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Welcome to the Furman Bioorganic Chemistry Wiki

This wiki is for students, by students... The chem teachers have never edited it.

Wiki Instructions:

Please do not post non-BioDraw images to the wiki.

They take up a lot of storage space and we cannot supply the personnel to confirm copyrights.

Font Color/Formatting

In general, use the default font and color provided by the "Edit" page. It just gets to be a little much if every other sentence is in lime green or neon pink, but feel free to use colored text for emphasis when it would be helpful. The only exceptions should be links and Headings. If you want to create a new heading for a topic on a page, you can do that by selecting the text in question and then using the pull-down menu in the upper left-hand corner of the editor.


You might notice that all the subject pages have a Table of Contents. You can create a new subject in the table of content by creating a heading. Main ideas should be made in Heading 4. Sub-points should be made in Heading 5, and a sub-sub-points in Heading 6. The other headings (1-3) won't show up in the table of contents.

Tables

Tables are a great way to express lots of data. They're very easy to make. When editing a page, click on the "Insert Table" Icon at the top of the editor:

This brings up a small screen on which you can edit the number of rows, columns, and whether or not you want the top row to be a heading (makes it purple, but will not affect the table of contents).

When you have a table selected, the buttons to the right of the insert table button (currently greyed out and unselectable in this picture) will magically become useful:


These are options to add/remove columns/rows, and (as we see selected) remove table.

Links can be created by using the Insert/Edit Link button:

Clicking this button will bring up a smaller screen from which you can decide what kind of link you want to post. You can create links to:

  • Files attached to this page.
  • Other pages contained in this wiki.
  • Pages external to this wiki (aka, the rest of the internet).

To link to a file attached to the page in question, click on the "Attachments" tab, then select the appropriate file.
For wiki pages, just click the "Search" tab, and type in the title, or keywords, or the page you want, and then select it from the list of returns.
For any other page, select the "External Link" tab and enter the url in the field where it says "Enter Hyperlink." This is useful if you want to link to say a Wikipedia page with relevant information.

When you place a link on the page, you can have the link displayed as the naked link itself, or you can give it an "Alias." This is the middle input field on the link setup page. If I want to create a link to Wikipedia page for PLP, I can do 1 of too things:
Plain link:http://en.wikipedia.org/wiki/Pyridoxal_phosphate

Or, give it an alias:PLP (Wikipedia)

Both of these links lead to the same place. Also, If you select text and then click the link button, it will make the selected text an alias for whatever you link it too. This has been done to the sentence directly below this about using the template.

Chem/BioDraw Instructions

Use the Template.

Few Captions in the Chemdraw Files

While it's necessary to have some text in the chemdraw files (for example, reactants over the reaction arrows), do not put whole sentences inside the Biodraw file. This will make the picture larger and the wiki will shrink larger images down to the size of others, and your text will be unreadably small.  Write explanations in the Edit page of the wiki, not in your chemdraw file. Labeling atoms or molecules is ok though.

Size your Pictures Correctly

The standard size of a chemdraw image posted to this website is 600 by 300 pixels (width and height, respectively). If a picture is too big it will be shrunk by the wiki in order to fit this size and will therefore be hard to view.

Compare these 2 chemdraws:

&lt;script&gt;//&lt;![CDATA[ cd_includeWrapperFile(&apos;/download/attachments/4653090/&apos;); //]]&gt; <script>//<![CDATA[ cd_insertObjectStr("<EMBED src='/download/attachments/10223643/$body' width='600' height='300' viewOnly='true' align='left' border='1' type='chemical/x-cdx' name='cdl'>"); //]]>

Download the chemdraw file above

&lt;script&gt;//&lt;![CDATA[ cd_includeWrapperFile(&apos;/download/attachments/4653090/&apos;); //]]&gt; <script>//<![CDATA[ cd_insertObjectStr("<EMBED src='/download/attachments/10223643/$body' width='600' height='300' viewOnly='true' align='left' border='1' type='chemical/x-cdx' name='cdl'>"); //]]>

Download the chemdraw file above

They are the same size, but the one on the right is much harder to read because it has been reduced in size in order to fit the 600 by 300 pixel requirement. You can do 1 of 2 things to avoid this:

Fit the all your structures into the the box in the template, and then delete the box and accompanying text (the instructions) before uploading. If all your structures can fit in the box, they'll fit the 600 by 300 space just fine.

Here is the template, please download it, and use it each time you create a new file.

Or

Edit the size of the chemdraw macro. A basic macro looks like this:

It will display a picture that is 600 by 300 pixels. However you can edit the size of the displayed image if you put a colon directly after the "w" in chemdraw and then type addition parameters. If I wanted the picture to be the same width but have a height of 800 pixels I could write the macro like this:

So that progression is "chemdraw:width|height" all in brackets. The symbol between the width an height is the vertical line that should be somewhere above the "Enter" button on your keyboard. It is on the same key as \. Here is the previously scrunched up chemdraw but set to 600 by 650 pixels:

Download the chemdraw file above

Much better.

Regardless of which of these methods you use, you should still use the template because of its formatting. It is formatted in such a way that your structures will look good and you will be able to fit more of them in.

File Names should be distinguishable

When you save a Biodraw file, name it so it can be distinguished from files with similar names.  Please title files as "YEAR-SEMESTER-INITIALS-SUBJECT.cdx" For example 2008-F-GGS-amino_acid_conformations.cdx.

fall = F, spring = S

Color in Chemdraws

You may use color in your chemdraw files. For example:

Download the chemdraw file above

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