Installing jmol

If you get the message below. Correct this fault as follows. This message is caused when the switch "security. This should open it with Firefox. This should open a web-page containing text and a graphics window. This should make two new files, one with the suffix. Open the. We will be using Jmol to view the PDB file 1qys. In the top right corner of the website there is a search bar similar to the image below.

This should bring you to the page for '1qys. Just below the search box on the right should be a list of four options similar to the image shown below. Click ' Download Files ' and you will see an expanded menu similar to the second image shown below. This file, named '1qys. Note: It is a good idea to create a new folder for each molecule you explore to organize all PDB files, images, articles and other related work. If you don't need additional information about the PDB file or don't wish to save a copy of the file on your computer, you can 'call up' the file in Jmol without downloading.

See Saving and Opening Files in Jmol for more details. To launch Jmol, click on the 'Jmol. Note: it should have an icon similar to one of the images below. Quick tip: You might wish to create a shortcut to the 'Jmol. For PC users: right click on the Jmol. Copy and paste the shortcut wherever you want to access Jmol quickly.

For Mac users: right click on the Jmol. However, if you need to change this:. Jmol as a standalone application. J S mol embedded in wikis or blogs. Borrowed JSmol , or running JSmol without your own server. Running Jmol using Java Web Start. JSmol in a Jupyter notebook. Jmol in an Android tablet. Get the files from SourceForge. Support and operating systems.

Try using the web based JSmol before attempting to install Java and Jmol. You will still need to download the molecular files needed, but your professor should make them available via Mycourses. JSmol allows you to open click the open link just below the image viewer files that have been downloaded to your computer. Once selected you will see the Choose file option and will be prompted to Open the file location of the molecules.

Once selected, hit the load button to view the selected file.