Welcome to this tutorial on Modify Display and View in Jmol Application.
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
To display the model with axes and bound box.
Save the image in various file formats.
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.
To record this tutorial, I am using:
Ubuntu OS version 12.04
Jmol version 12.2.2 and
Java version 7
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.
To rotate the model, click on the “Rotate molecule” icon on the tool bar.
Click on the model and observe that the cursor changes to a hand icon.
Holding down the mouse button, drag the mouse on the panel
You can see that the model is rotating.
To zoom-in and zoom-out, place the cursor on the panel.
Move the mouse wheel upwards to zoom-out and downwards to zoom-in.
To move the model on the panel, place the cursor on the model.
Hold the Shift button on the keyboard.
Double-click and drag the mouse.
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. Then select Jmol 12.2.2 and click on Mouse Manual.
If you are connected to the Internet,
a web page with “Mouse manual” appears on the screen.
Click on the panel to exit the Pop-up menu.
To automatically spin the molecule on the panel, open the Pop-up menu.
Scroll down to Spin and then click on option On.
We can see that the model is spinning on the panel.
To turn off the spin, open the Pop-up-menu again.
Scroll down to Spin and click on Off.
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.
As a hint: Use Set Z Rate option in the pop-up menu.
Your completed assignment should look as follows.
Let us now learn about the View menu.
View menu on the menu bar has options to view the model from various angles.
Click on the View menu.
Scroll down the menu and choose from the various options provided.
For example, I will choose Top view.
Click on the Top option.
The image on the screen shows how the molecule looks from the top.
We can save this view as an image in various file formats.
Click on the Save current view as an image icon.
A Save dialog box appears.
To select the file format, scroll down the options on the Image Type.
I will select JPEG format.
Open the folder in which you want the file to be saved.
I want it on Desktop.
Select Desktop and click on Open button.
In the File Name text-box, type “2-chloro-1-propanol” .
Go to “Files of Type” and select jpg.
Click on Save button.
The image will now be saved in JPEG format on the Desktop.
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.
We have an option to modify all the atoms in the molecule or a select set.
The default display of the model on the panel is of ball and stick.
To change the display into CPK Space fill, open the Pop-up-menu.
Go to Select and click on All to modify the whole molecule.
Open the Pop-up-menu again.
Scroll down to Style, select Scheme from the sub-menu.
And click on CPK Spacefill option.
The model on the screen is converted to CPK Spacefill model.
Let us now convert it back to ball and stick model.
Let's follow the same steps as before.
Open the Pop-up-menu.
Scroll down to Style, select Scheme and click on Ball and Stick option.
The model is now converted to ball and stick style display.
The size of the bonds can be changed using Pop-up menu, as well as Display menu on the menu bar.
Click on the Display menu and select Bond.
The sub-menu has options of bonds in different size diameter, in angstrom units.
For example, I will select 0.1 Angstrom and click on it.
Note the change in the thickness of the bonds.
We can also change the colour of atoms and bonds.
I want to change the colour of all the Carbon atoms in the model to yellow.
To do this, open the Pop-up menu and go to Select.
Scroll down to Element and click on Carbon.
Open the Pop-up menu again and select Color.
Then select Atoms and click on Yellow option.
All the Carbons in the model, now appear yellow in colour.
Let's see how to change the color of bonds.
Open the Pop-up-menu and select All.
Open the Pop-up-menu again.
Scroll down to Color, select Bonds from the sub-menu.
Scroll down and click on Blue option.
All the bonds are now blue in color.
We can display this model on the screen with X, Y and Z axes and within a bounding box.
Open the Pop-up menu, select Style
and Scroll down to Axes option.
From the sub-menu select Pixel Width .
I will choose 3 px. as pixel width.
We now have the model on the screen with all the axes.
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.
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.
Save the image and exit the program.
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.
We have also learnt to:
Display the image with axes and boundbox and
Save the image in different file formats.
For the Assignment-
Create a model of 3-amino-1-propanol.
Change the display to Sticks.
Change the color of hydrogens in the model to Green.
Change the color of all the bonds to yellow.
Your completed assignment should look as follows.
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