Proteopedia:Primer - Revision history

Jaime Prilusky at 10:58, 6 August 2014

Jaime Prilusky — Wed, 06 Aug 2014 10:58:45 GMT

←Older revision		Revision as of 10:58, 6 August 2014
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	'''4. Let's start with some text on a clean page:'''		'''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.
		+
		+	<!--
	For this tutorial, we want to have a clean and fresh page, so please select anything you find in the text input area and delete it, before starting.		For this tutorial, we want to have a clean and fresh page, so please select anything you find in the text input area and delete it, before starting.

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	We will now apply some boldface and italics. Scroll down the browser window, back to the wikitext box. Use the mouse to select (highlight) the word Proteopedia and click the button with the bold 'B'. Now, select (highlight) the words ''Hello World'', and click the button with the ''slanted I''. Click 'Save page' and behold: your first Proteopedia page is ready.		We will now apply some boldface and italics. Scroll down the browser window, back to the wikitext box. Use the mouse to select (highlight) the word Proteopedia and click the button with the bold 'B'. Now, select (highlight) the words ''Hello World'', and click the button with the ''slanted I''. Click 'Save page' and behold: your first Proteopedia page is ready.
-		+	-->

	'''5. Next, a rotating 3D protein structure:'''		'''5. Next, a rotating 3D protein structure:'''

-	Click the tab [edit this page] located on the top banner. Click in the text input area/wikitext box, and position the cursor one or two lines below the text you entered before.	+	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 <nowiki>' load='1stp' size=...’</nowiki> with the PDB id of a structure we'll use for testing, '''1acj'''. Once replaced, the line should start like this <nowiki>'load='1acj' size=...’</nowiki>
		+
		+	<!--
		+	Click in the text input area/wikitext box, and position the cursor one or two lines below the text you entered before.

	<blockquote>		<blockquote>
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	Click on the button labeled 3D. This button inserts a long line, but don't worry about understanding everything in it for now. We want to replace the selected text 'Insert PDB code or filename here' with the PDB id of a structure we'll use for testing, '''1acj'''. Once replaced, the line should start like this <nowiki>'<applet load='1acj' size=...’</nowiki>		Click on the button labeled 3D. This button inserts a long line, but don't worry about understanding everything in it for now. We want to replace the selected text 'Insert PDB code or filename here' with the PDB id of a structure we'll use for testing, '''1acj'''. Once replaced, the line should start like this <nowiki>'<applet load='1acj' size=...’</nowiki>
		+	-->

	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]].		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]].

Jaime Prilusky at 14:13, 2 December 2012

Jaime Prilusky — Sun, 02 Dec 2012 14:13:26 GMT

←Older revision		Revision as of 14:13, 2 December 2012
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	'''Note for teachers:'''		'''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 [http://proteopedia.org/support/ProteopediaPrimer.doc here].	+	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 [http://proteopedia.org/support/ProteopediaPrimer.doc here] ([http://proteopedia.org/support/Proteopedia_PrimerosPasos.docx español]).

	== A Proteopedia Worksheet ==		== A Proteopedia Worksheet ==

Eric Martz at 21:59, 23 September 2012

Eric Martz — Sun, 23 Sep 2012 21:59:08 GMT

←Older revision		Revision as of 21:59, 23 September 2012
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	'''3. Creating your first Proteopedia page:'''		'''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.	+	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.	+	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.		A little further down, you see the access link to SAT, the 'Scene authoring tools'. We will use them later on.

Jaime Prilusky at 05:59, 18 September 2012

Jaime Prilusky — Tue, 18 Sep 2012 05:59:37 GMT

←Older revision		Revision as of 05:59, 18 September 2012
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	'''Note for teachers:'''		'''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 [http://proteopedia.org/support/~~proteopediaPrimer~~.doc here].	+	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 [http://proteopedia.org/support/ProteopediaPrimer.doc here].

	== A Proteopedia Worksheet ==		== A Proteopedia Worksheet ==

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 18:16:02 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 18:16, 14 September 2012
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	'''12. … and beyond, the real fun:'''		'''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. The files ‘colorGROUP’ and ‘colorSTRUCTURE’ you used during the exercise, are examples of simple~~ scenes. To create ~~a slightly~~ complicated ~~one~~, ~~open on~~ a ~~separated~~ web browser ~~page Proteopedia.org~~, click on ‘Help’ (top left) and then click on ‘Proteopedia:DIY:Scenes’.	+	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, ~~to have~~ 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'.	+	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.		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 ~~enough support for displaying~~ a rotating 3D structure and ~~interact~~ with it.	+	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.		You may also want to display an applet with complete Functional, Evolutionary and Structural information of a PDB file. The following line shows how.
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	<nowiki>{{STRUCTURE_1acj \| PDB=1acj}}</nowiki>		<nowiki>{{STRUCTURE_1acj \| PDB=1acj}}</nowiki>

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

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 18:10:59 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 18:10, 14 September 2012
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	'''9. Adding some explanations to the page:'''		'''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 ~~line <scene name='colorSTRUCTURE'>structure</scene>~~ and click 'Save page'. here's a suggestion:	+	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:
-		+	<blockquote>
-	Let us color the two main forms of regular ~~secondary~~	+	Let us color the two main forms of regular
-	<scene name='colorSTRUCTURE'>structure</scene>	+	<scene name='colorSTRUCTURE'>secondary structure</scene>
	in this protein. Alpha helix appears in red, beta sheet in yellow.		in this protein. Alpha helix appears in red, beta sheet in yellow.
-		+	</blockquote>

	'''10. Quiz anyone?'''		'''10. Quiz anyone?'''

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 18:04:53 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 18:04, 14 September 2012
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	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.		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.
		+	{{Template:ColorKey_Helix}},
		+	{{Template:ColorKey_Strand}},
		+	{{Template:ColorKey_Turn}}.

	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.		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.

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 18:00:49 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 18:00, 14 September 2012
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	<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>		<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>
	</blockquote>		</blockquote>
-	</li><li>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 {{...}}.	+	</li><li>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 <nowiki>{{...}}</nowiki>.
-	</~~li><li>~~	+	</li><li>In your green link, change 'TextToBeDisplayed' to something that describes the scene, such as 'N to C sequence'.
-	~~</li><li~~>	+	</li><li>Save your page.
-	</li><li>	+
-	</li><li>	+
	</li></ol>		</li></ol>

-	~~<nowiki><scene name='colorGROUP'>~~N to C ~~terminus</scene></nowiki>~~	+	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.

-	~~Your page should have now~~ a green link, ~~able to interact with the Jmol applet~~. ~~Click on it. The 3D model should display~~ a ~~rainbow coloring, from dark blue signaling the N-terminal (start of the chain) to the C-terminal (end of~~ the ~~chain)~~.	+	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.

-	~~Edit your page again, type this line below the previous one, and save.~~	+	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.
-		+
-	~~<nowiki><scene name='colorSTRUCTURE'>structure</scene></nowiki>~~	+
-		+
-	By clicking on ~~this~~ new link, you can distinguish clearly the two main types of secondary structure in this model: alpha helix and beta strand. This ~~schema~~ uses ~~six~~ different colors to distinguish four types of protein secondary structures (helices, beta strands and sheets, turns, and loops) and DNA vs. RNA.	+

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 17:49:56 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 17:49, 14 September 2012
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	<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>		<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>
	</blockquote>		</blockquote>
		+	</li><li>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 {{...}}.
		+	</li><li>
		+	</li><li>
		+	</li><li>
		+	</li><li>
	</li></ol>		</li></ol>

Eric Martz: /* A Proteopedia Worksheet */

Eric Martz — Fri, 14 Sep 2012 15:38:27 GMT

A Proteopedia Worksheet

←Older revision		Revision as of 15:38, 14 September 2012
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	</li></ol>		</li></ol>

-	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~~.	+	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.

-	*Open a new browser tab and go to Proteopedia.Org.	+	Let's insert a color key to explain this color scheme.
-	*Type 'color keys' in the Search slot at the left side of the page and Enter.	+	{{Template:ColorKey_Amino2CarboxyRainbow}}
-	*One of the pages found is Help:Color_Keys. Click on this.	+
-	*At the Color Keys page, click on 'N to C rainbows'. There, click on the link to 'DRuMS'.	+	<ol type="a" start="m">
-	*At DRuMS, click on Rainbows. Select one of the wikitext templates and copy it, such as	+	<li>Open a new browser tab and go to Proteopedia.Org.
		+	</li><li>Type 'color keys' in the Search slot at the left side of the page and Enter.
		+	</li><li>One of the pages found is Help:Color_Keys. Click on this.
		+	</li><li>At the Color Keys page, click on 'N to C rainbows'. There, click on the link to 'DRuMS'.
		+	</li><li>At DRuMS, click on Rainbows. Select one of the wikitext templates and copy it, such as
	<blockquote>		<blockquote>
	<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>		<nowiki>{{Template:ColorKey_Amino2CarboxyRainbow}}</nowiki>
	</blockquote>		</blockquote>
		+	</li></ol>

	<nowiki><scene name='colorGROUP'>N to C terminus</scene></nowiki>		<nowiki><scene name='colorGROUP'>N to C terminus</scene></nowiki>