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

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| Welcome to this tutorial on '''Structures from Databases in Jmol'''
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| Welcome to this tutorial on '''Structures from Database''' in '''Jmol'''
  
 
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| 00:07
 
| 00:07
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| In this tutorial, we will learn to
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| In this tutorial, we will learn to:
  
 
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| * Load chemical structures from '''PubChem''' database and
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| * '''Load''' chemical structures from '''PubChem''' database and
  
 
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| To follow this tutorial you should be familiar with '''Jmol Application'''.
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| To follow this tutorial, you should be familiar with '''Jmol Application'''.
  
 
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| To record this tutorial I am using  
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| To record this tutorial, I am using:
  
 
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|00:44  
 
|00:44  
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| * '''Java''' version 7
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| * '''Java''' version 7.
  
 
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| '''Jmol''' has a feature to load structures of compounds listed in the database.
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| '''Jmol''' has a feature to '''load structure'''s of compounds listed in the '''database'''.
  
 
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| 01:07
 
| 01:07
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| The ''''File'''' menu on the menu bar, has an option ''''Get MOL'.'''
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| The ''''File'''' menu on the menu bar has an option ''''Get MOL'.'''
  
 
|-
 
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| 01:12
 
| 01:12
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| This loads molecules from chemical structure data base ''''PubChem'.'''
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| This loads molecules from chemical structure database ''''PubChem'.'''
  
 
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| 01:17
 
| 01:17
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| It also has another option ''''Get PDB'''' to load protein structures from '''Protein Data Bank'''.  
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| It also has another option ''''Get PDB'''' to load '''protein''' structures from '''Protein Data Bank'''.  
  
 
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| An ''''Input'''' dialog box opens on the screen.
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| An ''''Input'''' dialog box opens on the '''screen'''.
  
 
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| Common name or '''IUPAC''' name  
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| Common name or '''IUPAC''' name,
  
 
|-
 
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| 01:51
 
| 01:51
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|  '''CAS '''number  
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|  '''CAS '''number,
  
 
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| 01:54
 
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|  '''CID''' number  
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|  '''CID''' number,
  
 
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|'''SMILES identifier'''
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|'''SMILES identifier'''.
  
 
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| 02:01
 
| 02:01
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| Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical
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| Please visit '''Pubchem''' database website for information on identification numbers for a particular chemical.
  
 
|-
 
|-
 
| 02:09
 
| 02:09
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| let us display '''phenol''' on screen.
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| Let us display '''phenol''' on screen.
  
 
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| 02:13
 
| 02:13
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| So type ''''phenol'''' in the '''Input '''text box.
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| So, type: ''''phenol'''' in the '''Input '''text box.
  
 
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|02:30  
 
|02:30  
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| These options are listed in the '''Menu bar '''and '''Pop'''-'''up menu'''.  
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| These options are listed in the '''Menu bar '''and '''Pop-up''' menu.  
  
 
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| 02:41
 
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| First let us label the atoms in the model.
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| First, let us label the atoms in the '''model'''.
  
 
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| 02:45
 
| 02:45
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| Click on the '''display''' menu, and select''' label'''. Click on '''number '''option.  
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| Click on the '''Display''' menu and select''' Label'''. Click on '''Number '''option.  
  
 
|-
 
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| 02:52
 
| 02:52
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| Now, let's replace a '''hydrogen number 10 '''attached to the '''carbon atom number 4 '''with an amino group'''.'''
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| 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
 
|03:00
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| Open the '''modelkit menu''',  select '''nitrogen''' from the options.  
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| Open the '''modelkit''' menu,  select '''nitrogen''' from the options.  
  
 
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| On the panel we have a model of '''Para-Amino-phenol''' in sticks display.
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| On the panel, we have a model of '''Para-Amino-phenol''' in '''sticks''' display.
  
 
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| 03:36
 
| 03:36
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| Complex structures, which are difficult to create, can easily be loaded on the '''panel'''.
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| Complex structures which are difficult to create, can easily be loaded on the '''panel'''.
  
 
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| Click on '''File''' menu
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| Click on '''File''' menu.
  
 
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| 03:47
 
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| Click on '''Get Mol''' option,  in the text box type '''Cholesterol '''.
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| Click on '''Get Mol''' option,  in the text box type: '''Cholesterol '''.
  
 
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| We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule'''.'''
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| We can highlight the features like '''double-bond''' and '''side-chain '''in the molecule.
  
 
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| As an assignment,
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| As an assignment-
  
 
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| 05:24
 
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| We can convert 2D structures of molecules drawn in another software into 3D models.
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| We can convert '''2D structure'''s of molecules drawn in another software into '''3D model'''s.
  
 
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| 05:31
 
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| Here I have a model of '''aminoacid Alanine''' on the panel.
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| Here, I have a model of '''aminoacid Alanine''' on the panel.
  
 
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| The structure was saved as a '''.mol '''file.  
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| The structure was saved as a ''''.mol' '''file.  
  
 
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| To draw structures and save in .mol format, refer to Analysis of Compounds tutorial.
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| To draw structures and save in '.mol' format, refer to '''Analysis of Compounds''' tutorial.
  
 
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| Shown on this Gchempaint display area are 2D drawings of  
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| Shown on this Gchempaint display area are 2D drawings of-
  
 
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| * '''Saccharide -Alpha-D glucopyranose'''
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| * '''Saccharide -Alpha-D glucopyranose'''.
  
 
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| I have saved them in '''.mol '''format on my '''Desktop.'''
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| I have saved them in ''''.mol'''' format on my '''Desktop.'''
  
 
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| Click on ''''Open a file'''' icon in the tool bar.
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| Click on '''Open a file''' icon in the tool bar.
  
 
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| Open the '''modelkit menu '''and click on ''''fix hydrogens and minimize'''' option.
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| Open the '''modelkit''' menu and click on ''''fix hydrogens and minimize'''' option.
  
 
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| Let's summarize  
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| Let's summarize.
  
 
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| 07:27
 
| 07:27
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| In this tutorial we have learnt to
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| In this tutorial, we have learnt to:
  
 
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| # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''
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| # Draw 2D structures of the following '''Amino acids''' in '''GChemPaint'''-
  
 
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| # Save as '''.mol '''files.
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| # Save as ''''.mol' '''files.
  
 
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| Watch the video available at this URL.
 
| Watch the video available at this URL.
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[http://spoken-tutorial.org/What ttp://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial
+
http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial
  
 
|-
 
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| 08:16
 
| 08:16
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| 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
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| 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 http://spoken-tutorial.org/NMEICT-][http://spoken-tutorial.org/NMEICT-Intro Intro] ]
+
| More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro  
  
 
|-
 
|-
 
| 08:57
 
| 08:57
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| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
 
|}
 
|}

Revision as of 14:37, 14 September 2015

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

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