What is Jmol used for?

Overview. Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

How do I run Jmol?

The Jmol Console is used to input commands. To access the Console, right click anywhere in the Display Window to bring up the Display Window Menu. In this menu, click on the button ‘Console’ which will open the Jmol Console.

How do you reference Jmol?

The recommended way to cite Jmol is: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ JSmol: an open-source HTML5 viewer for chemical structures in 3D.

How do you pick a chain 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. Hemoglobin based on the file 1a3n.

How do I move to Jmol?

Moving the model

  1. To rotate the model, just put the mouse pointer over the J(S)mol panel and drag (move the mouse while you hold its button pressed down).
  2. To translate or move the model, hold down the Ctrl key while dragging.

What is the difference between summary judgment and directed verdict?

JMOL is also known as a directed verdict, which it has replaced in American federal courts. Judgment on the pleadings is a motion made after pleading and before discovery; summary judgment happens after discovery and before trial; JMOL occurs during trial.

How do I use Jmol commands?

Try some of these commonly useful commands:

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

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 you pick an amino acid in Jmol?

To select and display only the atoms of the sidechain of a specific amino acid, you want to use the select sidechain command followed by the amino acid name/number and end with the and (sidechain or alpha) text.

How do you show hydrogen bonds in Jmol?

By default, hydrogen bonds in Jmol are initially shown to connect the oxygen atom in one amino acid to the nitrogen atom in the second amino acids. However, if you are representing you protein with backbone format, these oxygen and nitrogen atoms are now visible and the hydrogen atoms appear to be floating in air.

How do I run Jmol on Windows?

Installing the application involves nothing more than putting one file, Jmol. jar, on your computer.

  1. Download the current Jmol . zip or .
  2. Take the one file Jmol. jar from the downloaded package.
  3. Windows users should also visit java.com and download the latest version of java.
  4. Double-click on the file Jmol.

What happens if you win a summary Judgement?

A summary judgment is a ruling by the court without a trial. Once the court enters summary judgment in favor of a party, the case is over, just as it would have been after a trial, and the losing party may either accept the judgment or appeal it.