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

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
00:36	be familiar with 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,
02:46	Open the Pop-up-menu again,
02:49	Scroll down to “Spin” and
02:51	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