CBI Molecule Workshop

From Proteopedia

Revision as of 05:10, 23 October 2013

Create Your Own Proteopedia Page

Use the right Internet browser

Proteopedia and Jmol requires Java for 64-bit browsers. Therefore, use Firefox (works best for page making) or Safari, and not Chrome.

Create a page

• At the 'Search' box on the left of any proteopedia page, type your page title. For a draft page for this class, type:

  Your Username/Sandbox1

You will be asked to click on a red linked caption to create your new page.

Edit the page

Create all your content in the 'edit this page' tab. Remember that you need to log in to edit a page. Changes are recorded and can be undone in the 'history' tab, just like Wikipages.

Create written content

Typography

Simple and useful basics...

• In the 'edit this page' tab, write something, then select your sentence or word. Click the appropriate buttons to create Bold or italics fonts, or "Headers".

== bla bla ==

• Click the button "Save page" at the page bottom, and you'll see how it will look like on your Proteopedia page.

When you create headers, Proteopedia automatically generates a content box at the top of the page to contain all the headers of the page.

Tip: To create more complicated constructions of your proteopedia page, browse other proteopedia pages, and observe the syntax used to create the special effects.

Link or reference other webpages

The 'External link' button lets you create a link to another webpage (other than Proteopedia pages). Example: Research articles related to your page.

• Click the 'External link' button. You'll see: [http://www.example.com link title]. Paste in your web address of interest. When you create a link title, it will show up as a blue linked caption like this: UMASS Amherst

The 'Internal link' button lets you create a link to another Proteopedia webpage. Example: a Proteopedia page that contains a PDB molecule related to your page, your Proteopedia profile page.

• Click the 'Internal link'. You'll see: [[Link title]]. Paste in the Proteopedia page of interest. It will show up as a blue linked caption like this: CBI Molecules

Create still images

The 'Embedded image' button lets you include images into your page. Example: gene pathways, chemical reactions, still structural images from Pymol.

• Click the 'Upload file' tab on the left of the page. Upload an image of interest. Copy the file name of the image.
• When in the 'edit this page tab', click the 'Embedded image' button and paste the file name into [[Image:Example.jpg]].
• You can change the size and position of the image by including further details such as: [[Image:Example.jpg||300px|left|]]

Create dynamic structural content

Here is where you create links to dynamic structural content that you create! It's really easy, believe us.

• In the 'edit this page' tab, click the 'show' button of

• Load a molecular structure onto your page by first clicking the 'load molecule' tab.

To find a known structure, you can type in its PDB code.

• For this workshop, type '7DFR'. Click 'load'. You'll see the DHFR protein molecule in the box on the right, as such:

• To display this molecule in your page, click the 'save scene' tab.
• Type into the 'Scene name' box, for example: Scene 1
• Click 'Save current scene'. A wikitext will appear as:

  Copy and paste the following line where you want the scene link to appear (scroll down if needed) and edit the TextToBeDisplayed:
  <scene name='56/565760/Scene_1/1'>TextToBeDisplayed</scene>

• Select and copy the line '<scene name='56/565760/Scene_1/1'>TextToBeDisplayed</scene>'

• In the main editing box of the 'edit this page' tab, paste '<scene name='56/565760/Scene_1/1'>TextToBeDisplayed</scene>'. 'TextToBeDisplayed' is where you can type a caption name that will turn into a green link that is used to initiate visualization of the molecule.
• Save page to view your output.

Favorite tips

Observe other molecules

Creating a great page is a reiterative process!

Remember to give credit to images appropriately, and avoid plagiarism like the plague by writing in your own words.

Your Heading Here (maybe something like 'Structure')

spinqualitylabelsall models Structure of HMG-CoA reductase (PDB entry 1dq8) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Anything in this section will appear adjacent to the 3D structure and will be scrollable.