Molecular Visualization Lab - Instructions

I. Hemoglobin and protein structure

II. Lipid Bilayers

The following interactive tutorials illustrate the principles of biochemistry using molecular visualization:

• http://www.umass.edu/microbio/chime

The JSmol tutorials should open immediately on your computer/phone. Try opening Hemoglobin:

• http://bioinformatics.org/jmol-tutorials/jtat/hemoglobin/contents/contents.htm (Chrome browser recommended)

Advanced Setup Instructions

Try opening the following tutorial; you will need to download Java (only works with Safari): http://www.umass.edu/molvis/tutorials/hemoglobin/glycine.htm

• Click on the 'Activate Java Applet' button.

• Select 'allow Java Applet to run' in the window that pops up. If it asks you to update Java, click Later. The tutorials seem to work better with older Java versions.

• A popup window may say Application Blocked by Security Settings, so you will likely need to lower your security setting for the site:

1. Give Java permission to run. Open your OS System Preferences and then open Other: Java. Under the Security tab, choose the lowest level available: medium or high.

2. Add exceptions for each site by clicking 'Edit Site List...' and then click 'Add'. Copy and paste this link into the box: http://www.umass.edu/molvis/tutorials/hemoglobin/glycine.htm and click 'Ok' followed by 'Continue' .

3. Lastly, click 'Ok' to apply the settings and restart your browser.

After closing and restarting Safari, open: http://www.umass.edu/molvis/tutorials/hemoglobin/glycine.htm and click 'Run'.

If a molecule doesn't load, you may need to configure your browser settings. Under the Plug-ins manager in your browser, check that the Java Applet is set to 'Ask to activate', e.g. Safari> Tools> Add-ons> Plugins> Java.. Note: Java no longer works with Chrome or Firefox internet browsers.

Mac OS 10.8 Mountain Lion: (tutorials 1 and 2)

• Chrome doesn't work (won't run new Java).

• Firefox and Safari will require the security settings above.

Mac OS 10.6 Snow Leopard (older Java):

• Hemoglobin runs in Chrome, Firefox and Safari

• Bilayers no longer seems to run

Install Java if you don't have it (ignore prompts to update your version).

• http://java.com/en/

Check out these other pages:

• www.proteopedia.org/wiki/index.php/Drug_Metabolism_by_CYP450_Enzymes. Answer Focus Questions at the bottom of the page.

• PDB - Molecule of the Month. Click on PDB entry links to explore a Health and Disease article (Zika Virus, Amyloids, Diabetes, etc.).