Instruction Sheet for Jmol Application

Spoken Tutorial Team

IIT Bombay

1 Online / Offline content Select Console from the list. Console window opens
with a prompt. At the prompt type zap and press
1. The online content of Spoken Tutorials can be ac- Enter.
cessed from :
https://spoken-tutorial.org/tutorial-search/
2. You can also download the Spoken Tutorials for of-
5 First tutorial: Overview of Jmol
fline learning from : Application
https://spoken-tutorial.org/cdcontent/
1. Locate the topic Overview of Jmol Application
3. From this link download the FOSS categories in the
and click on it.
language you wish to learn.
2. To view the tutorial, click on the Play icon which
4. The Spoken Tutorial content will be downloaded as
is located in the player.
a zip file on your machine.
3. For Ubuntu users at 4.19 min, the executable
5. Extract the contents of the zip file & access them. Jmol.jar file may not open sometimes because the
permissions to execute the file were not given. Do
2 The procedure to practise the following to give executable permission:
Right-click on the Jmol.jar file and select
1. You have been given a set of spoken tutorials and Properties option. In the dialog-box se-
files. lect Permissions tab, In the Execute field
check the check-box for Allow executing file as
2. You will typically do one tutorial at a time. program. Close the dialog-box. Now Double-click
3. You may listen to a spoken tutorial and reproduce on the Jmol.jar file to open the Jmol Application
all the commands shown in the video Side-by-Side interface.
Method.
4. If you find it difficult to do the above, you may con-
sider listening to the whole tutorial once and then
6 Second tutorial: Introduction
practise during the second hearing. to Jmol Application
1. Please locate the topic Introduction to Jmol
3 Jmol Application Application and click on it.
2. To view the tutorial, click on the Play icon which
1. Click on "Select FOSS" or "All FOSS is located in the player.
Categories" drop-down and choose "Jmol
Application". 3. The Pre-requisite will be visible below the player
(only for Online contents).
2. Click on "Select Language" or "All Languages"
drop-down and choose the language (English, Hindi, 4. Outline, Assignments, Code Files and
Marathi ...) in which you wish to learn. Slides are available below the player.
3. Click on "Submit" button. 5. Adjust the size of the browser in such a way that
you are able to practise in parallel.
4. You will see a list of tutorials based on your selec-
tion. 6. These tutorials are created on Ubuntu Linux - 12.04

5. Start with the first tutorial in the displayed list. 7. From 2.13 min to 2.34 min the tutorial shows how
to open Jmol Application
8. From 1.33 min to 2.12 the tutorial shows informa-
4 General Instructions for Jmol tion about installation of Jmol Application.
Please ignore this step if you have already installed
1. If you are unable to fetch/open the structure of Jmol on your system.
molecules from the database websites in Jmol,
please change the proxy settings and check firewall
settings. 6.1 Opening Jmol Application on
It generally works under No Proxy settings and Ubuntu
without firewall. 1. Open the extracted Jmol installer file.
2. Sometimes if you type a wrong command or if Jmol Double-click on the Jmol.jar file. This will open the
is unable to read the command you will see a zapped Jmol interface.
window and a error message. To refresh the win- You can also right click on the Jmol.jar file.
dow, open the Console by clicking on File menu. From the options select OpenJDK Java 8 Runtime
 from the list. 5. Save your work from time to time, instead of saving
it at the end of the task.
2. Opening Jmol using terminal: Open the ter- 6. Play-pause-practise the whole tutorial.
minal by pressing Ctrl, Alt and T keys simulta- 7. Once the tutorial is complete, choose the next tuto-
neously. rial from the playlist which is located on the right
Navigate to the Jmol installer file. For example if side or below the player.
you have downloaded and extracted the Jmol in-
staller file jmol-14.31.2 to the Desktop folder: 8. Follow all the above instructions, till you complete
Navigate to the Jmol installer file by typing the fol- all the tutorials in the series.
lowing command at the prompt: cd Desktop
Press Enter key on the key board.
To run the jar file, type the following command:
9 Common instructions for
java -jar Jmol.jar Assignments
Press enter on the keyboard. Jmol interface opens.
Please note: Do not close the terminal while you 1. Attempt the Assignments as instructed in the tu-
are working on Jmol interface. If you close the ter- torial.
minal, it will kill the process and Jmol interface will 2. Save your work in your folder.
close.

6.2 Opening Jmol Application on Win- 10 Common instructions to use

dows and Mac Code files
1. Go to the folder where you have extracted the Jmol 1. Click on the link "Code files" located below the
zip file. player and save it in your folder
Double-Click on the Jmol.jar file.
2. Extract the downloaded zip file.
3. You will see all the code/source files used in the
7 Eighth tutorial: Structures particular tutorial.
from Database 4. Use these files as per the instructions given in the
particular tutorial.
1. From 5.40 min to 7.23 min the tutorial describes
how 2D drawings created in GChemPaint software
can be viewed as 3D structures in Jmol. 11 Tutorials that need internet
2. Please visit the link given here to view tutorials on connection
GChemPaint.
https://spoken-tutorial.org/ The following tutorials need working internet connection
to practise:
8 Common Instructions to prac- 1. Overview of Jmol Application
tise 2. Modify Display and View
3. Script Console and Script Commands
1. Create a folder on the "Desktop" with
your "Name-RollNo-Component". (Eg. 4. Surfaces and Orbitals
"Priya-07-Jmol"). 5. Structures from Database
2. Give a unique name to the files you save, 6. Crystal Structure and Unitcell
so as to recognize it next time. (Eg.
7. Proteins and Macromolecules
"Practice-1-Priya").
3. Remember to save all your work in your folder. 8. 3D Models of Enzymes

4. This will ensure that your files don’t get over- 9. Symmetry and Pointgroup
written by someone else. 10. Animations using Script Commands