Proteopedia:Primer

From Proteopedia

Note for teachers: For teaching purposes, you may copy, adapt and distribute this document. Please remember to replace ‘_YOURSCHOOL’ by some unique identifier for your group, so Sandboxes from other courses will not interfere. Download this Primer as a Word document here (español).

A Proteopedia Worksheet

1. Getting to know each other:

Use a web browser to access http://proteopedia.org. Proteopedia's Main Page should greet you. Take a few minutes to familiarize yourself with the Proteopedia layout.

Proteopedia has a top banner, a left hand side bar and a central area. The left hand side bar has three sections, from top to bottom: navigation, search, toolbox.

From the navigation area, remember the 'Help' link. It will become handy.

From the toolbox, the 'Export this page' link allows you to save a self-contained version of a page, complete with interactive 3D molecules and working green links. Excellent for exporting pages for display or lessons, even when you don't have internet access.

The search area has two text input boxes. The top one uses Proteopedia's own searching engine and also allows for jumping directly to any page, as long as you enter it's full name. Let's call this input area 'Proteopedia's search'. The bottom text input area uses Google's powerful search engine to find pages in Proteopedia related to the word or words you enter. Let's call this bottom slot 'Google's search'.

2. Logging into Proteopedia:

Proteopedia allows free anonymous access, but editing and creation of pages is allowed only to registered users. To identify yourself to Proteopedia, click on the "Log in/request account" link on the top right hand side of the top banner.

Enter your Username, Password and click 'Log in'. For the purpose of this exercise, your instructor will provide you with a temporary Username and Password. You may also request your own Username by clicking on the "request one" link above the Username input field.

3. Creating your first Proteopedia page:

Type into the Proteopedia's search slot the name of the page you want to create. For the purpose of this exercise, enter Sandbox_YOURSCHOOL## (where ## is a unique number you will get from the instructor) and click 'Go'. From now own we'll use the name 'Sandbox_YOURSCHOOL##', but, of course, you will see the name you composed yourself.

After you click 'Go', as expected, you will get a message reporting that 'There is no page with the exact title...' and, a little further, a red link 'You can create a page titled Sandbox_YOURSCHOOL##'. Click the red link and Proteopedia will enter into editing mode. You should get a page entitled 'Editing Sandbox_YOURSCHOOL##' and a large central text input area, called the wikitext box. This is the area where you will enter the text for the page.

A little further down, you see the access link to SAT, the 'Scene authoring tools'. We will use them later on.

Then you will find three buttons: 'Save page', 'Show preview' and 'Show changes', that do exactly what they are named for. You can use 'Show preview' to evaluate the effect of the editing you are working on, and 'Save page' to permanently save the page, in its current state, into Proteopedia's database.

4. Let's start with some text on a clean page:

When starting a new page, Proteopedia provides you a default template. Click 'Save page' and behold: your first Proteopedia page is ready.

5. Next, a rotating 3D protein structure:

Click the tab [edit this page] located on the top banner.

The second line from the top is the one drawing the applet with the rotating structure. We want to replace the ' load='1stp' size=...’ with the PDB id of a structure we'll use for testing, 1acj. Once replaced, the line should start like this 'load='1acj' size=...’

Click 'Save page' and observe the result of your work. Your page should now contain text and a fully functional Jmol applet, displaying a rotating 3D representation of the protein structure of the Protein Data Bank entry 1acj.

Optional: You may edit the page again and play a little with the parameters for the <applet line. The value following size= sets the size in pixels for the applet; the text in quotes following caption= (if any) will be displayed as caption of the applet, under the rotating structure; the align= parameter can have values left, center, right, and will locate the applet on the page accordingly. Most of the time, align='right' is the best option.

6. Now a static image:

Click the tab [edit this page] located on the top banner, to go back into editing mode. As before, click in the text input area/wikitext box, and position the cursor one or two lines below the text you entered. Now click the button with the picture, the sixth from the left. You should get this line [[Image:Example.jpg]], with the word Example.jpg highlighted. You will replace this Example.jpg with the actual name of a sample Image already in Proteopedia: MW_Folding_Simulations.gif

Alternatively, you may copy and paste the following line: [[Image:MW_Folding_Simulations.gif]]

Click 'Save page' and you will now have text, image and a 3D representation of 1acj.

7. Looking into a structure more closely:

We will now start working with the 3D structure. But let's use 1pgb, a simpler structure than 1acj.

Edit the page and replace the PDB id '1acj' with '1pgb'. You should have <applet load='1pgb' ... and click 'Save page'. This loads and displays a smaller structure file. You may also want to replace the caption text with 1pgb ( caption='1pgb' ).

Click on 'Save page' and examine the structure. You may drag the structure with the mouse to rotate it. There are several accepted ways of representing and coloring a 3D structure to highlight different aspects related to functionality, structure, elements, etc. The current and default representation is called 'cartoon', where alpha helices are represented as helical ribbons and beta-strands as relatively straight ribbons. Each secondary structure element (helix or strand) has an arrowhead at one end, pointing from the N to the C terminus.

8. Using color to bring the molecule to life:

Let's create a green link in your page to color the 3D structure with colors that emphasizes the N terminus to C terminus sequence of the whole structure.

1. Enter the edit mode with the tab [edit this page].
2. Below the text input box/wikitext box, click on [show] at Scene Authoring Tools.
3. Click the 'load molecule' tab and type 1pgb into the PDB code slot, and click the 'load' button closest to the PDB slot.
4. Click the 'select all' button below the molecule.
5. Click the 'colors' tab and there, the button 'N->C rainbow (named chain)'.
6. Click the 'save scene' tab, and type 'N to C rainbow' in the 'Scene name' slot.
7. Use the mouse to drag the molecule into a pleasing orientation. The green link will start in whatever orientation you have when you save the scene.
8. Click the button 'save current scene'.
9. Copy the <scene ...>...</scene> that appears in the Wikitext box.
10. Scroll up, and paste it into the main text input/wikitext box above.
11. Above the Scene Authoring Tools, click [hide].
12. Click 'Save page'.

Now you should see a green link TextToBeDisplayed. When you click this green link, the N->C rainbow color scheme will be applied to the molecule.

Let's insert a color key to explain this color scheme.

1. Open a new browser tab and go to Proteopedia.Org.
2. Type 'color keys' in the Search slot at the left side of the page and Enter.
3. One of the pages found is Help:Color_Keys. Click on this.
4. At the Color Keys page, click on 'N to C rainbows'. There, click on the link to 'DRuMS'.
5. At DRuMS, click on Rainbows. Select one of the wikitext templates and copy it, such as

   {{Template:ColorKey_Amino2CarboxyRainbow}}

6. Go back to your Sandbox page, and paste the color key template into the text input/wikitext box. Make sure you have double curly brackets at each end {{...}}.
7. In your green link, change 'TextToBeDisplayed' to something that describes the scene, such as 'N to C sequence'.
8. Save your page.

Now you have a green link that colors the protein ribbon trace with the N to C rainbow color scheme, and a color key that explains that scheme.

In a similar manner, you could follow the steps above to create a green link for a different color scheme, such as 'Secondary Structure'. Also you can paste in a template with a color key for the secondary structure color scheme. Alpha Helices,  Beta Strands , Turns.

By clicking on such a new green link, you can distinguish clearly the two main types of secondary structure in this model: alpha helix and beta strand. This scheme uses four different colors to distinguish four types of protein secondary structures (helices, beta strands and sheets, turns, and loops) and DNA vs. RNA.

9. Adding some explanations to the page:

Proteopedia's green links are much like the standard links on a HTML page, where you frame a word with a start/end tag to make it 'hot' and responsive to a mouse click. Try to enter some explanation around the last link you created. Enter the edit mode, and type some text before and after the green link and click 'Save page'. here's a suggestion:

Let us color the two main forms of regular in this protein. Alpha helix appears in red, beta sheet in yellow.

10. Quiz anyone?

Now, we will create a simple quiz for self-evaluation. Enter the edit mode, click in the text input area, to have the cursor located one or two lines below the text you entered and copy these lines:

<quiz display=simple>
{How many alpha helices are in this structure?
|type="[]"}
- None.
+ One.
- Four.
</quiz>

Save the page and have fun by testing it. More possibilities are explained at Help:Quiz.

11. This is the END.

This marks the end of this exercise. With it, you should be able to create a Proteopedia page with text, static images and 3D models of protein structures. You should be able to interact with the model and create quizzes for student evaluation.

A more complete description is available on Proteopedia.org, by clicking the 'Help' link on the top left hand-side of the screen.

12. … and beyond, the real fun:

How to create your own scenes: The Scene Authoring Tool (SAT) is a unique and powerful Proteopedia feature for easily creating 3D scenes. To create additional and more complicated scenes, go to Proteopedia.org in a new web browser tab, click on ‘Help’ (top left) and then click on ‘Proteopedia:DIY:Scenes’.

On your page, enter the edit mode with the tab [edit this page], click in the text input area, position the cursor located one or two lines below the text you entered, click on the ‘3D’ button and type 1acj where the selected text states 'Insert PDB code or filename here'.

Click on [show] Scene authoring tools (SAT), and follow the step-by-step instructions on the Tacrine section of the Proteopedia:DIY:Scenes page.

An annotated applet: The line ‘<Structure…’ created when you click on the button 3D provides a rotating 3D structure that can be dragged and zoomed with the mouse, or popped up into a separate resizable window with the 'popup' button below the molecule.

You may also want to display an applet with complete Functional, Evolutionary and Structural information of a PDB file. The following line shows how.

{{STRUCTURE_1acj | PDB=1acj}}

Enter this line and replace ‘1acj’ with the PDB id you want to display. Automatic data mining processes refresh the added information every week.