Help:Media - ChemPRIME

Help:Media

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This Help page is designed to provide assistance in using different media forms on the wiki, including videos, jmols, and Lewis diagrams. Jmols are an easy way to represent molecules in a three-dimensional form.


Contents


Representing Molecules

Introduction to Molecular Structures

The most common media item used on ChemPRIME is the Jmol applet, which displays a rotatable 3D diagram of a molecule. The use of 3D molecules is encouraged, especially when describing molecular structure and intermolecular and intramolecular forces, or when you simply would like a reader to further explore a molecule you are describing.

Jmol molecules have several levels of complexity that can be tacked on with extra code. Usually, a relatively simple depiction is used with the following code:

<chemeddl-jmol>molecule name|size=150</chemeddl-jmol>

For example, to show methane in Jmol:

Jmol Wiki Code
<chemeddl-jmol>CH4|size=150</chemeddl-jmol>

Jmol diagrams can be placed into a small table for organization, as seen on CoreChem:Alkanes. On this page we describe additional options when using Jmol and how to use other media sources from ChemED DL. A List of available Molecules is here.

A simple TwirlyMol version of methane is shown below. This light-weight JavaScript representation is preferable when you have a large molecule and do not wish to use any of the fancy (and slower) utilities that Jmol provides, or have many molecules to display on one page, where the greater complexity of Jmols slows the load time.

<chemeddl-jmol>CH4|simple</chemeddl-jmol>

3D Structures of Molecules (Jmol)

Jmols are an easy way to add 3D rotatable, interactive molecules to a page. Two examples of this are shown below. See Models 360

The page ChemEd DL Jmol Applets gives a very detailed description of jmols, including what tags can be used to display features.

If you have difficulty adding your own Jmol to the wiki page (one that is not in the ChemEd DL repository) for now contact Jshorb).

The Jmol provides many useful and illustrative functions for visualizing molecules. If you want to add visualization for vibrations, Molecular Orbitals, Symmetry Elements or various other representations, then insert a Jmol using the corresponding tag. Below we have a water molecule with the associated representation menu, as well as the vibrational modes menu.

<chemeddl-jmol>Water|genmenu|vib</chemeddl-jmol>

Various options for inserting molecules with the various menus is done using a set of simple tags.

Wrapping Jmol structures

It is often desirable to wrap text around Jmol structures and other images in the text. Inserted Jmol structures do not allow you to do this even when their size is smaller than the screen width. To overcome this limitation, the Jmol structure can be inserted in a wiki table with no borders and floating alignment.


Example

Wiki Code Table
{| style="border-collapse:collapse;float:left;margin:1em;"
|<chemeddl-jmol>phosphoric_acid|size=200|caption='''Phosphoric Acid'''</chemeddl-jmol>
|}
We often require to wrap Jmol structures and other images in the text. Inserted Jmol structures do not allow you to do this even when their size is smaller than the screen width.
Phosphoric Acid

To overcome this limitation, the Jmol structure can be inserted in a wikitable with no borders and floating alignment.

2-D Images of Molecules and Lewis Structures

Using the "image" attribute, you can insert a simple 2D, non-manipulable picture of a molecule:

<chemeddl-jmol>CH3COOH|image|size=100,150,200</chemeddl-jmol>

Each of the above molecules can be viewed in its Lewis Structure corresponding to the resonance structure that contributes most to the overall resonance hybrid. An example of a Lewis structure is shown below.

<chemeddl-jmol>CH3COOH|Lewis|small</chemeddl-jmol>

Videos

Videos can be used to show chemical reactions, lab techniques or other chemical concepts difficult to convey in text or images. Two sources for adding videos are currently used on ChemPRIME. It is especially important to provide context to inserted videos in the text, as not everyone may be able to view video content.

ChemED DL Streaming Video

The Chemical Education Digital Library(ChemEd DL) hosts a large collection of videos which cover a broad range of chemical topics. This includes the Chemistry Comes Alive!(CCA) collection, published by the Journal of Chemical Education. The following steps show how to take advantage of the CCA library:

1) On the right side of the CCA collection page are a set of tools for searching for videos. The search function can be used to enter your query. The keyword link is also quite useful, as it has already categorized videos by topic.

2) Once you find a good video, find the information on its location. For instance, the Nitrogen Triiodide video, is found on the page http://jce.divched.org/JCESoft/CCA/CCA3/MVHTM/NITRO3I/NI3IOD.HTM

From the URL: The video is in CCA volume 3 The listed path is: MOVIES/NITRO3I The video name is: NI3IOD.MOV

This information is also found at the bottom of the page.

The unique identifier for this video is: CCA3/MOVIES/NITRO3I/NI3IOD

Sometimes the unique identifier cannot be deduced from the URL. For instance, the video on http://jce.divched.org/JCESoft/CCA/CCA6/MAIN/2QuantMenu/Weighing/SPOON/SPOON1_2/MOVIE.HTM has the unique identifier:

CCA6/MOVIES/volumetric/SPOON1_2

This identifier can actually be found just to the right of the movie on the page.

3)To insert a video onto the page, simply place the unique identifier inside the <chemeddl-video></chemeddl-video> tag, as shown below:

Wiki Code Video
<chemeddl-video>CCA3/MOVIES/NITRO3I/
NI3IOD</chemeddl-video>

<chemeddl-video>CCA6/MOVIES/
volumetric/SPOON1_2</chemeddl-video>


In addition to CCA videos, new (non-CCA) videos found here use the same syntax. These videos use a video ID instead of the CCA identifier. All CCA videos also have video IDs in addition to CCA identifiers. In the future, there will be an easy search for videos and their video IDs. For now, the Textbook Table of Contents page can be used to search for videos. Upon finding a video, click on it, to take you to the video page. The Video ID appears in the URL. For instance, the Ketene generator video:

http://content.chemeddl.org/alfresco/service/org/chemeddl/video.html?options=false&ID=vid:3309&guest=true

has a video ID of 3309.

4) After inserting a video, make sure that the context of the video is explained in the text, since some users may not be able to display videos on their machines.

More Information

More information on displaying videos in the wiki can be found at Wikipedia

Using YouTube Video

Another source for videos is YouTube, to which a number of chemistry related videos have been uploaded, and to which a ChemPRIME user could upload their own video of a chemical concept. YouTube videos cannot currently be inserted into ChemPRIME webpages. However, by creating a link to the video of interest, that video will be inserted into the Chempaths page automatically. The syntax for linking to a website in wiki-code is:

[website_address hyperlink text]

A good example of linking to YouTube videos can be seen on CoreChem:Titrations.

As always, make sure the content and context of the added video is explained in the text.

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