How do I run Jmol?
In order to run Jmol, you will need to install Java 8 in order to run it.
- Download Java for your Operating System: For macOS: jre-8u231-macosx-x64.
- Navigate to your downloads folder and open the downloaded file.
- Follow the steps in the installer to install Java.
- Once Java is installed, you may proceed to installing Jmol.
What is Jmol application?
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 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 open a jmol jar?
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.
Who created Jmol?
Dan Gezelter
The origins of Jmol For example, the SGI version of XMol did not run on IRIX 6. x because IRIX switched to a new executable format. XMol’s demise left a need for a similar tool. Dan Gezelter, the originator of Jmol, chose to avoid the same problems by making Jmol open source.
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 are jmol distances measured?
To measure a distance (such as a bond length), double-click on an atom; when you move the pointer, a dotted line will be shown, and when it is positioned on a second atom the distance will be displayed. If you double-click on the second atom, the measurement will be permanently displayed.
How do you select amino acids in Jmol?
You can use the or Boolean Operator to select all the amino acids that are either part of alpha helices or the atoms that are part of the backbone. The phrase ‘select helix or backbone’ means ‘select all atoms that are either a helix or in the backbone (or both)’.
How do you see 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 you cite Jmol software?
Which is the standalone version of Jmol?
Jmol Application “Jmol Application” is the version of Jmol that runs as a standalone program, in its own window.
How is the memory available in Jmol determined?
Memory available to Jmol is determined by Java. Less or more memory can be allocated by using: java -Xmx###m -jar Jmol.jar where the ### must be substituted by a number in megabytes (hence the “m” after it).
How to use JMOL in a kiosk mode?
By default it opens in full screen, but you can use the -goption above to set a certain window size. Communication with the application in kiosk mode uses ports with JSON commands (see http://chemapps.stolaf.edu/jmol/docs/misc/appsync.txt).
How to set the window size in Jmol?
To set the application’s window size, use either of these: Jmol.jar -g WIDTHxHEIGHTJmol.jar –geometry WIDTHxHEIGHT using lowercase ‘x’ and no spaces, e.g. Jmol.jar -g 500×250. By default, size is the last size used or else 500×500.
