Organic Chemistry at Penn State: Viewing Instructions

We are not computer scientists! We are just organic chemists. We construct our Organic Chemistry pages using the simplest means available. Yet, we try to design our pages in such a way that they are educational, and that they give you contents not available in textbooks, especially in the area of visualization of molecules and interactive learning. And, of course, we try to make them pleasant to look at and explore. After all, we want you to use them and to learn organic chemistry in the process.

There is a big difference between what could be done, and what we are willing to do. The technical limitations we face are browser related. The most popular browsers (Microsoft Internet Explorer (IE) and Firefox (FF) have more than 95% of market share) do not work in the same way. Since we are not able (we are non-profit after all) to prepare several versions of our pages, we are limited to techniques that will be, at least partially, effective on all machines. That usually means the lowest common denominator. We have designed these pages for viewing with IE, still the most popular browser in use.

We assume that you are internet-suave and can resolve simple browser problems. The browser requirements, additional software plug-ins and compatibility issues are discussed on a separate page. We strongly recommend that you read these comments before downloading and installing any software. All the software that you need is available free of charge. Note that the PSU computer labs have restrictions on what programs can be installed.

For now, we use only a few plugins (Chime, Acrobat, MS-Windows Media Player, and Flash Player) from the long list of those commonly available. The plugins are additional programs that have to be obtained separately. Many other interesting sites use them extensively. If you use the web frequently from the same machine (for example, you own your computer) we recommend getting at least some of them. We plan to incorporate some Java applets. Their "start up" time is sometimes a little longer, but they provide interactivity that is difficult to obtain by other means.

To help you use our organic site better we have introduced many icons to indicate that there is something hiding under the front page: an extra pop-up window, a molecular visualizer requiring a plug-in, or an java applet. Here is the list of our "road signs" set up to illustrate our approach. Try them! With your cursor over the icon watch the tool-tip (the little yellow pop-up window) and monitor the status bar at the bottom of the browser for extra info.

	This icon indicates that there is a file available (pdf) that can be viewed and printed (or downloaded) using Acrobat Reader. In some cases the file is just a printer-ready version of the page material, in other instances it contains material not available in other formats (such as practice exams). You need to get extra software to use it (it's free).
	This sign alerts you to the fact that a picture, or some other element of the page, is interactive. If you click on the appropriate area (observe the changing cursor) you will get an extra window with additional information. Read about extra windows below.
	Click on this icon only if you want to be questioned. You will get an extra window (or two) with questions probing your understanding of the material you are currently exploring. On occasion, you may even get an answer and learn something new.
	This profile should tell you that we have some hidden info on the scientists behind the concepts or reactions that we study. We even include some anecdotes. You can check the full list in our "Who is who?"
	Some extra windows will last for only a few seconds. They are just for fun.
	To give you a better idea about the three-dimensional nature of molecules we use Chime plug-in. The molecular visualizer is interactive, but require a little time to learn how to use it (and it takes a little longer to load). They are worth it! You need to make sure that you have Chime installed properly with your browser. We provide a brief tutorial page on how to use it.
	We have a movie for you. You will need Microsoft Windows Media Player to view it. It is available (free) from Microsoft. The music note symbol indicates that sound is included.
	Sometimes we have a video or animation presentation requiring Flash Player.
	For truly interactive experience we are using java scripts and some java applets. Java scripts (brief pieces of code in a programming language resembling Java) are usually executed by the newest browsers without any difficulties. They allow for introduction of some degree of interactivity. Java applets are small programs that execute on your computer after downloading. They use "true" Java, are compiled and take some time to load (be patient). They do not provide security problems because they run on their own "virtual" machine. They allow for much more interactivity. Make sure your browser has the newest Java (especially if you are using IE on XP Window computer) and is Java script and Java enabled.
	The vibrating methane molecule displayed in the left top corner of your page will always take you to the main page. Use it if you are lost (we mean, navigationally).

It helps if you "personalize" your browser for you own preferences. A selection of some options for browser "looks" or behavior often makes things more readable. The final effect (including colors) will depend on your screen resolution (the higher the better, we recommend at least 800x600), the speed of your processor, and preferences that you set up. Start with options provided by us, but do not be afraid to experiment. Most of the options can be set under "Internet Options" or "Preferences" menus of your browser.

Some recommendations that may help you with viewing our pages (grouped by topics):

We provide the navigational frame on the right side (We know that there are frame-haters between us, but for now there are some advantages in using frames). Our frame should help you to find your way to the major subsections of our page. The width of that side frame can be adjusted by moving the inside border with the mouse. If you desperately want to get rid of that navigational side frame, click here. At the bottom of each page there is an additional index of main sections, and clicking on the vibrating methane at the top of each page will take you to the main page.
We do not have our links underlined, but you will recognize them easily by their bold face and dark blue color. In IE, and FF, the links will change color to red when the cursor hovers above them. Remember there are also links hidden under icons or (occasionally) under some other pictures. You will recognize them easily since the cursor changes its shape when you move it above them. It helps if you monitor the status line (at the bottom of the browser) for additional information.
We provide brief alternative descriptions to most of the pictures. You may see them if you keep the cursor above the picture (or the icon) for one second. They help navigating, and provide (sometimes) some surprises.
We occasionally use extra windows to illustrate some additional concepts. These (usually) small windows can be moved around and resized. They will "disappear" if you perform any action in the main window, but they really only hide under the main window. To get them back "on the top" click on the appropriate button on the task bar (Windows) or under the Windows menu (Mac). Remember to close them before you move on, because you may run out of memory, if you have too many windows open. There is an exception: windows that pop up when you click on butterflies will disappear on their own after a few seconds (7-15 s). You will find some surprises in these windows.
If you want to print the contents of the whole page (and not that of the navigational bar) make sure that the frame containing that page is active (click on it anywhere), and that the appropriate selections are made in "Print" menu. With IE you may also select a section of the text (by highlighting it with the mouse) and print only your selection by choosing the appropriate option in the "Print" menu. Make sure that your printing does not include background colors (check it off under "Internet Options"). Occasionally, we provide an already formatted (printable) version of the material. You will recognize it by the Acrobat Reader icon (see above). If you have a slow internet connection, for printing large files (especially old exam pdf files) it is easier to first save them to your computer, and then print them off line.
To view our Java applets, make sure that your browser is Java-enabled. If the applets freeze or crashes your computer try to view them on freshly-restarted system (clean RAM). If it does not help, disable Java in your browser and forget about it. It is time to buy a new computer.
If your connection is really slow, and you are not sure what you want to examine, turn off the loading of images (pictures). After you are sure that the material is worth your time, turn the image loading on again, and refresh (reload) the page. The pictures will appear while you start reading.
If you are going to view the materials from the same computer over and over again, it pays off to setup a large enough cache to be able to keep your pages from session to session. It will minimize downloads, especially if you set your option to compare the cached document with one on the network to once per visit (recommended).

Please report all viewing problems to us, especially if you cannot view the pages correctly (tell us what the problem is, and what hardware and software are you using).

Technical limitations	How to view our pages	Viewing software	Frames
Browsers	How to speed it up	Plugins	Images
Website navigation	Personalize	Java	Extra windows
Screen resolution	Links	Icons	Cache
Printing		Construction tools	Report problems