We will be using a web application called Protein Explorer to make protein three dimensional structures visible and allow you to alter the display. The app also serves as the basis of a very helpful online tutorial about protein structure. There are other protein visualization apps, but this one in particular is needed to run the tutorial, and no other that I'm aware of allows you to manipulate the display without complications.Unfortunately, Protein Explorer is a Java applet, and a couple of years ago, browsers began removing support for Java applets. Protein Explorer will not run on the current version of Firefox, Chrome, and Safari for Windows. It also will not run on Internet Explorer (for another reason). It may run on Safari for Mac OS X, I'm not sure.
The sure choice for Windows users is to install a legacy version of Firefox that still supports Java applets. That version is Firefox ESR version 52. Version 60 will not work.
If you're a Mac user, your current version of Safari may be good enough.
How to install portable Firefox ESR version 52 (Windows users only)
Firefox ESR (Extended Support Release) version 52, 32-bit, is an legacy version of Firefox that should not be used except to run the tutorial and Protein Explorer, because it lacks security features of later Firefox versions. I've provided hints on how to install portable Firefox ESR version 52 for two reasons.Procedure
- It is available, while the non-portable version is not
- It can be installed on a portable memory device, allowing you to run it on a public computer
- Go to the Portable Firefox Legacy 52 download page
- The page will advise you that Firefox ESR is for organizations, while individuals who want the latest features should use normal Firefox.
Ignore this. You do not want the latest features. Amongst the latest features is removal of support for Java.
- Click Download from DuckGoGo Version 52.9.0 for Windows.
- Save the file and execute it
- During the installation you'll be asked for the directory in which to install Firefox ESR. Choose a directory on a portable memory device.
- Version 52.9.0 is a configured by default to run in 32-bit or 64-bit mode, depending on your machine. However, Java applets run only in 32-bit mode, so you must change the default to force 32-bit mode. To do this, download this Firefox configuration file and put it in the Firefox ESR directory. Open it up to verify that it contains a directive to force 32-bit mode.
- CHECK: Once Firefox ESR is installed, run it. You can tell you've got the right version by clicking Help and then About Firefox. If you see:
- "Firefox ESR 52.9.0 (32 bit)": GOOD!
- "Firefox ESR 52.9.0 (64 bit)": BAD! Go back to the previous step and make sure FirefoxPortable.ini is in the ESR directory, i.e. the same place that FirefoxPortable.exe lives.
- "Firefox ESR 60.2...": BAD! You either downloaded the wrong version or it somehow got updated to the current version (which won't work).
- "Firefox Quantum 62.0...": BAD! You're running the wrong version. Exit all Firefox windows, go to the Firefox ESR directory and run FirefoxPortable.exe. If you don't have a Firefox ESR directory, then you didn't download the right version or you didn't execute the installation file.
- Never update this version. If Firefox takes it upon itself to update, then you'll have to go back to the installation file you downloaded and reinstall Firefox 52.9.0.
(If you have any other advice that would work better than the above, please let me know)
Test if there are any Java issues to resolve
- Go to the Hemoglobin tutorial
- If you see:
All OK 
Just asking permission... OK 
PROBLEM! How to resolve Java problem
- Update Java. Download the file and execute it, installing it in the default directory (which on Windows will be Program Files (x86)\Java)
- CHECK: Once Java is installed, exit all Firefox windows and restart Firefox ESR. Then click Tools, Add-ons, Plugins. You should see Java Deployment Toolkit... and maybe other Java plugins. If you don't, look in the Program Files (x86) directory on your computer to make sure that it has a Java subdirectory. If it doesn't, then you didn't install Java to the right directory.
- Put the tutorial server on Java's whitelist
- Go to Windows Control Panel and click Java
- Go to the Security tab
- Click Edit Site List
- Click Add
- Copy/type in the resulting blank box: http://www.umass.edu (the beginning of the URL that gets you to the tutorial)
- Press OK
- Exit all Firefox windows and re-enter Firefox ESR.
- Test to see if any Java problems remain (see above)
(If you have any other advice that would work better than the above, please let me know)