Difference between revisions of "Jmol-Application/C2/Modify-Display-and-View/English-timed"

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{| border=1
 
{| border=1
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! <center>Time</center>
+
|'''Time'''
−
! <center>Narration</center>
+
|'''Narration'''
  
 
|-
 
|-
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| 00:01
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|00:01
 
|Welcome to this tutorial on '''Modify Display and View '''in '''Jmol Application.'''  
 
|Welcome to this tutorial on '''Modify Display and View '''in '''Jmol Application.'''  
  
 
|-
 
|-
−
| 00:08
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|00:08
−
| In this tutorial, we will learn to:
+
|In this tutorial, we will learn to:
  
 
|-
 
|-
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| 00:11
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|00:11
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|* Rotate, zoom, move and spin the model on screen
+
|Rotate, zoom, move and spin the model on screen
  
 
|-
 
|-
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| 00:17
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|00:17
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|* Modify the view  
+
|Modify the '''view'''
  
 
|-
 
|-
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| 00:19
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|00:19
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|* Change the style of the display
+
|Change the style of the '''display'''
  
 
|-
 
|-
−
| 00:22
+
|00:22
−
|* Change the size and color of atoms and bonds
+
|Change the size and color of atoms and '''bond'''s
  
 
|-
 
|-
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| 00:26
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|00:26
−
|* To display the model with axes and bound box.
+
|To display the model with '''axes''' and '''bound box'''.
  
 
|-
 
|-
−
| 00:30
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|00:30
−
|* Save the image in various file formats.
+
|Save the image in various '''file format'''s.
  
 
|-
 
|-
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| 00:34
+
|00:34
−
| To follow this tutorial, you should be familiar with
+
|To follow this tutorial, you should be familiar with
  
 
|-
 
|-
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| 00:37
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|00:37
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| '''Jmol Application''' Window and
+
|'''Jmol Application''' window and
  
 
|-
 
|-
−
| 00:40
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|00:40
−
| know to create and edit models using '''modelkit function'''.
+
|know to '''create''' and '''edit model'''s using '''modelkit function'''.
  
 
|-
 
|-
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| 00:45
+
|00:45
 
|If not, watch the relevant tutorials available at the following link.  
 
|If not, watch the relevant tutorials available at the following link.  
  
 
|-
 
|-
−
| 00:51
+
|00:51
−
| To record this tutorial, I am using:
+
|To record this tutorial, I am using:
  
 
|-
 
|-
−
| 00:53
+
|00:53
−
|* '''Ubuntu '''OS version. 12.04
+
|'''Ubuntu '''OS version 12.04
  
 
|-
 
|-
−
| 00:58
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|00:58
−
|* '''Jmol''' version 12.2.2 and  
+
|'''Jmol''' version 12.2.2 and  
  
 
|-
 
|-
−
| 01:02
+
|01:02
−
|* Java version 7
+
|'''Java''' version 7
  
 
|-
 
|-
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| 01:05
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|01:05
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| I have opened a new '''Jmol '''window with a model of '''2-chloro-1-propanol '''on the '''panel'''.
+
|I have opened a new '''Jmol '''window with a model of '''2-chloro-1-propanol '''on the '''panel'''.
  
 
|-
 
|-
−
| 01:12
+
|01:12
−
| We can rotate and zoom the model to get a better perspective of the structure.
+
|We can rotate and zoom the model to get a better perspective of the structure.
  
 
|-
 
|-
−
| 01:18
+
|01:18
−
| To rotate the model, click on the “'''Rotate molecule'''” icon on the tool bar.
+
|To rotate the model, click on the “'''Rotate molecule'''” icon on the '''tool bar'''.
  
 
|-
 
|-
−
| 01:24
+
|01:24
−
| Click on the model and observe that the cursor changes to a hand icon.
+
|Click on the model and observe that the cursor changes to a hand icon.
  
 
|-
 
|-
−
| 01:29
+
|01:29
−
| Holding down the '''mouse button''', drag the '''mouse''' on the '''panel'''
+
|Holding down the '''mouse button''', drag the '''mouse''' on the '''panel'''
  
 
|-
 
|-
−
| 01:34
+
|01:34
−
|You can see the '''model''' is rotating.
+
|You can see that the '''model''' is rotating.
  
 
|-
 
|-
−
| 01:37
+
|01:37
−
| To zoom-in and zoom-out, place the cursor on the '''panel'''.
+
|To zoom-in and zoom-out, place the cursor on the '''panel'''.
  
 
|-
 
|-
−
| 01:42
+
|01:42
−
|Move the '''mouse wheel''' upwards to zoom-out and downwards to zoom-in.
+
|Move the '''mouse wheel''' upwards to '''zoom-out''' and downwards to '''zoom-in'''.
  
 
|-
 
|-
−
| 01:49
+
|01:49
−
| To move the model on the '''panel''', place the cursor on the model.
+
|To move the model on the '''panel''', place the cursor on the model.
  
 
|-
 
|-
−
| 01:54
+
|01:54
 
|Hold the '''Shift''' button on the keyboard.
 
|Hold the '''Shift''' button on the keyboard.
  
 
|-
 
|-
−
| 01:57
+
|01:57
 
|Double-click and drag the '''mouse'''.
 
|Double-click and drag the '''mouse'''.
  
 
|-
 
|-
−
| 02:00
+
|02:00
−
| For a detailed description, refer to the '''Mouse Manual''' provided in the Pop-up-menu.
+
|For a detailed description, refer to the '''Mouse Manual''' provided in the '''Pop-up-menu'''.
  
 
|-
 
|-
−
| 02:06
+
|02:06
−
|Open the Pop-up-menu and scroll down to '''About''' then select '''Jmol 12.2.2'''  and click on '''Mouse Manual'''.
+
|Open the Pop-up-menu and scroll down to '''About'''. Then select '''Jmol 12.2.2'''  and click on '''Mouse Manual'''.
  
 
|-
 
|-
−
| 02:17
+
|02:17
−
| If you are connected to the Internet,
+
|If you are connected to the Internet,
  
 
|-
 
|-
−
| 02:19
+
|02:19
 
|a web page with “'''Mouse manual'''” appears on the screen.
 
|a web page with “'''Mouse manual'''” appears on the screen.
  
 
|-
 
|-
−
| 02:24
+
|02:24
−
|Click on the '''panel''' to exit the Pop-up menu.
+
|Click on the panel to exit the Pop-up menu.
  
 
|-
 
|-
−
| 02:28
+
|02:28
−
| To automatically spin the molecule on the '''panel''', open the Pop-up menu.
+
|To automatically '''spin''' the molecule on the panel, open the Pop-up menu.
  
 
|-
 
|-
−
| 02:34
+
|02:34
 
|Scroll down to  '''Spin''' and then click on  option '''On'''.
 
|Scroll down to  '''Spin''' and then click on  option '''On'''.
  
 
|-
 
|-
−
| 02:40
+
|02:40
−
| We can see that the model is spinning on the '''panel'''.
+
|We can see that the model is spinning on the '''panel'''.
  
 
|-
 
|-
−
| 02:44
+
|02:44
−
| To turn off the spin, Open the Pop-up-menu again.  
+
|To turn off the spin, open the Pop-up-menu again.  
  
 
|-
 
|-
−
| 02:49
+
|02:49
 
|Scroll down to '''Spin''' and click on '''Off'''.  
 
|Scroll down to '''Spin''' and click on '''Off'''.  
  
 
|-
 
|-
−
| 02:54
+
|02:54
−
| As an assignment-  
+
|As an assignment-  
  
 
|-
 
|-
−
| 02:56
+
|02:56
−
| Create a model of '''2-chloro-3-Iodo-pentane'''.
+
|Create a model of '''2-chloro-3-Iodo-pentane'''.
  
 
|-
 
|-
−
| 03:00
+
|03:00
−
| Explore the '''Spin''' option in the Pop-up menu.
+
|Explore the '''Spin''' option in the Pop-up menu.
  
 
|-
 
|-
−
| 03:04
+
|03:04
−
| Change the direction of spin to '''Z'''-axis and rate of spin to '''40'''.
+
|Change the direction of spin to '''Z-axis''' and rate of spin to '''40'''.
  
 
|-
 
|-
−
| 03:10
+
|03:10
−
| As a hint: Use '''Set Z Rate '''option in the pop-up menu
+
|As a hint: Use '''Set Z Rate '''option in the pop-up menu.
  
 
|-
 
|-
−
| 03:16
+
|03:16
 
|Your completed assignment should look as follows.  
 
|Your completed assignment should look as follows.  
  
 
|-
 
|-
−
| 03:22
+
|03:22
−
| Let us now learn about the '''View''' menu.
+
|Let us now learn about the '''View''' menu.
  
 
|-
 
|-
−
| 03:25
+
|03:25
−
| '''View''' menu on the menu bar, has options to view the model from various angles.
+
|'''View''' menu on the menu bar has options to view the model from various angles.
  
 
|-
 
|-
−
| 03:31
+
|03:31
−
| Click on the '''View''' menu.
+
|Click on the '''View''' menu.
  
 
|-
 
|-
−
| 03:33
+
|03:33
−
| Scroll down the menu and choose from the various options provided.
+
|Scroll down the menu and choose from the various options provided.
  
 
|-
 
|-
−
| 03:38
+
|03:38
−
| For example, I will choose '''Top''' view.  
+
|For example, I will choose '''Top''' view.  
  
 
|-
 
|-
−
| 03:42
+
|03:42
 
|Click on the '''Top''' option.
 
|Click on the '''Top''' option.
  
 
|-
 
|-
−
| 03:45
+
|03:45
−
| The '''image''' on the '''screen''' shows how the molecule looks from the top.
+
|The '''image''' on the '''screen''' shows how the molecule looks from the top.
  
 
|-
 
|-
−
| 03:50
+
|03:50
−
| We can '''save''' this '''view''' as an image in various file formats.
+
|We can '''save''' this '''view''' as an image in various file formats.
  
 
|-
 
|-
−
| 03:55
+
|03:55
−
| Click on the '''Save current view as an image''' icon.
+
|Click on the '''Save current view as an image''' icon.
  
 
|-
 
|-
−
| 03:59
+
|03:59
−
| A '''Save''' dialog box appears.
+
|A '''Save''' dialog box appears.
  
 
|-
 
|-
−
| 04:03
+
|04:03
−
| To select the file format, scroll down the options on the '''Image Type'''.
+
|To select the file format, scroll down the options on the '''Image Type'''.
  
 
|-
 
|-
−
| 04:09
+
|04:09
−
| I will select  '''JPEG''' format.
+
|I will select  '''JPEG''' format.
  
 
|-
 
|-
−
| 04:13
+
|04:13
 
|Open the folder in which you want the file to be saved.
 
|Open the folder in which you want the file to be saved.
  
 
|-
 
|-
−
| 04:17
+
|04:17
−
| I want it on '''Desktop.'''  
+
|I want it on '''Desktop.'''  
  
 
|-
 
|-
−
| 04:19
+
|04:19
 
|Select '''Desktop''' and click on '''Open''' button.
 
|Select '''Desktop''' and click on '''Open''' button.
  
 
|-
 
|-
−
| 04:24
+
|04:24
−
| In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''.
+
|In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''.
  
 
|-
 
|-
−
| 04:30
+
|04:30
−
| Go to “'''Files of Type'''” and select '''jpg'''.
+
|Go to “'''Files of Type'''” and select '''jpg'''.
  
 
|-
 
|-
−
| 04:35
+
|04:35
−
| Click on '''Save '''button.
+
|Click on '''Save '''button.
  
 
|-
 
|-
−
| 04:38
+
|04:38
−
| The image will now be saved in '''JPEG '''format on the '''Desktop'''.
+
|The image will now be saved in '''JPEG '''format on the '''Desktop'''.
  
 
|-
 
|-
−
| 04:44
+
|04:44
−
| The style of display of molecular model can be modified in various ways.
+
|The style of display of '''molecular model''' can be modified in various ways.
  
 
|-
 
|-
−
| 04:50
+
|04:50
 
|Size and color of atoms and '''bond'''s in this molecule can be changed, if required.
 
|Size and color of atoms and '''bond'''s in this molecule can be changed, if required.
  
 
|-
 
|-
−
| 04:57
+
|04:57
−
| We have an option to modify all the atoms in the molecule or a select set.  
+
|We have an option to modify all the atoms in the molecule or a select set.  
  
 
|-
 
|-
−
| 05:03
+
|05:03
−
| The default display of the model on the panel is of '''ball and stick.'''
+
|The default display of the model on the panel is of '''ball and stick.'''
  
 
|-
 
|-
−
| 05:09
+
|05:09
−
| To change the display into '''CPK Space fill''', open the Pop-up-menu.
+
|To change the display into '''CPK Space fill''', open the Pop-up-menu.
  
 
|-
 
|-
−
| 05:15
+
|05:15
−
| Go to '''Select''' and click on '''All''' to modify the whole molecule.
+
|Go to '''Select''' and click on '''All''' to modify the whole molecule.
  
 
|-
 
|-
−
| 05:22
+
|05:22
−
| Open the Pop-up-menu again.
+
|Open the Pop-up-menu again.
  
 
|-
 
|-
−
| 05:25
+
|05:25
 
|Scroll down to '''Style''',  select '''Scheme''' from the sub-menu.
 
|Scroll down to '''Style''',  select '''Scheme''' from the sub-menu.
  
 
|-
 
|-
−
| 05:30
+
|05:30
−
| And click on '''CPK Spacefill''' option.
+
|And click on '''CPK Spacefill''' option.
  
 
|-
 
|-
−
| 05:35
+
|05:35
−
| The model on the screen is converted to '''CPK Spacefill''' model.
+
|The model on the screen is converted to '''CPK Spacefill''' model.
  
 
|-
 
|-
−
| 05:40
+
|05:40
 
|Let us now convert it back to '''ball and stick''' model.
 
|Let us now convert it back to '''ball and stick''' model.
  
 
|-
 
|-
−
| 05:44
+
|05:44
−
| Let's follow the same steps as before.
+
|Let's follow the same steps as before.
  
 
|-
 
|-
 
|05:48
 
|05:48
−
| Open the Pop-up-menu.  
+
|Open the Pop-up-menu.  
  
 
|-
 
|-
−
| 05:50
+
|05:50
 
|Scroll down to '''Style''', select '''Scheme''' and click on '''Ball and Stick''' option.
 
|Scroll down to '''Style''', select '''Scheme''' and click on '''Ball and Stick''' option.
  
 
|-
 
|-
−
| 05:56
+
|05:56
−
| The model is now converted to''' ball and stick '''style display.
+
|The model is now converted to''' ball and stick '''style display.
  
 
|-
 
|-
−
| 06:01
+
|06:01
−
| The size of the bonds can be changed using Pop-up menu, as well as '''Display''' menu on the menu bar.  
+
|The size of the bonds can be changed using Pop-up menu, as well as '''Display''' menu on the menu bar.  
  
 
|-
 
|-
−
| 06:08
+
|06:08
 
|Click on the '''Display''' menu and select '''Bond'''.
 
|Click on the '''Display''' menu and select '''Bond'''.
  
 
|-
 
|-
−
| 06:12
+
|06:12
 
|The sub-menu has options of bonds in different size diameter, in '''angstrom units. '''
 
|The sub-menu has options of bonds in different size diameter, in '''angstrom units. '''
  
 
|-
 
|-
−
| 06:19
+
|06:19
−
| For example, I will select '''0.1 Angstrom''' and click on it.
+
|For example, I will select '''0.1 Angstrom''' and click on it.
  
 
|-
 
|-
−
| 06:26
+
|06:26
−
| Note the change in the thickness of the bonds.  
+
|Note the change in the thickness of the bonds.  
  
 
|-
 
|-
−
| 06:30
+
|06:30
−
| We can also change the colour of atoms and bonds.
+
|We can also change the colour of atoms and bonds.
  
 
|-
 
|-
−
| 06:34
+
|06:34
−
| I want to change the colour of all the '''Carbon''' atoms in the model to yellow.
+
|I want to change the colour of all the '''Carbon''' atoms in the model to yellow.
  
 
|-
 
|-
−
| 06:39
+
|06:39
−
| To do this, open the Pop-up menu and go to '''Select'''.  
+
|To do this, open the Pop-up menu and go to '''Select'''.  
  
 
|-
 
|-
−
| 06:44
+
|06:44
−
| Scroll down to '''Element''' and click on '''Carbon'''.
+
|Scroll down to '''Element''' and click on '''Carbon'''.
  
 
|-
 
|-
−
| 06:48
+
|06:48
−
| Open the Pop-up menu again and select '''Color'''.
+
|Open the Pop-up menu again and select '''Color'''.
  
 
|-
 
|-
−
| 06:52
+
|06:52
−
|Then select '''Atoms''' and click on '''Yellow'''  options.  
+
|Then select '''Atoms''' and click on '''Yellow'''  option.  
  
 
|-
 
|-
 
|06:57
 
|06:57
−
|| All the '''Carbons''' in the model, now appear yellow in colour.  
+
|All the '''Carbons''' in the model, now appear yellow in colour.  
  
 
|-
 
|-
−
| 07:02
+
|07:02
−
| Let's see how to change the color of bonds.
+
|Let's see how to change the color of bonds.
  
 
|-
 
|-
−
| 07:06
+
|07:06
−
| Open the Pop-up-menu and select '''All'''
+
|Open the Pop-up-menu and select '''All'''.
  
 
|-
 
|-
−
| 07:10
+
|07:10
−
| Open the Pop-up-menu again.
+
|Open the Pop-up-menu again.
  
 
|-
 
|-
−
| 07:12
+
|07:12
 
|Scroll down to '''Color''', select '''Bonds''' from the sub-menu.
 
|Scroll down to '''Color''', select '''Bonds''' from the sub-menu.
  
 
|-
 
|-
−
| 07:16
+
|07:16
−
| Scroll down and click on '''Blue''' option.
+
|Scroll down and click on '''Blue''' option.
  
 
|-
 
|-
−
| 07:20
+
|07:20
−
| All the bonds are now blue in color.
+
|All the bonds are now blue in color.
  
 
|-
 
|-
−
| 07:23
+
|07:23
−
| We can display the image with '''X,Y '''and''' Z''' axes and within a bounding box.
+
|We can display this model on the screen with X, Y and Z axes and within a bounding box.
  
 
|-
 
|-
−
| 07:31
+
|07:31
−
| Open the Pop-up menu, select '''Style'''.
+
|Open the Pop-up menu, select '''Style'''
  
 
|-
 
|-
−
| 07:34
+
|07:34
−
|And Scroll down to '''Axes''' option.
+
|and Scroll down to '''Axes''' option.
  
 
|-
 
|-
−
| 07:37
+
|07:37
−
| From the sub-menu select '''Pixel Width '''.
+
|From the sub-menu select '''Pixel Width '''.
  
 
|-
 
|-
−
| 07:40
+
|07:40
−
| I will choose '''3 px.''' as pixel width.
+
|I will choose '''3 px.''' as pixel width.
  
 
|-
 
|-
−
| 07:44
+
|07:44
−
| We now have the model on screen with all the axes.  
+
|We now have the model on the screen with all the axes.  
  
 
|-
 
|-
−
| 07:49
+
|07:49
−
| To draw a bound box around the image, open the Pop-up-menu.
+
|To draw a '''bound box''' around the image, open the Pop-up-menu.
  
 
|-
 
|-
−
| 07:54
+
|07:54
 
|Scroll down to '''Style''' and select '''Boundbox''' from the options.  
 
|Scroll down to '''Style''' and select '''Boundbox''' from the options.  
  
 
|-
 
|-
−
| 07:59
+
|07:59
 
|Select '''Pixel width''' and click on the pixel width '''3 px'''.  
 
|Select '''Pixel width''' and click on the pixel width '''3 px'''.  
  
 
|-
 
|-
−
| 08:05
+
|08:05
−
| On the screen, we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.'''
+
|On the screen, we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.'''
  
 
|-
 
|-
−
| 08:12
+
|08:12
 
|To view the '''Boundbox''' clearly, we may have to zoom-in or zoom out.
 
|To view the '''Boundbox''' clearly, we may have to zoom-in or zoom out.
  
 
|-
 
|-
−
| 08:17
+
|08:17
−
| '''Save''' the '''image''' and exit the program.
+
|'''Save''' the '''image''' and exit the program.
  
 
|-
 
|-
−
| 08:21
+
|08:21
−
| Let's summarize what we have learnt.
+
|Let's summarize what we have learnt.
  
 
|-
 
|-
−
| 08:23
+
|08:23
 
|In this tutorial, we have learnt to:  
 
|In this tutorial, we have learnt to:  
  
 
|-
 
|-
−
| 08:26
+
|08:26
−
|* Rotate, zoom, move and spin the model on screen.
+
|Rotate, zoom, move and spin the model on screen.
  
 
|-
 
|-
−
| 08:31
+
|08:31
−
|* View the model from various angles.
+
|View the model from various angles.
  
 
|-
 
|-
−
| 08:34
+
|08:34
−
|* Change the style of the display.  
+
|Change the style of the display.  
  
 
|-
 
|-
−
| 08:36
+
|08:36
−
|* Change the color of atoms and bonds.
+
|Change the color of atoms and bonds.
  
 
|-
 
|-
 
|08:39
 
|08:39
−
| We have also learnt to:
+
|We have also learnt to:
  
 
|-
 
|-
−
| 08:41
+
|08:41
−
|* Display the image with axes and boundbox and
+
|Display the image with axes and boundbox and
  
 
|-
 
|-
−
| 08:44
+
|08:44
−
|* Save the image in different file formats.
+
|Save the image in different file formats.
  
 
|-
 
|-
−
| 08:48
+
|08:48
−
| For the Assignment-
+
|For the Assignment-
  
 
|-
 
|-
−
| 08:50
+
|08:50
 
|Create a model of '''3-amino-1-propanol.'''
 
|Create a model of '''3-amino-1-propanol.'''
  
 
|-
 
|-
−
| 08:53
+
|08:53
−
| Change the display to '''Sticks'''.
+
|Change the display to '''Sticks'''.
  
 
|-
 
|-
−
| 08:56
+
|08:56
−
| Change the color of all the hydrogens in the model to Green.
+
|Change the color of hydrogens in the model to Green.
  
 
|-
 
|-
−
| 09:00
+
|09:00
−
| Change the color of all the bonds to yellow.
+
|Change the color of all the bonds to yellow.
  
 
|-
 
|-
−
| 09:04
+
|09:04
 
|Your completed assignment should look as follows.
 
|Your completed assignment should look as follows.
  
 
|-
 
|-
−
| 09:12
+
|09:12
−
| Watch the video available at the following link.
+
|Watch the video available at the following link.
  
 
|-
 
|-
−
| 09:15
+
|09:15
 
|It summarizes the Spoken Tutorial project.
 
|It summarizes the Spoken Tutorial project.
  
 
|-
 
|-
−
| 09:19
+
|09:19
 
|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.  
  
 
|-
 
|-
−
| 09:24
+
|09:24
−
| The Spoken Tutorial Project team:  
+
|The Spoken Tutorial Project team:  
  
 
|-
 
|-
−
| 09:26
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|09:26
−
|* Conducts workshops using spoken tutorials.
+
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 09:29
+
|09:29
−
|* Gives certificates to those who pass an on-line test.  
+
|Gives certificates to those who pass an on-line test.  
  
 
|-
 
|-
−
| 09:34
+
|09:34
−
|For more details, please write to: contact@spoken-tutorial.org  
+
|For more details, please write to: '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
−
| 09:41
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|09:41
 
|'''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.  
  
 
|-
 
|-
−
| 09:44
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|09:44
 
|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.
  
 
|-
 
|-
−
| 09:51
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|09:51
 
|More information on this mission is available at the following link.
 
|More information on this mission is available at the following link.
  
 
|-
 
|-
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| 09:57
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|09:57
−
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
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|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
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+
 
|}
 
|}

Latest revision as of 16:31, 28 March 2017

Time Narration
00:01 Welcome to this tutorial on Modify Display and View in Jmol Application.
00:08 In this tutorial, we will learn to:
00:11 Rotate, zoom, move and spin the model on screen
00:17 Modify the view
00:19 Change the style of the display
00:22 Change the size and color of atoms and bonds
00:26 To display the model with axes and bound box.
00:30 Save the image in various file formats.
00:34 To follow this tutorial, you should be familiar with
00:37 Jmol Application window and
00:40 know to create and edit models using modelkit function.
00:45 If not, watch the relevant tutorials available at the following link.
00:51 To record this tutorial, I am using:
00:53 Ubuntu OS version 12.04
00:58 Jmol version 12.2.2 and
01:02 Java version 7
01:05 I have opened a new Jmol window with a model of 2-chloro-1-propanol on the panel.
01:12 We can rotate and zoom the model to get a better perspective of the structure.
01:18 To rotate the model, click on the “Rotate molecule” icon on the tool bar.
01:24 Click on the model and observe that the cursor changes to a hand icon.
01:29 Holding down the mouse button, drag the mouse on the panel
01:34 You can see that the model is rotating.
01:37 To zoom-in and zoom-out, place the cursor on the panel.
01:42 Move the mouse wheel upwards to zoom-out and downwards to zoom-in.
01:49 To move the model on the panel, place the cursor on the model.
01:54 Hold the Shift button on the keyboard.
01:57 Double-click and drag the mouse.
02:00 For a detailed description, refer to the Mouse Manual provided in the Pop-up-menu.
02:06 Open the Pop-up-menu and scroll down to About. Then select Jmol 12.2.2 and click on Mouse Manual.
02:17 If you are connected to the Internet,
02:19 a web page with “Mouse manual” appears on the screen.
02:24 Click on the panel to exit the Pop-up menu.
02:28 To automatically spin the molecule on the panel, open the Pop-up menu.
02:34 Scroll down to Spin and then click on option On.
02:40 We can see that the model is spinning on the panel.
02:44 To turn off the spin, open the Pop-up-menu again.
02:49 Scroll down to Spin and click on Off.
02:54 As an assignment-
02:56 Create a model of 2-chloro-3-Iodo-pentane.
03:00 Explore the Spin option in the Pop-up menu.
03:04 Change the direction of spin to Z-axis and rate of spin to 40.
03:10 As a hint: Use Set Z Rate option in the pop-up menu.
03:16 Your completed assignment should look as follows.
03:22 Let us now learn about the View menu.
03:25 View menu on the menu bar has options to view the model from various angles.
03:31 Click on the View menu.
03:33 Scroll down the menu and choose from the various options provided.
03:38 For example, I will choose Top view.
03:42 Click on the Top option.
03:45 The image on the screen shows how the molecule looks from the top.
03:50 We can save this view as an image in various file formats.
03:55 Click on the Save current view as an image icon.
03:59 A Save dialog box appears.
04:03 To select the file format, scroll down the options on the Image Type.
04:09 I will select JPEG format.
04:13 Open the folder in which you want the file to be saved.
04:17 I want it on Desktop.
04:19 Select Desktop and click on Open button.
04:24 In the File Name text-box, type “2-chloro-1-propanol” .
04:30 Go to “Files of Type” and select jpg.
04:35 Click on Save button.
04:38 The image will now be saved in JPEG format on the Desktop.
04:44 The style of display of molecular model can be modified in various ways.
04:50 Size and color of atoms and bonds in this molecule can be changed, if required.
04:57 We have an option to modify all the atoms in the molecule or a select set.
05:03 The default display of the model on the panel is of ball and stick.
05:09 To change the display into CPK Space fill, open the Pop-up-menu.
05:15 Go to Select and click on All to modify the whole molecule.
05:22 Open the Pop-up-menu again.
05:25 Scroll down to Style, select Scheme from the sub-menu.
05:30 And click on CPK Spacefill option.
05:35 The model on the screen is converted to CPK Spacefill model.
05:40 Let us now convert it back to ball and stick model.
05:44 Let's follow the same steps as before.
05:48 Open the Pop-up-menu.
05:50 Scroll down to Style, select Scheme and click on Ball and Stick option.
05:56 The model is now converted to ball and stick style display.
06:01 The size of the bonds can be changed using Pop-up menu, as well as Display menu on the menu bar.
06:08 Click on the Display menu and select Bond.
06:12 The sub-menu has options of bonds in different size diameter, in angstrom units.
06:19 For example, I will select 0.1 Angstrom and click on it.
06:26 Note the change in the thickness of the bonds.
06:30 We can also change the colour of atoms and bonds.
06:34 I want to change the colour of all the Carbon atoms in the model to yellow.
06:39 To do this, open the Pop-up menu and go to Select.
06:44 Scroll down to Element and click on Carbon.
06:48 Open the Pop-up menu again and select Color.
06:52 Then select Atoms and click on Yellow option.
06:57 All the Carbons in the model, now appear yellow in colour.
07:02 Let's see how to change the color of bonds.
07:06 Open the Pop-up-menu and select All.
07:10 Open the Pop-up-menu again.
07:12 Scroll down to Color, select Bonds from the sub-menu.
07:16 Scroll down and click on Blue option.
07:20 All the bonds are now blue in color.
07:23 We can display this model on the screen with X, Y and Z axes and within a bounding box.
07:31 Open the Pop-up menu, select Style
07:34 and Scroll down to Axes option.
07:37 From the sub-menu select Pixel Width .
07:40 I will choose 3 px. as pixel width.
07:44 We now have the model on the screen with all the axes.
07:49 To draw a bound box around the image, open the Pop-up-menu.
07:54 Scroll down to Style and select Boundbox from the options.
07:59 Select Pixel width and click on the pixel width 3 px.
08:05 On the screen, we have the model of 2-chloro-1-propanol in Boundbox with Axes.
08:12 To view the Boundbox clearly, we may have to zoom-in or zoom out.
08:17 Save the image and exit the program.
08:21 Let's summarize what we have learnt.
08:23 In this tutorial, we have learnt to:
08:26 Rotate, zoom, move and spin the model on screen.
08:31 View the model from various angles.
08:34 Change the style of the display.
08:36 Change the color of atoms and bonds.
08:39 We have also learnt to:
08:41 Display the image with axes and boundbox and
08:44 Save the image in different file formats.
08:48 For the Assignment-
08:50 Create a model of 3-amino-1-propanol.
08:53 Change the display to Sticks.
08:56 Change the color of hydrogens in the model to Green.
09:00 Change the color of all the bonds to yellow.
09:04 Your completed assignment should look as follows.
09:12 Watch the video available at the following link.
09:15 It summarizes the Spoken Tutorial project.
09:19 If you do not have good bandwidth, you can download and watch it.
09:24 The Spoken Tutorial Project team:
09:26 Conducts workshops using spoken tutorials.
09:29 Gives certificates to those who pass an on-line test.
09:34 For more details, please write to: contact@spoken-tutorial.org
09:41 Spoken Tutorial project is a part of the Talk to a Teacher project.
09:44 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
09:51 More information on this mission is available at the following link.
09:57 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Ranjana, Sandhya.np14

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