PoojaMoolya: Created page with ' {| border=1 ! Time ! Narration |- | 00:01 |Welcome to this tutorial on '''Modify Display and View '''in Jmol Application.''' ''' |- | 00:08 |…'

2014-08-12T10:42:38Z

Created page with ' {| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 |Welcome to this tutorial on '''Modify Display and View '''in Jmol Application.''' ''' |- | 00:08 |…'

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! <center>Time</center>
! <center>Narration</center>

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| 00:01
|Welcome to this tutorial on '''Modify Display and View '''in Jmol Application.''' '''

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| 00:08
| In this tutorial, we will learn to

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| 00:11
|Rotate, zoom, move and spin the model on screen

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| 00:17
| Modify the view

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| 00:19
| Change the style of the display.

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| 00:22
| Change the size and color of atoms and bonds

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| 00:26
| To display the model with axes and bound box.

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| 00:30
| Save the image in various file formats.

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| 00:34
| To follow this tutorial you should

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| 00:36
| be familiar with '''Jmol Application''' Window and

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| 00:40
| know to create and edit models using '''modelkit function'''.

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| 00:45
|If not, watch the relevant tutorials available at the following link.

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| 00:51
| To record this tutorial, I am using

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| 00:53
| '''Ubuntu '''OS version. 12.04

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| 00:58
| '''Jmol''' version 12.2.2 and

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| 01:02
|Java version 7

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| 01:05
| I have opened a new '''Jmol '''window with a model of '''2-chloro-1-propanol '''on the '''panel'''.

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| 01:12
| We can rotate and zoom the model, to get a better perspective of the structure.

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| 01:18
| To rotate the model, click on the “'''Rotate molecule'''” icon on the tool bar.

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| 01:24
| Click on the model and Observe that the cursor changes to a hand icon.

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| 01:29
| Holding down the mouse button, drag the mouse on the '''panel'''

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| 01:34
|You can see the model is rotating.

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| 01:37
| To zoom-in and zoom-out, place the cursor on the '''panel'''.

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| 01:42
|Move the mouse wheel upwards to zoom-out, and downwards to zoom-in.

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| 01:49
| To move the model on the '''panel''', place the cursor on the model.

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| 01:54
|Hold the '''Shift''' button on the keyboard.

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| 01:57
|Double-click and drag the mouse.

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| 02:00
| For a detailed description, refer to the “'''Mouse Manual'''” provided in the Pop-up-menu.

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| 02:06
|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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| 02:17
| If you are connected to the Internet,

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| 02:19
|a web page with “'''Mouse manual'''” appears on the screen.

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| 02:24
|Click on the '''panel''' to exit the Pop-up menu.

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| 02:28
| To automatically spin the molecule on the '''panel''', open the Pop-up menu.

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| 02:34
|Scroll down to “'''Spin'''” and then click on option “'''On'''”.

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| 02:40
| We can see that the model is spinning on the '''panel'''.

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| 02:44
| To turn off the spin,

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| 02:46
|Open the Pop-up-menu again,

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| 02:49
|Scroll down to “'''Spin'''” and
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| 02:51
|click on “Off”.

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| 02:54
| As an assignment,

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| 02:56
| Create a model of '''2-chloro-3-Iodo-pentane'''.

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| 03:00
| Explore the “'''Spin'''” option in the Pop-up menu.

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| 03:04
| Change the direction of spin to “'''Z'''” axis and rate of spin to “'''40'''”.

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| 03:10
| As a hint: Use '''Set Z Rate '''option in the pop-up menu

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| 03:16
|Your completed assignment should look as follows.

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| 03:22
| Let us now learn about the '''View''' menu.

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| 03:25
| “'''View'''” menu on the menu bar, has options to view the model from various angles.

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| 03:31
| Click on the ''''View'''' menu.

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| 03:33
| Scroll down the menu and choose from the various options provided.

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| 03:38
| For example, I will choose “'''Top'''” view.

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| 03:42
|Click on the ''''Top'''' option.

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| 03:45
| The image on the screen shows how the molecule looks from the top.

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| 03:50
| We can save this view as an image in various file formats.

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| 03:55
| Click on the “'''Save current view as an image'''” icon.

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| 03:59
| A “'''Save'''” dialog box appears.

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| 04:03
| To select the file format, scroll down the options on the “'''Image Type'''”.

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| 04:09
| I will select '''JPEG''' format.

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| 04:13
|Open the folder in which you want the file to be saved.

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| 04:17
| I want it on '''Desktop.'''

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| 04:19
|Select '''Desktop''' and click on '''Open''' button.

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| 04:24
| In the '''File Name '''text-box, type '''“2-chloro-1-propanol” '''

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| 04:30
| Go to “'''Files of Type'''” and select '''jpg'''.

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| 04:35
| Click on '''Save '''button.

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| 04:38
| The image will now be saved in '''JPEG '''format on the '''Desktop'''.

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| 04:44
| The style of display of molecular model can be modified in various ways.

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| 04:50
|Size and color of atoms and bonds in this molecule can be changed, if required.

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| 04:57
| We have an option to modify all the atoms in the molecule or a select set.

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| 05:03
| The default display of the model on the panel is of '''ball and stick.'''

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| 05:09
| To change the display into “'''CPK Space fill'''”, open the Pop-up-menu.

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| 05:15
| Go to “'''Select'''” and click on '''All''' to modify the whole molecule.

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| 05:22
| Open the Pop-up-menu again.

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| 05:25
|Scroll down to ''''Style'''', select ''''Scheme'''' from the sub-menu.

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| 05:30
| And click on '''CPK Spacefill''' option.

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| 05:35
| The model on the screen is converted to '''CPK Spacefill''' model.

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| 05:40
|Let us now convert it back to '''ball and stick''' model.

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| 05:44
| Let's follow the same steps as before.

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|05:48
| Open the Pop-up-menu.

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| 05:50
|Scroll down to “'''Style'''”, select '''Scheme''' and click on '''Ball and Stick''' option.

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| 05:56
| The model is now converted to''' ball and stick '''style display.

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| 06:01
| The size of the bonds can be changed using Pop-up menu, as well as '''Display''' menu on the menu bar.

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| 06:08
|Click on the '''Display''' menu and select '''Bond'''.

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| 06:12
|The sub-menu has options of bonds in different size diameter, in '''angstrom units. '''

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| 06:19
| For example, I will select “'''0.1 Angstrom'''” and click on it.

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| 06:26
| Note the change in the thickness of the bonds.

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| 06:30
| We can also change the colour of atoms and bonds.

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| 06:34
| I want to change the colour of all the '''Carbon''' atoms in the model, to yellow.

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| 06:39
| To do this, open the Pop-up menu and go to '''Select'''.

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| 06:44
| Scroll down to '''Element''' and click on '''Carbon'''.

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| 06:48
| Open the Pop-up menu again and select '''Color'''.

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| 06:52
|Then select '''Atoms''' and click on '''Yellow''' options.

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|06:57
|| All the '''Carbons''' in the model, now appear yellow in colour.

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| 07:02
| Let's see how to change the color of bonds.

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| 07:06
| Open the Pop-up-menu and select '''All'''

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| 07:10
| Open the Pop-up-menu again.

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| 07:12
|Scroll down to '''Color''', select '''Bonds''' from the sub-menu.

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| 07:16
| Scroll down and click on '''Blue''' option.

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| 07:20
| All the bonds are now blue in color.

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| 07:23
| We can display the image with '''“X,Y '''and''' Z'''” axes and within a bounding box.

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| 07:31
| Open the Pop-up menu, select '''Style'''.

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| 07:34
|And Scroll down to '''Axes''' option.

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| 07:37
| From the sub-menu select '''Pixel Width '''.

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| 07:40
| I will choose '''3 px.''' as pixel width.

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| 07:44
| We now have the model on screen with all the axes.

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| 07:49
| To draw a bound box around the image, open the Pop-up-menu.

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| 07:54
|Scroll down to '''Style''', and select '''Boundbox''' from the options.

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| 07:59
|Select '''Pixel width''' and click on the pixel width '''3 px'''.

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| 08:05
| On the screen we have the model of '''2-chloro-1-propanol''' in '''Boundbox''' with '''Axes.'''

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| 08:12
|To view the '''Boundbox''' clearly, we may have to zoom-in or zoom out.

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| 08:17
| Save the image and exit the program.

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| 08:21
| Let's summarize what we have learnt.

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| 08:23
|In this tutorial,we have learnt to

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| 08:26
| Rotate, zoom, move and spin the model on screen.

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| 08:31
|View the model from various angles.

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| 08:34
|Change the style of the display.

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| 08:36
| Change the color of atoms and bonds.

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|08:39
| We have also learnt to,

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| 08:41
| Display the image with axes and boundbox and

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| 08:44
| Save the image in different file formats.

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| 08:48
| For the Assignment

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| 08:50
|Create a model of '''3-amino-1-propanol.'''

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| 08:53
| Change the display to “Sticks”.

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| 08:56
| Change the color of all the hydrogens in the model to “Green”.

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| 09:00
| Change the color of all the bonds to yellow.

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| 09:04
|Your completed assignment should look as follows.

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| 09:12
| Watch the video available at the following link

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| 09:15
|It summarizes the Spoken Tutorial project

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| 09:19
|If you do not have good bandwidth, you can download and watch it

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| 09:24
| The Spoken Tutorial Project Team:

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| 09:26
|Conducts workshops using spoken tutorials

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| 09:29
|Gives certificates to those who pass an on-line test

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| 09:34
|For more details, please write to contact@spoken-tutorial.org

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| 09:41
|Spoken Tutorial Project is a part of the Talk to a Teacher project

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| 09:44
|It is supported by the National Mission on Education through ICT, MHRD, Government of India

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| 09:51
|More information on this Mission is available at the following link

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| 09:57
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

Jmol Application/C2/Modify-Display-and-View/English-timed - Revision history

PoojaMoolya: Created page with ' {| border=1 ! Time ! Narration |- | 00:01 |Welcome to this tutorial on '''Modify Display and View '''in Jmol Application.''' ''' |- | 00:08 |…'