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

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| 00:01
 
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|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
 
| 00:08
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| In this tutorial, we will learn to
+
| In this tutorial, we will learn to:
  
 
|-
 
|-
 
| 00:11
 
| 00:11
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|Rotate, zoom, move and spin the model on screen
+
|* Rotate, zoom, move and spin the model on screen
  
 
|-
 
|-
 
| 00:17
 
| 00:17
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| Modify the view  
+
|* Modify the view  
  
 
|-
 
|-
 
| 00:19
 
| 00:19
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| Change the style of the display.
+
|* Change the style of the display
  
 
|-
 
|-
 
| 00:22
 
| 00:22
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| Change the size and color of atoms and bonds  
+
|* Change the size and color of atoms and bonds  
  
 
|-
 
|-
 
| 00:26
 
| 00:26
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| To display the model with axes and bound box.
+
|* To display the model with axes and bound box.
  
 
|-
 
|-
 
| 00:30
 
| 00:30
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| Save the image in various file formats.
+
|* Save the image in various file formats.
  
 
|-
 
|-
 
| 00:34
 
| 00:34
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| To follow this tutorial you should be familiar with
+
| To follow this tutorial, you should be familiar with
  
 
|-
 
|-
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|-
 
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| 00:51
 
| 00:51
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| To record this tutorial, I am using
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| To record this tutorial, I am using:
  
 
|-
 
|-
 
| 00:53
 
| 00:53
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| '''Ubuntu '''OS version. 12.04
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|* '''Ubuntu '''OS version. 12.04
  
 
|-
 
|-
 
| 00:58
 
| 00:58
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| '''Jmol''' version 12.2.2 and  
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|* '''Jmol''' version 12.2.2 and  
  
 
|-
 
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| 01:02
 
| 01:02
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|Java version 7
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|* Java version 7
  
 
|-
 
|-
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|-
 
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| 01:12
 
| 01:12
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| We can rotate and zoom the model, to get a better perspective of the structure.
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| We can rotate and zoom the model to get a better perspective of the structure.
  
 
|-
 
|-
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|-
 
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| 01:24
 
| 01:24
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|  Click on the model and Observe that the cursor changes to a hand icon.
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|  Click on the model and observe that the cursor changes to a hand icon.
  
 
|-
 
|-
 
| 01:29
 
| 01:29
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| Holding down the mouse button, drag the mouse on the '''panel'''
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| Holding down the '''mouse button''', drag the '''mouse''' on the '''panel'''
  
 
|-
 
|-
 
| 01:34
 
| 01:34
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|You can see the model is rotating.
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|You can see the '''model''' is rotating.
  
 
|-
 
|-
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|-
 
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| 01:42
 
| 01:42
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|Move the mouse wheel upwards to zoom-out, and downwards to zoom-in.
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|Move the '''mouse wheel''' upwards to zoom-out and downwards to zoom-in.
  
 
|-
 
|-
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|-
 
|-
 
| 01:57
 
| 01:57
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|Double-click and drag the mouse.
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|Double-click and drag the '''mouse'''.
  
 
|-
 
|-
 
| 02:00
 
| 02:00
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|  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
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|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'''.
  
 
|-
 
|-
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|-
 
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| 02:34
 
| 02:34
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|Scroll down to  “'''Spin'''” and then click on  option “'''On'''”.
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|Scroll down to  '''Spin''' and then click on  option '''On'''.
  
 
|-
 
|-
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|-
 
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| 02:44
 
| 02:44
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|  To turn off the spin, Open the Pop-up-menu again,
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|  To turn off the spin, Open the Pop-up-menu again.
  
 
|-
 
|-
 
| 02:49
 
| 02:49
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|Scroll down to “'''Spin'''” and click on “Off”.  
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|Scroll down to '''Spin''' and click on '''Off'''.  
  
 
|-
 
|-
 
| 02:54
 
| 02:54
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|  As an assignment,
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|  As an assignment-
  
 
|-
 
|-
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|-
 
|-
 
| 03:00
 
| 03:00
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| Explore the “'''Spin'''” option in the Pop-up menu.
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| Explore the '''Spin''' option in the Pop-up menu.
  
 
|-
 
|-
 
| 03:04
 
| 03:04
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| Change the direction of spin to “'''Z'''” axis and rate of spin to “'''40'''”.
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| Change the direction of spin to '''Z'''-axis and rate of spin to '''40'''.
  
 
|-
 
|-
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|-
 
|-
 
| 03:25
 
| 03:25
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|  “'''View'''” menu on the menu bar, has options to view the model from various angles.
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|  '''View''' menu on the menu bar, has options to view the model from various angles.
  
 
|-
 
|-
 
| 03:31
 
| 03:31
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|  Click on the ''''View'''' menu.
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|  Click on the '''View''' menu.
  
 
|-
 
|-
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|-
 
|-
 
| 03:38
 
| 03:38
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|  For example, I will choose “'''Top'''” view.  
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|  For example, I will choose '''Top''' view.  
  
 
|-
 
|-
 
| 03:42
 
| 03:42
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|Click on the ''''Top'''' option.
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|Click on the '''Top''' option.
  
 
|-
 
|-
 
| 03:45
 
| 03:45
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|  The image on the screen shows how the molecule looks from the top.
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|  The '''image''' on the '''screen''' shows how the molecule looks from the top.
  
 
|-
 
|-
 
| 03:50
 
| 03:50
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|  We can save this view as an image in various file formats.
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|  We can '''save''' this '''view''' as an image in various file formats.
  
 
|-
 
|-
 
| 03:55
 
| 03:55
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|  Click on the “'''Save current view as an image'''” icon.
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|  Click on the '''Save current view as an image''' icon.
  
 
|-
 
|-
 
| 03:59
 
| 03:59
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|  A “'''Save'''” dialog box appears.
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|  A '''Save''' dialog box appears.
  
 
|-
 
|-
 
| 04:03
 
| 04:03
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|  To select the file format, scroll down the options on the “'''Image Type'''”.
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|  To select the file format, scroll down the options on the '''Image Type'''.
  
 
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|-
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| 04:24
 
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|  In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''
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|  In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''.
  
 
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| 04:50
 
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|Size and color of atoms and bonds in this molecule can be changed, if required.
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|Size and color of atoms and '''bond'''s in this molecule can be changed, if required.
  
 
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|-
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|-
 
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| 05:09
 
| 05:09
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|  To change the display into “'''CPK Space fill'''”, open the Pop-up-menu.
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|  To change the display into '''CPK Space fill''', open the Pop-up-menu.
  
 
|-
 
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| 05:15
 
| 05:15
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|  Go to “'''Select'''” and click on '''All''' to modify the whole molecule.
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|  Go to '''Select''' and click on '''All''' to modify the whole molecule.
  
 
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| 05:25
 
| 05:25
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|Scroll down to ''''Style'''',  select ''''Scheme'''' from the sub-menu.
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|Scroll down to '''Style''',  select '''Scheme''' from the sub-menu.
  
 
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| 05:50
 
| 05:50
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|Scroll down to “'''Style'''”, select '''Scheme''' and click on '''Ball and Stick''' option.
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|Scroll down to '''Style''', select '''Scheme''' and click on '''Ball and Stick''' option.
  
 
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| 06:19
 
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|  For example, I will select “'''0.1 Angstrom'''” and click on it.
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|  For example, I will select '''0.1 Angstrom''' and click on it.
  
 
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|  I want to change the colour of all the '''Carbon''' atoms in the model, to yellow.
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|  I want to change the colour of all the '''Carbon''' atoms in the model to yellow.
  
 
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| 07:23
 
| 07:23
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|  We can display the image with '''“X,Y '''and''' Z'''” axes and within a bounding box.
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|  We can display the image with '''X,Y '''and''' Z''' axes and within a bounding box.
  
 
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| 07:54
 
| 07:54
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|Scroll down to '''Style''', and select '''Boundbox''' from the options.  
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|Scroll down to '''Style''' and select '''Boundbox''' from the options.  
  
 
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| 08:05
 
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|  On the screen we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.'''
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|  On the screen, we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.'''
  
 
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| 08:17
 
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|  Save the image and exit the program.
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|  '''Save''' the '''image''' and exit the program.
  
 
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|-
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|-
 
|-
 
| 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
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|  For the Assignment
+
|  For the Assignment-
  
 
|-
 
|-
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| 08:53
 
| 08:53
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| Change the display to “Sticks”.
+
| Change the display to '''Sticks'''.
  
 
|-
 
|-
 
| 08:56
 
| 08:56
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| Change the color of all the hydrogens in the model to “Green”.
+
| Change the color of all the hydrogens in the model to Green.
  
 
|-
 
|-
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| 09:12
 
| 09:12
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| 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
 
| 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
 
| 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
 
| 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
 
| 09:51
−
|More information on this Mission is available at the following link
+
|More information on this mission is available at the following link.
  
 
|-
 
|-
 
| 09:57
 
| 09:57
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 22:01, 13 September 2015

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 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 options.
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 the image 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 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 all the 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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