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

Title of script: Modify Display and View

Author: Snehalatha Kaliappan

Keywords: Molecular models, 3-D models of chemical structures, video tutorial, Jmol tutorial

Outline:-

• Rotate, zoom, move and spin the model
• Modify the view
• Change the style of the display.
• Change the size and color of atoms and bonds.
• Axes and bound box
• Save the image in various file formats.

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Modify Display and View in Jmol Application.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to Rotate, zoom, move and spin the model on screen Modify the view Change the style of the display. Change the size and color of atoms and bonds
Slide Number 3 Learning Objectives	We will also learn to, Display the model with axes and bound box. Save the image in various file formats.
Slide Number 4 Pre-requisites	To follow this tutorial you should be familiar with Jmol Application Window and know to create and edit models using modelkit function. If not, watch the relevant tutorials available at the following link.
Slide Number 5 System Requirement	To record this tutorial, I am using Ubuntu OS version. 12.04 Jmol version 12.2.2 and Java version 7
Cursor on Jmol panel. Cursor on 2-chloro-1-propanol molecule.	I have opened a new Jmol window with a model of 2-chloro-1-propanol on the panel.
	We can rotate and zoom the model to get a better perspective of the structure.
Cursor on 2-chloro-1-propanol molecule Click on“Rotate molecule” icon on the tool bar.	To rotate the model, click on the “Rotate molecule” icon on the tool bar.
Click on the molecule.	Click on the model. Observe that the cursor changes to a hand icon.
Drag the mouse.	Holding down the mouse button, drag the mouse on the Jmol panel. You can see the model is rotating.
Place the cursor on the model. Move the mouse wheel up and down.	To zoom-in and zoom-out, place the cursor on the panel. Move the mouse wheel upwards to zoom-out, downwards to zoom-in.
Cursor on the panel. Cursor on the model on the Jmol panel. Hold the shift key on the key board.	To move the model on the panel, place the cursor on the model. Hold the shift button on the key board. Double click and drag the mouse.
Cursor on the Jmol panel. Open the Pop-up-menu >>scroll down to “About Jmol 12.2.2” . Cursor on the “Mouse Manual” Click on the “MouseManual”	For a detailed description, refer to the “Mouse Manual” provided in the Pop-up-menu. Open the Pop-up-menu and scroll down to “About Jmol 12.2.2” . Scroll down to the “Mouse Manual” and click on it.
Cursor on the web page	If you are connected to the Internet a web page with “Mouse manual” appears on screen.
Click on the panel.	Click on the panel to exit the Pop-up menu.
Right click on the mouse. Scroll down , select “Spin” and click “On”.	To automatically spin the molecule on the panel, open the “Pop-up menu”. Scroll down, select “Spin” and then click on the option “On”.
Click on the panel.	We can see that the model is spinning on the panel.
Scroll down Pop-up-menu, select “Spin” and click “Off”.	To turn off the spin, open the Pop-up-menu and select “Spin” and click on “Off”.
Slide 6 Assignment	As an assignment, Create a model of 2-chloro-3-Iodo-pentane. Explore the “Spin” option in the Pop-up menu. Change the direction of spin to “Z” axis and rate of spin to “40”. Hint: Use Set Z Rate option Your completed assignment should look as follows.
Cursor on the panel	Let's now learn about the View menu.
Click on the “View” icon.	“View” menu on the menu bar has options to view the model from various angles.
Click on the 'View' menu.	Click on the 'View' menu.
Scroll down the menu.	Scroll down the menu and choose from the various options provided.
Click on “Top”	For example, I will choose “Top” view. Click on the 'Top' option.
Cursor on the panel	The image on the screen shows how the molecule looks from the top.
Cursor on the panel	We can save this view as an image in various formats.
Click on the “Save current view as an image” icon.	Click on the “Save current view as an image” icon.
Cursor on the dialog box.	A “Save” dialog box appears.
Scroll down “Image type”	To select the file format, scroll down the options on the “Image Type”.
Click on JPEG	I select will JPEG format.
Cursor on the dialog box.	Open the folder in which you want the file to be saved.
Select Desktop.	I want it on Desktop. So select 'Desktop' and click on 'open' button.
Cursor on the “file name”	In the File Name text-box, type “2-chloro-1-propanol”
Click on jpg	Go to “Files of Type” and select jpg.
Click on Save button.	Click on Save button.
Cursor on the Jmol panel	The image will now be saved in JPEG format on the Desktop. <PAUSE>
Cursor on the Jmol panel.	The style of display of molecular model can be modified in various ways. Size and color of atoms and bonds in this molecule can be changed, if required.
Scroll down the Pop-up-menu	We have an option to modify all the atoms in the molecule or a select set.
Cursor on the Jmol panel.	The default display of the model on the panel is of ball and stick.
Open Pop-up-menu	To change the display into “CPK Space fill”, open the Pop-up-menu.
Go to “Select” and click “All” .	Go to “Select” and click “All” to modify the whole molecule.
Open the Pop-up-menu. Scroll down.	Open the Pop-up-menu again scroll down to 'Style' and select 'Scheme' from the sub-menu.
Select first “Style” go to “Scheme” >>click on “CPK Spacefill”.	And click on “CPK Spacefill”.
Cursor on the panel	The model on the screen is converted to “CPK Spacefill” model.
	Let us now convert it back to ball and stick model.
Cursor on the panel. Open Pop-up-menu, >>“Select” click on “All”.	Let's follow the same steps as before.
Open the Pop-up-menu>> “style”, >>“scheme”>> click on “ball and stick”.	Open the Pop-up-menu scroll down to “Style”, then to “Scheme” and click on “Ball and Stick”.
Cursor on the model.	The model is now converted to ball and stick style display.
Cursor on the model.	Size of the bonds can be changed using Pop-up menu, as well as “Display” menu on the menu bar.
Open display menu in the menu bar. Scroll down the display menu.	Click on the “Display” menu and select “Bond”. The sub-menu has options of bonds in different size diameter in angstrom units.
Click on “0.01 A”.	For example, I will select “0.10 A” and click on it.
Cursor on the panel.	Note the change in the thickness of the bonds.
Cursor on the panel.	We can also change the color of atoms and bonds.
Cursor on 2-chloro-propanol	I want to change the color of all the Carbon atoms in the model to yellow.
Right-click, go to “select”.	Open the “Pop-up” menu and go to “Select”.
Scroll down to “element” >> click on “carbon”.	Now, scroll down to “Element” and click on “C-carbon”.
Right-click>>select “Color”, select “Atoms”.	Open the “Pop-up” menu again and select “Color”. Then select “Atoms” and click on “Yellow” from the options.
Cursor on the bond	All the carbons in the model now appear in yellow colour.
Cursor on the Panel	Let's see how to change the color of bonds.
Open the Pop-up-menu go to 'Select' and click on 'All'.	Open the Pop-up-menu and select 'All'
Open the Pop-up-menu>> select “Color”>> select “Bonds” from the sub-menu.	Open the Pop-up-menu again, and scroll down to “Color” and select “Bonds” from the sub-menu.
Click on 'Blue' option.	Click on “Blue” from the option.
Cursor on the panel	All the bonds are now blue in color.
Cursor on the panel	We can display the image with “X,Y and Z” axes and within a bounding box.
Right-click on the panel, select “style” scroll down the sub-menu and select “axes” .	Open the Pop-up menu and select “Style”. Scroll down to “Axes” option.
Cursor on the sub-menu	From the sub-menu select Pixel Width among the options given.
Click on 3 pixel.	I will choose 3 px. as pixel width.
Cursor on the panel.	We have the model on screen with all the axes.
Right-click on the panel,>> select “Style” . scroll down the sub-menu >> select “Boundbox” . Click on “3 px”	To draw a bound box around the image, open the pop-up-menu. Scroll down to “Style”, and select “Boundbox” from the options. Select 'Pixel width' and click on the Pixel Width “3 px”.
Cursor on the panel.	On the screen we have the model of 2-chloro-1-propanol in ”Boundbox” with “Axes”. To view the “Boundbox” clearly, we may have to zoom-in or zoom out.
Cursor on the panel	Save the image and exit the program.
Slide Number 7 Summary	Let's summarize what we have learnt. In this tutorial,we have learnt to Rotate, zoom, move and spin the model on screen. View the model from various angles. Change the style of the display. Change the color of atoms and bonds.
Slide Number 8 Summary	W We have also learnt to, Display the image with axes and boundbox and Save the image in different file formats.
Slide Number 9 Assignment	For the Assignment Create a model of 3-amino-1-propanol. Change the display to “Sticks”. Change the color of all the hydrogens in the model to “Green”. Change the color of all the bonds to “Yellow. Your completed assignment should look as follows.
Slide Number 10 Acknowledgement	Watch the video available at this URL. http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial It summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it
Slide Number 11	The Spoken Tutorial Project Team: Conducts workshops using spoken tutorials Gives certificates to those who pass an on-line test For more details, please write to contact@spoken-tutorial.org
Slide number 11	Spoken Tutorial Project is a part of the Talk to a Teacher project It is supported by the National Mission on Education through ICT, MHRD, Government of India More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro
	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak