-
−
| 04:24
+
|04:24
−
| A yellow halo appears around the atoms.
+
|A yellow halo appears around the atoms.
  
 
|-
 
|-
−
| 04:28
+
|04:28
−
| Open the Pop-up-menu.
+
|Open the Pop-up-menu.
  
 
|-
 
|-
−
| 04:30
+
|04:30
−
| Scroll down to '''Color''', select '''Atoms''' and click on '''Orange''' option.  
+
|Scroll down to '''Color''', select '''Atoms''' and click on '''Orange''' option.  
  
 
|-
 
|-
−
| 04:37
+
|04:37
−
| Now click on ''' “Rotate molecule”''' option in the tool bar.
+
|Now click on ''' “Rotate molecule”''' option in the tool bar.
  
 
|-
 
|-
−
| 04:42
+
|04:42
−
| The double-bond in the '''cholesterol '''model is now in orange color.
+
|The double-bond in the '''cholesterol '''model is now in orange color.
  
 
|-
 
|-
−
| 04:49
+
|04:49
−
| Similarly, we can highlight the '''carbons '''in the side-chain.
+
|Similarly, we can highlight the '''carbons '''in the side-chain.
  
 
|-
 
|-
−
| 04:54
+
|04:54
−
| Using '''Pop-up'''-menu, change the color to violet.
+
|Using '''Pop-up'''-menu, change the color to violet.
  
 
|-
 
|-
 
|04:59
 
|04:59
−
| On the panel, we have a model of '''Cholesterol '''with important features highlighted.  
+
|On the panel, we have a model of '''Cholesterol '''with important features highlighted.  
  
 
|-
 
|-
−
| 05:06
+
|05:06
−
| As an assignment-
+
|As an assignment-
  
 
|-
 
|-
−
| 05:08
+
|05:08
 
|'''Load''' structure of '''caffeine''' from '''Pubchem''' database.
 
|'''Load''' structure of '''caffeine''' from '''Pubchem''' database.
  
 
|-
 
|-
−
| 05:11
+
|05:11
 
|Highlight the important features in the molecule.
 
|Highlight the important features in the molecule.
  
 
|-
 
|-
−
| 05:15
+
|05:15
 
|Modify the display to '''wireframe'''.
 
|Modify the display to '''wireframe'''.
  
 
|-
 
|-
−
| 05:19
+
|05:19
−
| Now I will discuss another important feature of '''Jmol.'''
+
|Now I will discuss another important feature of '''Jmol.'''
  
 
|-
 
|-
−
| 05:24
+
|05:24
−
| We can convert '''2D structure'''s of molecules, drawn in another software, into '''3D model'''s.
+
|We can convert '''2D structure'''s of molecules, drawn in another software, into '''3D model'''s.
  
 
|-
 
|-
−
| 05:31
+
|05:31
−
| Here, I have a model of '''amino acid Alanine''' on the panel.
+
|Here, I have a model of '''amino acid Alanine''' on the panel.
  
 
|-
 
|-
−
| 05:36
+
|05:36
−
| '''2D structure''' of this molecule was drawn in a software called '''GChemPaint.'''
+
|'''2D structure''' of this molecule was drawn in a software called '''GChemPaint.'''
  
 
|-
 
|-
−
| 05:42
+
|05:42
−
| The structure was saved as a ".mol" file.  
+
|The structure was saved as a ".mol" file.  
  
 
|-
 
|-
−
| 05:46
+
|05:46
−
| '''GchemPaint '''is an '''Open source software''' for drawing '''2D''' chemical structures.
+
|'''GchemPaint '''is an '''Open source software''' for drawing '''2D''' chemical structures.
  
 
|-
 
|-
−
| 05:51
+
|05:51
−
| Tutorials on '''GChemPaint '''are available at the following link.
+
|Tutorials on '''GChemPaint '''are available at the following link.
  
 
|-
 
|-
−
| 05:56
+
|05:56
−
| To draw structures and '''save''' in ".mol" format, refer to '''Analysis of Compounds''' tutorial.
+
|To draw structures and '''save''' in ".mol" format, refer to '''Analysis of Compounds''' tutorial.
  
 
|-
 
|-
−
| 06:05
+
|06:05
−
| Shown on this '''Gchempaint''' display area are 2D drawings of-  
+
|Shown on this '''Gchempaint''' display area are 2D drawings of-  
  
 
|-
 
|-
−
| 06:10
+
|06:10
−
| '''Amino acid -Alanine'''
+
|'''Amino acid -Alanine'''
  
 
|-
 
|-
−
| 06:12
+
|06:12
−
| '''Nuclioside -Adenosine''' and
+
|'''Nuclioside -Adenosine''' and
  
 
|-
 
|-
−
| 06:14
+
|06:14
−
| '''Saccharide -Alpha-D glucopyranose'''.
+
|'''Saccharide -Alpha-D glucopyranose'''.
  
 
|-
 
|-
−
| 06:19
+
|06:19
−
| I have saved them in '.mol' format on my '''Desktop.'''
+
|I have saved them in '.mol' format on my '''Desktop.'''
  
 
|-
 
|-
−
| 06:24
+
|06:24
−
| First let's view the 2D structure of '''Alanine '''as 3D model, in '''Jmol Application'''.
+
|First let's view the 2D structure of '''Alanine '''as 3D model, in '''Jmol Application'''.
  
 
|-
 
|-
−
| 06:32
+
|06:32
−
| So, I will open a new '''Jmol '''window.
+
|So, I will open a new '''Jmol '''window.
  
 
|-
 
|-
−
| 06:36
+
|06:36
−
| Click on '''Open a file''' icon in the tool bar.
+
|Click on '''Open a file''' icon in the tool bar.
  
 
|-
 
|-
−
| 06:40
+
|06:40
−
| I will choose '''Desktop''' folder and click on '''Open'''. Choose the file 'Alanine.mol' and click on '''Open''' button.
+
|I will choose '''Desktop''' folder and click on '''Open'''. Choose the file 'Alanine.mol' and click on '''Open''' button.
  
 
|-
 
|-
−
| 06:51
+
|06:51
−
| A '''3D model''' of '''Alanine''' opens on screen.
+
|A '''3D model''' of '''Alanine''' opens on screen.
  
 
|-
 
|-
−
| 06:55
+
|06:55
−
| Open the '''modelkit''' menu and click on '''fix hydrogens and minimize''' option.
+
|Open the '''modelkit''' menu and click on '''fix hydrogens and minimize''' option.
  
 
|-
 
|-
 
|07:03
 
|07:03
−
| '''Hydrogens''' are added to the structure and the energy minimized.
+
|'''Hydrogens''' are added to the structure and the energy minimized.
  
 
|-
 
|-
−
| 07:08
+
|07:08
−
| As with any ".mol" file, we can change the display using menu bar and also '''Pop-up '''menu.  
+
|As with any ".mol" file, we can change the display using menu bar and also '''Pop-up '''menu.  
  
 
|-
 
|-
−
| 07:15
+
|07:15
−
| Here is the 3D model of '''Adenosine.mol '''in '''Jmol.'''
+
|Here is the 3D model of '''Adenosine.mol '''in '''Jmol.'''
  
 
|-
 
|-
−
| 07:19
+
|07:19
 
|And this is a 3D model of '''Alpha-D-glucopyranose.mol '''in '''Jmol.'''
 
|And this is a 3D model of '''Alpha-D-glucopyranose.mol '''in '''Jmol.'''
  
 
|-
 
|-
−
| 07:25
+
|07:25
−
| Let's summarize.  
+
|Let's summarize.  
  
 
|-
 
|-
−
| 07:27
+
|07:27
−
| In this tutorial, we have learnt to:
+
|In this tutorial, we have learnt to:
  
 
|-
 
|-
−
| 07:32
+
|07:32
 
|'''Load''' chemical structures from '''Pubchem''' data base.  
 
|'''Load''' chemical structures from '''Pubchem''' data base.  
  
 
|-
 
|-
−
| 07:34
+
|07:34
 
|Modify the display of '''Phenol''' and '''Cholesterol'''.  
 
|Modify the display of '''Phenol''' and '''Cholesterol'''.  
  
 
|-
 
|-
−
| 07:38
+
|07:38
 
|Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.
 
|Convert 2D structures drawn in '''GChemPaint''' to 3D models in '''Jmol'''.
  
 
|-
 
|-
−
| 07:44
+
|07:44
 
|Convert 2D structures of '''Alanine, Adenosine''' and '''Alpha-D-glucopyranose '''to 3D models.
 
|Convert 2D structures of '''Alanine, Adenosine''' and '''Alpha-D-glucopyranose '''to 3D models.
  
 
|-
 
|-
−
| 07:53
+
|07:53
−
| Here is another assignment for you.
+
|Here is another assignment for you.
  
 
|-
 
|-
−
| 07:56
+
|07:56
 
|Draw 2D structures of the following '''Amino acids''' in '''GChemPaint'''-
 
|Draw 2D structures of the following '''Amino acids''' in '''GChemPaint'''-
  
 
|-
 
|-
−
| 08:01
+
|08:01
 
|'''Cysteine '''
 
|'''Cysteine '''
  
 
|-
 
|-
−
| 08:03
+
|08:03
 
|'''Histidine ''' '''Phenylalanine'''
 
|'''Histidine ''' '''Phenylalanine'''
  
 
|-
 
|-
−
| 08:06
+
|08:06
 
|Save as '.mol' files.
 
|Save as '.mol' files.
  
 
|-
 
|-
−
| 08:09
+
|08:09
 
|Open the files in '''Jmol''' and modify the display.  
 
|Open the files in '''Jmol''' and modify the display.  
  
 
|-
 
|-
−
| 08:12
+
|08:12
−
| Watch the video available at this URL:http://spoken-tutorial.org/What_is_a_Spoken_Tutorial  
+
|Watch the video available at this URL:http://spoken-tutorial.org/What_is_a_Spoken_Tutorial  
  
 
|-
 
|-
−
| 08:16
+
|08:16
−
| It summarizes the '''Spoken Tutorial''' project.
+
|It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 08:19
+
|08:19
−
| If you do not have good bandwidth, you can download and watch it.  
+
|If you do not have good bandwidth, you can download and watch it.  
  
 
|-
 
|-
−
| 08:23
+
|08:23
 
|The Spoken Tutorial Project team:  
 
|The Spoken Tutorial Project team:  
  
 
|-
 
|-
−
| 08:26
+
|08:26
 
|Conducts workshops using spoken tutorials.
 
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 08:29
+
|08:29
 
|Gives certificates to those who pass an on-line test.  
 
|Gives certificates to those who pass an on-line test.  
  
 
|-
 
|-
−
| 08:33
+
|08:33
−
| For more details, please write to:'''contact@spoken-tutorial.org'''  
+
|For more details, please write to:'''contact@spoken-tutorial.org'''  
  
 
|-
 
|-
−
| 08:40
+
|08:40
−
| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.  
+
|'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.  
  
 
|-
 
|-
−
| 08:45
+
|08:45
−
| It is supported by the National Mission on Education through ICT, MHRD, Government of India.
+
|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
−
| 08:52
+
|08:52
−
| More information on this mission is available at this link:http://spoken-tutorial.org/NMEICT-Intro   
+
|More information on this mission is available at this link:http://spoken-tutorial.org/NMEICT-Intro   
  
 
|-
 
|-
−
| 08:57
+
|08:57
−
| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
+
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
 
|}
 
|}

Latest revision as of 17:48, 28 March 2017

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: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

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