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.
|
|
---|---|
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
|
Slide Number 3
Learning Objectives contd. |
|
Slide Number 4
Pre-requisites |
To follow this tutorial you should
If not, watch the relevant tutorials available at the following link. |
Slide Number 5
System Requirement |
To record this tutorial, I am using
|
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
|
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.
|
Place the cursor on the model.
|
To zoom-in and zoom-out, place the cursor on the panel.
|
Cursor on the panel.
Cursor on the model on the Jmol panel.
|
To move the model on the panel, place the cursor on the model.
|
Cursor on the Jmol panel.
|
For a detailed description, refer to the “Mouse Manual” provided in the Pop-up-menu.
|
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.
|
To automatically spin the molecule on the panel, open the Pop-up menu.
|
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,
|
Slide 6
Assignment
|
As an assignment,
Your completed assignment should look as follows. |
Cursor on the panel | Let us 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 file 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 will select 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.
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.
|
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 on 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 option. |
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”, select Scheme and click on Ball and Stick option. |
Cursor on the model. | The model is now converted to ball and stick style display. |
Cursor on the model. | The 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.
|
Click on the Display menu and select Bond.
|
Click on “0.01 A”. | For example, I will select “0.1 Angstrom” 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 colour of atoms and bonds. |
Cursor on 2-chloro-propanol | I want to change the colour of all the Carbon atoms in the model, to yellow. |
Right-click, go to “select”. | To do this, open the Pop-up menu and go to Select. |
Scroll down to “element” >> click on “carbon”. | Scroll down to Element and click on C-carbon. |
Right-click>>select “Color”, select Atoms.
|
Open the Pop-up menu again and select Color.
|
Cursor on the bond | All the Carbons in the model, now appear yellow in 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.
Scroll down to Color and select Bonds from the sub-menu. |
Click on 'Blue' option. | Scroll down and click on Blue 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.
|
Cursor on the sub-menu | From the sub-menu select Pixel Width . |
Click on 3 pixel. | I will choose 3 px. as pixel width. |
Cursor on the panel. | We now 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.
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.
|
Cursor on the panel | Save the image and exit the program. |
Slide Number 7
Summary |
Let's summarize what we have learnt.
|
Slide Number 8
Summary |
We have also learnt to,
|
Slide Number 9
Assignment |
For the Assignment
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. |