Proteopedia:Cookbook

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Contents

Side by side still images

To arrange still images side by side on a page, insert them in a table

{| 
| [[Image:1cjq.png|left|200px]] 
| [[Image:1stp.png|left|200px]]
|}

Rectangular Jmol Structure Applets

jslibrary describes:
For a rectangular Jmol structure applet, an array containing two elements, width and height; this is usually easiest to do using JavaScript square bracket notation for array constants, as in [400, 200], ["50%", "100%"] or [0.5, 1.0]. Proteopedia currently only accepts integers, as in this example size='[800,200]'

Insert caption here

Synchronizing molecules

Please see Jmol/Synchronization

Movies mp4

Click the Play icon below to start the sample movie.

<html5media height="300" width="300">/mp4/file.mp4</html5media>

Shows the movie with the with a width of 300 and a height of 300 pixels.

A movie controller is also displayed at the bottom beneath the movie. If the height is too small, the controller will not be displayed. Clicking on the movie stops playing, and double clicking resumes playing in both Mac OS X and Windows. This is useful in case the controller is not displayed ("controller=false").

Embedded Youtube

<html5media height="300" width="300">https://www.youtube.com/watch?v=3uBqnVs2ywc</html5media>

Quiz

The special implementation of Quiz in Proteopedia includes an email feedback to the teacher. See overview at Help:Quiz and the full explanation and examples on How To Use at Help:Quiz at Wikiversity.

<quiz display=simple>
{  
|type="{}"}
Name a famous Greek philosopher. 
{ Aristotle|Plato }

{Question
|type="[]"}
+ Correct answer.
- Incorrect answer.
+ Correct answer.
- Incorrect answer.
</quiz>

Imagemaps

In the image map below, clicking on the computer screen should lead you to 2ace, the keyboard to 1rat,
and the thinking balloon to Believe It or Not!. A click on the person's head goes to the external article on Student at Wikipedia.
The (i) goes to the image info.

2ace1rathttp://en.wikipedia.org/wiki/StudentBelieve It or Not!
picture of a fooAbout this image
<imagemap>
Image:Foo.jpg|200px|picture of a foo
poly 131 45 213 41 210 110 127 109 [[2ace]]
poly 104 126 105 171 269 162 267 124 [[1rat]]
rect 15 95 94 176   [http://en.wikipedia.org/wiki/Student]
# A comment, this line is ignored
circle 57 57 20    [[Believe_It_or_Not!]]
desc bottom-left
</imagemap>

Here's a nice tool for finding the coordinates in an image.

Theoretical Models

On pages that largely or entirely concern theoretical model structures, please insert {{Theoretical_model}} in the top of the wikitext box. It will generate this banner:

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

If a page shows largely empirical models, but also one or more theoretical models, please put Theoretical Model in the text, and/or as a caption in Jmol whenever the model is theoretical:

  • The wikitext is: '''<font color='red'>Theoretical Model</font>'''
  • To add the red caption to a scene, use the "labels" tab in the Scene Authoring Tools and open the "caption" section.

Policy concerning theoretical models is at Proteopedia:Policy#Theoretical_Models, where you will also find links to examples.

Anchors

Section headings automatically act as anchors, with the heading text as the "anchor_name". Links of the form #anchor_name will link to the first anchor on the page matching that "anchor_name", usually the first identical section heading.

For example, try #Quiz ( [[#Quiz]] ) and #KiNG ( [[#KiNG]] ) to jump to those sections.

Floating quote Box

Alice's Adventures in Wonderland by Lewis Carroll
Project Gutemberg

There was nothing so very remarkable in that; nor did Alice think it so very much out of the way to hear the Rabbit say to itself, `Oh dear! Oh dear! I shall be late!' (when she thought it over afterwards, it occurred to her that she ought to have wondered at this, but at the time it all seemed quite natural); but when the Rabbit actually took a watch out of its waistcoat-pocket, and looked at it, and then hurried on, Alice started to her feet, for it flashed across her mind that she had never before seen a rabbit with either a waistcoat-pocket, or a watch to take out of it, and burning with curiosity, she ran across the field after it, and fortunately was just in time to see it pop down a large rabbit-hole under the hedge.

{{Quote box
 | quote  =
 | source =
 | width  =
 | align  =
}}

ConSurf

To insert the ConSurf panel, type the following line

{{subst:ConSurf|1stp|st}}

where the 2 parameters, 1stp and st, need to be adjusted to your case:

  • First parameter is the PDB ID of the model.
  • Second parameter is the 2nd and 3rd characters of the PDB ID.

The result will look like below and will be made a hard-coded content of the page (i.e. the template wikitext is removed and the result is inserted into the page source).


Evolutionary Conservation

Check , as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Eric Martz, Wayne Decatur, Angel Herraez, Eran Hodis, Karl Oberholser

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