How do I use Jmol commands?

Try some of these commonly useful commands:

Table of Contents

“spin on” will cause the molecule to start spinning.
“spin off” will stop the molecule from spinning.
“moveto 0 {0 0 0} 0” will return to the default view.
“select carbon” will select the carbon atoms in the file.
“select hydrogen” will select the hydrogen atoms in the file.

How do you reference Jmol?

How to cite Jmol. Remember to always use uppercase ‘J’, lowercase ‘mol’ (explanation). If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section of the Jmol Wiki.

What is Jmol application?

Jmol as a standalone application. J(S)mol as a web applet or HTML5 object. compatibility with JavaScript frameworks or libraries.

How do I change the atom color in Jmol?

You can explicitly assign atom colors using JavaScript standard color names, octal equivalents, or RGB triples.

select carbon; color atoms forestgreen.
select hydrogen; color atoms [xFF00FF]
select oxygen; color atoms [0,255,0]
select *;color white; select carbon and atomno<8; color atoms green.

How do I run Jmol on Windows?

Steps

Download the Chem119 compressed folder.
Right click the folder and drag it to your Desktop or Documents folder and choose to Extract…
Once it finishes extracting, open the Chem119 folder.
Double click Jmol.jar.
Jmol should launch, opening to a black screen.

How do you zoom in on Jmol?

To zoom the image in Jmol put the mouse cursor over the Jmol image then hold down the shift key and the left mouse button while dragging down to zoom in or up to zoom out.

How do I start Jmol?

How do you get to Jmol?

Downloading Jmol You need to have Java on your computer to run the desktop version of Jmol. Most computers will already have Java installed, but if you do not, you can download it for free from https://java.com/en/download/.

How do you select chains in jmol?

Select Chain With select :, followed by the letter of the chain you would like to select, only the chain you select will be affected by future commands. Note: The Top 7 protein is a protein with only a single chain, so all atoms are colored red with the commands used above.

What is CPK jmol?

CPK. This is the default color scheme used in Jmol and was developed by Corey and Pauling and later improved by Kultin. In the CPK color scheme, carbon is gray, hydrogen is white, oxygen is red, nitrogen is blue and sulfur is yellow. This is the standard color code utilized in many textbooks.

How do I download and install jmol?

Where is the jmol menu?

The Jmol Menu provides access to a wide range of Jmol’s capabilities. Open Jmol’s menu by clicking on Jmol (to the lower right of the molecule; or right-click anywhere in Jmol). The menu is good for exploring what Jmol can do, or for making a small number of changes to the molecular view.