// ===========================================================================
// 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 = true;
slabSliderLabel = "Cut"; // Optionally, may be changed to "Slab".

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

  // CHAPTER TITLE IS REQUIRED
chapterTitle = '7. MHC Class II';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = 'Human HLA-DR1';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
// Be sure to include paragraphs within <p></p> tags. This gives them margins.
chapterIntro =
	'<p> \n\
The peptide in this structure is \n\
<a href="http://en.wikipedia.org/wiki/Influenza_hemagglutinin" \n\
target="_blank">influenza hemagglutinin</a> \n\
306-318 (13 amino acids), \n\
<a href="http://proteopedia.org/wiki/index.php/Amino_Acids" \n\
title="Pro Lys Tyr Val  Lys Glu Asn Thr  Leu Lys Leu Ala Thr" \n\
target="_blank">PKYV KQNT LKLAT</a>. \n\
	<\/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";

  // Leave blank if this is the first chapter.
previousChapterButtonGoesTo = "../chapter06/chapter.htm";

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

  // If the View buttons define the orientation/zoom, no Replay/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.
	// For more explanation, see "Add Chapters ..." in the
	// Authoring Instructions.
provideResetButton = true; // ignored when isContents.

	// The next variable applies only when provideResetButton is true.
	// If showResetInitialViewButtonAtTop is true,
	// there will be a Replay/Reset button at the top of the page
	// as well as at the bottom. If false, it will be only at the bottom.
showResetInitialViewButtonAtTop = true;


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

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1dlh.pdb.gz", // ATOMIC COORDINATE FILE
		"script view00.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Polypeptide chains of MHC II. \n\
<br>&nbsp; &nbsp; <font color="#c3d3ff">Alpha Chain</font>,\n\
<br>&nbsp; &nbsp; <font color="#ffa0a0">Beta Chain</font>,\n\
<br>&nbsp; &nbsp; <font color="#009600">Antigenic Peptide</font>,\n\
<br>&nbsp; &nbsp; <font color="#FFC832">Disulfide bonds</font>.\n\
';

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

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

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
//	buttons[buttonNumber][iPreButtonText] =
//'[Optionally, pre-button text can go here.] \n\
//<br>';

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Structure of MHC II.\n\
<br>&nbsp; &nbsp;\n\
<font color="#009600"> <!--green, dkgreen-->\n\
	Antigenic Peptide,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#a04000"> <!--brown-->\n\
	Alpha chain, domain 1,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#887000"> <!--ckchartreuse-->\n\
	Alpha chain, domain 2,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#E08000"> <!--orange-->\n\
	Beta chain, domain 1,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#b01800"> <!--brick-->\n\
	Beta chain, domain 2,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#FFC832">\n\
	Disulfide bonds,\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<font color="#6000ff"> <!--violet-->\n\
	Carbohydrate.\n\
</font>\n\
\n\
<br>&nbsp; &nbsp;\n\
<div id="jcontrol1" name="jcontrol1"></div>\n\
';

	// MOLECULAR VIEW DETAILS
//	buttons[buttonNumber][iDetailsTitle] = "[Optional Details Title]";
//	buttons[buttonNumber][iDetailsText] =
//'[Optional details text goes here.]  \n\
//';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
//	buttons[buttonNumber][iPostButtonText] =
//	'<br> \n\
//[Optional post-button text goes here.] \n\
//';

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

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

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'T cell antigen receptor\'s view.<br><i>\
Use the above checkboxes here too!</i>\
<br><br><div id="jcontrol2" name="jcontrol2"></div>';

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

	setupButton(2,                 // NUMBER OF MOLECULES

		"../molecules4all/2vaa.pdb.gz", // ATOMIC COORDINATE FILE
		"script ../chapter06/view04.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningOff,  // spinningStart, spinningOn, spinningSame, or spinningOff

		"../molecules4all/1dlh.pdb.gz", // ATOMIC COORDINATE FILE
		"script view03.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningOff);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Epitope comparison: MHC I vs. II.';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
	buttons[buttonNumber][iPostButtonText] =
'<br><br><span class="lightGreenText"> \n\
<center>What do you see?</center> \n\
<ol start="17"><li> \n\
How many polypeptide chains make up the cleft of MHC II, \n\
<i>excluding the antigenic peptide</i>? \n\
</li><li> \n\
How many Ig-like domains are present in one molecule of MHC II? \n\
</li><li> \n\
How many sequence-invariant chains are present in MHC class II? \n\
</li><li> \n\
What holds the alpha and beta chains of class II together? \n\
</li><li> \n\
For MHC II, are the ends of the peptide buried or exposed? \n\
</li></ol> \n\
</span> \n\
';

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

	// CHAPTER CONCLUSION
//	chapterConclusion =
//	'<p> \n\
//[Optionally, conclusion text can go here.] \n\
//	<\/p> \n\
//';

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