Difference between revisions of "Jmol-Application/C2/Measurements-and-Labeling/English-timed"

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|-
 
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| 00:06
 
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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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|-
 
|-
 
| 00:14
 
| 00:14
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|* Label atoms in a model with symbol and number.
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|* Label atoms in a '''model''' with symbol and number.
  
 
|-
 
|-
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|-
 
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| 00:27
 
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|* how to create and edit molecular models  in '''Jmol Application.'''
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| how to create and '''edit''' molecular models  in '''Jmol Application.'''
  
 
|-
 
|-
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|-
 
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| 00:39
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|'''Ubuntu '''OS version. 12.04
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|* '''Ubuntu '''OS version. 12.04
  
 
|-
 
|-
 
| 00:44
 
| 00:44
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|'''Jmol''' version 12.2.2
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|* '''Jmol''' version 12.2.2
  
 
|-
 
|-
 
| 00:47
 
| 00:47
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|'''Java''' version 7
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|* '''Java''' version 7.
  
 
|-
 
|-
 
| 00:50
 
| 00:50
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| Let's go through the steps on how to build a '''carboxyl''' group using this animation.
+
| Let's go through the steps on how to build a '''carboxyl''' group using this '''animation'''.
  
 
|-
 
|-
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|-
 
|-
 
| 01:11
 
| 01:11
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|Substitute two '''hydrogens''' attached to the same '''carbon atom '''with '''hydroxy''' group.
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|Substitute two '''hydrogen'''s attached to the same '''carbon''' atom with '''hydroxy''' group.
  
 
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|-
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|-
 
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| 01:23
 
| 01:23
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|Convert '''Carbon-Oxygen''' bond to a double bond.
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|Convert '''Carbon-Oxygen''' bond to a double-bond.
  
 
|-
 
|-
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|-
 
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| 01:42
 
| 01:42
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| This is a model of '''Ethane''' on '''Jmol panel.'''
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| This is a model of '''Ethane''' on '''Jmol panel'''.
  
 
|-
 
|-
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|-
 
|-
 
| 01:50
 
| 01:50
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| Select '''oxygen''' from the '''Modelkit menu'''.
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| Select '''oxygen''' from the '''Modelkit''' menu.
  
 
|-
 
|-
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|-
 
|-
 
| 01:58
 
| 01:58
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| Now, check against '''delete atom''' option in the '''modelkit menu.'''
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| Now, check against '''Delete atom''' option in the '''modelkit''' menu.
  
 
|-
 
|-
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|-
 
|-
 
| 02:11
 
| 02:11
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| Then, let us introduce a double bond between '''carbon''' and '''oxygen.'''
+
| Then, let us introduce a double-bond between '''carbon''' and '''oxygen.'''
  
 
|-
 
|-
 
| 02:16
 
| 02:16
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|So, check '''double''' option in the '''modelkit menu. '''
+
|So, check '''double''' option in the '''modelkit''' menu.
  
 
|-
 
|-
 
| 02:20
 
| 02:20
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|And click on the bond connecting '''carbon '''and '''oxygen'''.  
+
|And click on the '''bond''' connecting '''carbon '''and '''oxygen'''.  
  
 
|-
 
|-
 
| 02:25
 
| 02:25
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| We have a model of '''Acetic acid '''on screen.
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| We have a model of '''Acetic acid '''on '''screen'''.
  
 
|-
 
|-
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|-
 
|-
 
| 02:37
 
| 02:37
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| Here is the Jmol panel with a model of '''ethane.'''
+
| Here is the '''Jmol''' panel with a model of '''ethane.'''
  
 
|-
 
|-
 
| 02:40
 
| 02:40
−
| Now let us convert this molecule to '''nitro-ethane.'''
+
| Now, let us convert this molecule to '''nitro-ethane.'''
  
 
|-
 
|-
 
| 02:45
 
| 02:45
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| Click on the '''modelkit menu '''and check against '''Nitrogen'''.
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| Click on the '''modelkit''' menu and check against '''Nitrogen'''.
  
 
|-
 
|-
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|-
 
|-
 
| 03:04
 
| 03:04
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|Click on the '''modelkit menu '''and check against '''oxygen.'''
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|Click on the '''modelkit''' menu and check against '''Oxygen (O).'''
  
 
|-
 
|-
 
| 03:10
 
| 03:10
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|Then click on the '''hydrogens attached to the nitrogen.'''
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|Then click on the '''hydrogen'''s attached to the '''nitrogen'''.
  
 
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|-
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|-  
 
|-  
 
|03:26
 
|03:26
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|Now we will introduce a double bond between '''nitrogen '''and '''oxygen '''atom.
+
|Now, we will introduce a double-bond between '''nitrogen '''and '''oxygen '''atoms.
  
 
|-
 
|-
 
| 03:32
 
| 03:32
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|Check the “'''double'''” option in the '''modelkit menu.'''  
+
|Check the “'''double'''” option in the '''modelkit''' menu.
  
 
|-
 
|-
 
| 03:36
 
| 03:36
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|Click on the bond connecting '''nitrogen''' and '''oxygen''' atom.  
+
|Click on the bond connecting '''nitrogen''' and '''oxygen''' atoms.  
  
 
|-
 
|-
 
| 03:40
 
| 03:40
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| This is a model of '''nitroethane''' on the panel'''.'''
+
| This is a model of '''nitroethane''' on the panel.
  
 
|-
 
|-
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|-
 
|-
 
| 04:08
 
| 04:08
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| Let us learn to label the '''atoms''' in the model.  
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| Let us learn to label the atoms in the model.  
  
 
|-
 
|-
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|-
 
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|04:17
 
|04:17
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| Open the display menu, and select '''Label''' from the scroll down menu.  
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| Open the '''Display''' menu and select '''Label''' from the scroll down menu.  
  
 
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|-
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|-
 
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| 04:29
 
| 04:29
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| “'''Name'''” option will give both symbol and number.
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| "'''Name'''” option will give both symbol and number.
  
 
|-
 
|-
 
|04:34
 
|04:34
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|“'''Number'''” option will give only numbering of atoms.
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|"'''Number'''" option will give only numbering of atoms.
  
 
|-
 
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| 04:37
 
| 04:37
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| One can erase the labels from the model, using the “'''None'''” option.
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| One can erase the labels from the model using the "'''None'''" option.
  
 
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|Right click on the '''panel''' to open the Pop-up menu and check the various options.
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|Right-click on the '''panel''' to open the Pop-up menu and check the various options.
  
 
|-
 
|-
 
| 04:55
 
| 04:55
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| Distance between any two atoms in a molecule, can be measured using “'''Tools'''” menu.
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| Distance between any two atoms in a molecule can be measured using '''Tools''' menu.
  
 
|-
 
|-
 
| 05:01
 
| 05:01
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| Before we measure, open the '''modelkit menu''' and click on “'''minimize'''”.
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| Before we measure, open the '''modelkit''' menu and click on '''minimize'''.
  
 
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|-
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| 05:14
 
| 05:14
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| Now, click on “'''Tools'''” menu, select “'''Distance Units'''”.
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| Now, click on '''Tools''' menu, select '''Distance Units'''.
  
 
|-
 
|-
 
| 05:20
 
| 05:20
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|Select options from the sub-menu, according to the requirement.
+
|Select options from the sub-menu according to the requirement.
  
 
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| 05:34
 
| 05:34
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| Click on rotate molecule icon. And bring the cursor to the '''panel'''.
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| Click on '''Rotate molecule''' icon and bring the cursor to the '''panel'''.
  
 
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| 05:46
 
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|First double-click on the starting atom, which is atom number 9.
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|First double-click on the starting atom which is atom number 9.
  
 
|-
 
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| 05:52
 
| 05:52
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|To fix the measurement, double-click on the ending atom, which is atom number 4.  
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|To fix the measurement, double-click on the ending atom which is atom number 4.  
  
 
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|06:19
 
|06:19
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| Similarly, let's measure the '''carbon '''and '''oxygen '''single bond distance.  
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| Similarly, let's measure the '''carbon '''and '''oxygen '''single-bond distance.  
  
 
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| For example we will measure the '''bond angle''' between atoms 9, 4 and 1.
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| For example- we will measure the '''bond angle''' between atoms 9, 4 and 1.
  
 
|-
 
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| 06:51
 
| 06:51
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|Double-click on atom number 9, and then click on atom 4.
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|Double-click on atom number 9 and then click on atom 4.
  
 
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|Click on the atom number 4, and then on atom number 1.
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|Click on the atom number 4 and then on atom number 1.
  
 
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| “'''Measurements'''” dialog box opens on the '''panel'''.
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| '''Measurements''' dialog box opens on the '''panel'''.
  
 
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| We can now save the image and exit the application.
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| We can now '''save''' the image and exit the application.
  
 
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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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| 08:48
 
| 08:48
 
| Watch the video available at this URL.
 
| Watch the video available at this URL.
−
[http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial
+
http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial
  
 
|-
 
|-
 
| 08:51
 
| 08:51
−
|It summarizes the Spoken Tutorial project
+
|It summarizes the Spoken Tutorial project.
  
 
|-
 
|-
 
| 08:54
 
| 08:54
−
|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.
  
 
|-
 
|-
 
| 08:59
 
| 08:59
−
| The Spoken Tutorial Project Team:  
+
| The Spoken Tutorial Project team:  
  
 
|-
 
|-
 
| 09:01
 
| 09:01
−
|Conducts workshops using spoken tutorials
+
|* Conducts workshops using spoken tutorials.
  
 
|-
 
|-
 
| 09:04
 
| 09:04
−
|Gives certificates to those who pass an on-line test  
+
|* Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
 
| 09:08
 
| 09:08
−
|For more details, please write to contact@spoken-tutorial.org  
+
|For more details, please write to: contact@spoken-tutorial.org  
  
 
|-
 
|-
 
| 09:15
 
| 09:15
−
| 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.
  
 
|-
 
|-
 
| 09:19
 
| 09:19
−
|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.
  
 
|-
 
|-
 
| 09:26
 
| 09:26
−
|More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ]
+
|More information on this mission is available at this link.
 +
http://spoken-tutorial.org/NMEICT-Intro  
  
 
|-
 
|-
 
| 09:31
 
| 09:31
−
| 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 08:28, 14 September 2015

Time Narration
00:01 Welcome to this tutorial on Measurements and Labeling in Jmol Application.
00:06 In this tutorial, we will learn to:
00:09 * Create models of carboxylic acid and nitroalkane.
00:14 * Label atoms in a model with symbol and number.
00:19 * Measure bond lengths, bond angles and dihedral angles.
00:24 To follow this tutorial, you should know
00:27 how to create and edit molecular models in Jmol Application.
00:32 If not, watch the relevant tutorials available on our website.
00:37 To record this tutorial, I am using:
00:39 * Ubuntu OS version. 12.04
00:44 * Jmol version 12.2.2
00:47 * Java version 7.
00:50 Let's go through the steps on how to build a carboxyl group using this animation.
00:56 As an example, we will create a model of Ethanoic acid, commonly known as Acetic acid.
01:03 We will begin with a model of Ethane.
01:06 We have to convert one of the methyl groups to a carboxyl group.
01:11 Substitute two hydrogens attached to the same carbon atom with hydroxy group.
01:18 Delete hydrogens attached to one of the oxygen and Carbon.
01:23 Convert Carbon-Oxygen bond to a double-bond.
01:26 Methyl group is converted to a Carboxyl group.
01:31 Observe that Ethane is converted to Ethanoic acid.
01:35 We will follow the above steps and create the model of Ethanoic acid in Jmol application.
01:42 This is a model of Ethane on Jmol panel.
01:46 Let us convert a methyl group to a carboxyl group.
01:50 Select oxygen from the Modelkit menu.
01:54 Click on the hydrogens attached to the same carbon atom.
01:58 Now, check against Delete atom option in the modelkit menu.
02:02 Delete the hydrogen attached to the oxygen.
02:07 And also, delete hydrogen attached to the carbon.
02:11 Then, let us introduce a double-bond between carbon and oxygen.
02:16 So, check double option in the modelkit menu.
02:20 And click on the bond connecting carbon and oxygen.
02:25 We have a model of Acetic acid on screen.
02:28 Do the energy minimization to optimize the structure.
02:32 We will follow a similar strategy to create a nitro group.
02:37 Here is the Jmol panel with a model of ethane.
02:40 Now, let us convert this molecule to nitro-ethane.
02:45 Click on the modelkit menu and check against Nitrogen.
02:50 Click on the hydrogen atom in the ethane molecule.
02:54 Nitrogen atom is represented as blue sphere.
02:58 Next, we will substitute two hydrogens attached to nitrogen with hydroxy group.
03:04 Click on the modelkit menu and check against Oxygen (O).
03:10 Then click on the hydrogens attached to the nitrogen.
03:14 Delete the hydrogens attached to the oxygen atoms.
03:18 Open modelkit menu and check against delete atom.
03:23 Click on the hydrogen attached to oxygen atoms.
03:26 Now, we will introduce a double-bond between nitrogen and oxygen atoms.
03:32 Check the “double” option in the modelkit menu.
03:36 Click on the bond connecting nitrogen and oxygen atoms.
03:40 This is a model of nitroethane on the panel.
03:44 As an assignment-
03:45 * Create models of 1-butanoic acid and ethylacetate.
03:50 * Optimize the structure by doing energy minimization and
03:53 * Save the image.
03:56 Your completed assignment should look as follows.
04:02 Let's go back to the Jmol panel.
04:04 This is the model of 1-butanoic acid on screen.
04:08 Let us learn to label the atoms in the model.
04:12 We do this with symbols corresponding to the element and number.
04:17 Open the Display menu and select Label from the scroll down menu.
04:22 Select “Symbol” option to label all the atoms with the symbol corresponding to the element.
04:29 "Name” option will give both symbol and number.
04:34 "Number" option will give only numbering of atoms.
04:37 One can erase the labels from the model using the "None" option.
04:43 We can also use the Pop-up menu to do all the above modifications.
04:48 Right-click on the panel to open the Pop-up menu and check the various options.
04:55 Distance between any two atoms in a molecule can be measured using Tools menu.
05:01 Before we measure, open the modelkit menu and click on minimize.
05:07 Energy minimization is now done and the model is in the most stable conformation.
05:14 Now, click on Tools menu, select Distance Units.
05:20 Select options from the sub-menu according to the requirement.
05:25 For example, I will choose Angstrom.
05:28 So, the bond lengths I measure, will be in Angstrom units.
05:34 Click on Rotate molecule icon and bring the cursor to the panel.
05:42 I will measure the distance between atoms 9 and 4.
05:46 First double-click on the starting atom which is atom number 9.
05:52 To fix the measurement, double-click on the ending atom which is atom number 4.
05:58 The bond length is now displayed on the screen.
06:02 Let's do some more measurements of bond lengths.
06:05 Let's measure the bond-length between carbon and oxygen double-bond.
06:10 So, double-click on atom 5 and bring the cursor to atom number 7 and double-click on it.
06:19 Similarly, let's measure the carbon and oxygen single-bond distance.
06:25 So, double-click on atom 5 and bring the cursor to atom 6 and double-click on it.
06:34 We can see on the panel all the bond lengths are displayed.
06:39 We can also measure bond-angles and dihedral angles in a model.
06:44 For example- we will measure the bond angle between atoms 9, 4 and 1.
06:51 Double-click on atom number 9 and then click on atom 4.
06:56 To fix the angle measurement, double-click on atom number 1.
07:01 We can see the bond-angle displayed on the screen.
07:05 Let's measure another bond-angle, say, between atoms 1, 5 and 6.
07:12 Double-click on atom 1, click on atom 5 and lastly double-click atom number 6.
07:23 Measurement of torsional or dihedral angle involves 4 atoms.
07:29 So, we will choose atoms 8, 4,1 and 2.
07:34 For measurement of dihedral angle, first double-click on atom number 8.
07:39 Click on the atom number 4 and then on atom number 1.
07:43 Lastly, to fix the dihedral angle measurement, double-click on atom number 2.
07:50 We can see the dihedral angle measurement displayed on the screen.
07:55 Values of all measurements made, can be viewed in a tabular form.
08:00 Click on “Click atom to measure distances” icon in the tool bar.
08:06 Measurements dialog box opens on the panel.
08:10 It has a list of all the measurements made so far.
08:14 We can now save the image and exit the application.
08:17 Let's summarize:
08:19 In this tutorial, we have learnt to-
08:22 * Create models of carboxylic acid and nitroalkane.
08:26 * Label atoms in a model with symbol of the element and number.
08:31 * Measure bond lengths, bond angles and dihedral angles.
08:36 For the assignment-
08:38 * Create models of molecules with single, double and triple bonds.
08:43 * Measure bond lengths between the carbon atoms.
08:45 * And compare them.
08:48 Watch the video available at this URL.

http://spoken-tutorial.org/What]_is_a_Spoken_Tutorial

08:51 It summarizes the Spoken Tutorial project.
08:54 If you do not have good bandwidth, you can download and watch it.
08:59 The Spoken Tutorial Project team:
09:01 * Conducts workshops using spoken tutorials.
09:04 * Gives certificates to those who pass an on-line test.
09:08 For more details, please write to: contact@spoken-tutorial.org
09:15 Spoken Tutorial project is a part of the Talk to a Teacher project.
09:19 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
09:26 More information on this mission is available at this link.

http://spoken-tutorial.org/NMEICT-Intro

09:31 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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