// ===========================================================================
// This file, chapter.js, must be provided for each chapter.htm.
// Each chapter.js file contains the settings and content for one chapter.
// Each chapter should be in a separate directory (folder).
// Each chapter directory should contain one and only one chapter.htm file.
//
// Lines beginning "//" are comments for authors. They are ignored by JTAT.
// ===========================================================================

  // ========== SECTION I: PROVIDE SLIDERS? ============

  // These control whether this Chapter has a Slab ("Cut")
  // slider, in addition to a Zoom slider, or neither.
  // You cannot have a Slab slider without also having the Zoom slider.
  // The label on the slab slider (typically "Cut" or "Slab")
  // is defined in _jsutil/config2.js
showZoomSlider = true;
showSlabSlider = false;

  // ========== SECTION II: CHAPTER TITLE, INTRODUCTION ============

  // CHAPTER TITLE IS REQUIRED
chapterTitle = 'Subtitles, Replays, Images, and Text Everywhere.';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = '';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
// Be sure to include paragraphs within <p></p> tags. This gives them margins.
chapterIntro =
	'<p> \n\
Neuraminidase, on the surface of the influenza virus (see image below), \n\
is critical to its ability to infect cells. The type of neuraminidase \n\
on avian influenza (&quot;bird flu&quot;) is called &quot;N1&quot;. \n\
	<\/p> \n\
<a href="http://en.wikipedia.org/wiki/Influenza" \n\
title="Click for Influenza at Wikipedia" \n\
target="_blank"> \n\
\n\
	<center><img \n\
	src="../images4all/3d_influenza_virus.png"></a></center> \n\
	\n\
	<p><small><center> \n\
Click on image above for &quot;influenza&quot; \n\
at Wikipedia. \n\
	<br> \n\
(<a href="http://en.wikipedia.org/wiki/Image:3D_Influenza_virus.png"  \n\
target="_blank">Public domain image</a>.) \n\
	</center></small></p> \n\
	\n\
	<p> \n\
	<span class="aboutJTAT"> \n\
In addition to <i>Descriptions</i> of molecular views, separate \n\
paragraphs of text can be placed at the top or bottom of each chapter, and \n\
before or after molecular view buttons/descriptions. \n\
Hyperlinks and images can be placed wherever desired, \n\
including in <i>Details</i>. \n\
	</span> \n\
	<\/p> \n\
	\n\
	<p> \n\
	<span class="aboutJTAT"> \n\
Text here, between the Title and the Replay/Reset button, is called \n\
the chapter\'s Introduction. It is optional. \n\
	</span> \n\
	<span class="forAuthors"> \n\
It is defined in \n\
the variable <tt><big>chapterIntro</big></tt> (in jtat/tutorialName/chapterName/chapter.js). \n\
' + noIdea + '\n\
	<\/span><\/p> \n\
';

  // ========== SECTION III: NAVIGATION (NEXT, PREVIOUS, CONTENTS, RESET) ============

  // The 3 URL's below must be relative to the current chapter.
  // The position and style of the navigation bar are set in config.js

  // Leave blank if there is only one chapter, and no contents page.
contentsButtonGoesTo = "../contents/contents.htm";

  // If the View buttons define the orientation/zoom, 
  // no Reset button is needed, so provideResetButton should be false.
  // In contrast, some chapters are designed to maintain the orientation and
  // zoom set previously by the user when a new view is displayed.
  // These need a Reset button, so provideResetButton should be true.
  // When provided, a Reset button runs reset.spt in the chapter's directory.
  // It allows Reset to do something different than the "View 1" button does.
provideResetButton = true; // ignored when isContents.

  // Leave blank if this is the first chapter.
previousChapterButtonGoesTo = "../ch_view1/chapter.htm";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../ch_anims/chapter.htm";


  // ========== SECTION IV: MOLECULAR VIEW BUTTONS ============

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/2hu4_1mm.pdb", // ATOMIC COORDINATE FILE
		"script view01.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPreButtonText] =
'<i>Tamiflu</i> is an anti-viral drug being stockpiled around the \n\
world in case of a bird flu pandemic. \n\
	<span class="aboutJTAT"> \n\
This paragraph is an example of text placed before a molecular view button. \n\
	</span> \n\
	<span class="forAuthors"> \n\
It is defined in \n\
<tt><big>buttons[buttonNumber][iPreButtonText]</big></tt> \n\
(in chapterName/chapter.js). \n\
	</span> \n\
	<br>';

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Here is a \n\
	<span class="protein"> \n\
single protein chain \n\
	</span> \n\
of bird flu neuraminidase N1, complexed with \n\
	<span class="ligand"> \n\
tamiflu</span>. \n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Induced Fit..";
	buttons[buttonNumber][iDetailsText] =
'<center><b>Induced Fit</b></center> \n\
Tamiflu was designed to fit the neuriminadases N2 or N9. The \n\
structure of the binding \n\
pocket differs in N1, so it was surprising that tamiflu works on \n\
bird flu. The structure in View 1 \n\
(<a href="http://www.ncbi.nlm.nih.gov/pubmed/16915235" \n\
target="_blank">Russell <i>et al.</i>, 2005</a>) \n\
shows that it works by pulling \n\
one loop of the protein into position, that is, by &quot;induced fit&quot;. \n\
';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPostButtonText] =
	'<br><span class="aboutJTAT"> \n\
New tutorial users may click the <i>View 1</i> button first, \n\
not realizing that <i>View 1</i> is already showing. \n\
When you click any button for a view that is already showing, the legend <i>Now \n\
Showing View [Number]</i>, beneath the molecule at left, \n\
flashes in colors. <big><font color="yellow">Try it!</font></big> \n\
(This can be suppressed: See the chapter \n\
on <i>Animations</i>.) \n\
This paragraph is an example of text placed after a molecular view button. \n\
	</span> \n\
	<span class="forAuthors"> \n\
Text placed after the molecular view description is defined in \n\
<tt><big>buttons[buttonNumber][iPostButtonText]</big></tt> \n\
(in chapterName/chapter.js). \n\
	</span> \n\
';

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/2hu4_1mm.pdb", // ATOMIC COORDINATE FILE
		"script view02.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPreButtonText] =
'<center><big>Unexpected Cavity</big></center> \n\
	<br> \n\
	<span class="aboutJTAT"> \n\
<big>Subtitles:</big> \n\
Note that the option to place text before a view button can be \n\
used to insert a subtitle like the one just above. \n\
	</span><br> \n\
';

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'An unexpected <font color="#ffa600"><b>cavity (solid gold)</b></font>\n\
is present in the N1, adjacent to the bound tamiflu.\n\
This provides an opportunity to design better drugs, specific for bird flu.\n\
Tamiflu is shown as sticks colored by element: ' + element_key("c o n", "", ".");

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsText] =
'';

// End of View Buttons ===== ===== ===== ===== ===== ===== ===== ===== =====

	// CHAPTER CONCLUSION
	chapterConclusion =
	'<p><center><table width="85%" cellpadding="7" class="tnice"><tr>\n\
<td class="tdnice"> \n\
Elsewhere are available an \n\
<a href="http://www.umass.edu/molvis/martz/lectures/labmolgen07/n1tami.htm" \n\
target="_blank">introduction to avian influenza neuraminidase \n\
and tamiflu</a> and a related \n\
<a href="http://www.umass.edu/molvis/martz/lectures/labmolgen07/index.htm" \n\
target="_blank">lesson plan</a> with considerably more detail. \n\
	</td></tr></table></center></p> \n\
<p><span class="aboutJTAT"> \n\
The <i>Replay/Reset Initial View</i> buttons (at the top and bottom of \n\
this Control Panel) are optional. When each \n\
molecular view script specifies the molecule\'s orientation and zoom, they are \n\
unnecessary (as they are here). See Chapter 4 for an example where these \n\
buttons are omitted. In contrast, in \n\
Chapter 1, the orientation and zoom set by the user\'s \n\
mouse are maintained between views. This design benefits from \n\
having <i>Replay/Reset Initial View</i> buttons. \n\
	<span class="forAuthors"> \n\
Their presence is controlled by <tt><big>provideResetButton</big></tt> \n\
in chapter.js. \n\
	</span> \n\
<br><br> \n\
The box above and the previous paragraph (and this one) use the option for \n\
&quot;conclusion&quot; text, following the final molecular view button. \n\
	</span> \n\
	<span class="forAuthors"> \n\
The chapter\'s conclusion text is defined in \n\
the variable <tt><big>chapterConclusion</big></tt> (in chapter.js). \n\
	<\/span><\/p> \n\
';

  // ========== END OF chapter.js ============
