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

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

  // CHAPTER TITLE IS REQUIRED
chapterTitle = '6. Viral Peptides in MHC I';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = 'Mouse H-2K</sup>b</sup>';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
// Be sure to include paragraphs within <p></p> tags. This gives them margins.
chapterIntro = '';
//	'<p> \n\
//[Optionally, introductory text can go here.] \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 = "../chapter05/chapter.htm";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../chapter07/chapter.htm";

  // 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/2vab.pdb.gz", // ATOMIC COORDINATE FILE
		"script view01.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningOn);  // 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] =
'<a href="http://en.wikipedia.org/wiki/Sendai_virus" \n\
target="_blank">Sendai virus</a> \n\
nucleoprotein 324-332, nonamer \n\
<a href="http://proteopedia.org/wiki/index.php/Amino_Acids" \n\
title="Phe Ala Pro Gly Asn Tyr Pro Ala Leu" \n\
target="_blank">FAPGNYPAL</a>.\n\
<br> \n\
&nbsp; Buried: Tyr6, Leu9 \n\
<br> \n\
&nbsp; Up: Phe1, Asn5 \n\
<br> \n\
Peptide: ' + element_key("c n o") +
'<br> \n\
MHC: ' + ss_key() +
'<br><br><div id="jcontrol1" name="jcontrol1"></div>';

	// 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/2vaa.pdb.gz", // ATOMIC COORDINATE FILE
		"script view02.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningOn);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'<a href="http://en.wikipedia.org/wiki/Vesicular_stomatitis_virus" \n\
target="_blank">Vesicular stomatitis virus</a> \n\
nucleoprotein 52-59, octamer \n\
<a href="http://proteopedia.org/wiki/index.php/Amino_Acids" \n\
title="Arg Gly Tyr Val Tyr Gln Gly Leu" \n\
target="_blank">RGYVYQGL</a> \n\
<br> \n\
&nbsp; Buried: Tyr5, Leu8 \n\
<br> \n\
&nbsp; Up: Arg1, Val4, Gln6 \n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepboth.pdb", // ATOMIC COORDINATE FILE
		"script view03.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningOn);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Both peptides.\n\
<div id="jcontrol2" name="jcontrol2"></div>';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
	buttons[buttonNumber][iPostButtonText] =
'<span class="lightGreenText"> \n\
<center>What do you see?</center> \n\
<ol start="14"><li> \n\
How does a 9 amino acid chain fit in the same cleft as does an \n\
8 amino acid chain? \n\
</li><li> \n\
What two sidechains, identical for both peptides, point into the floor \n\
of the cleft? \n\
These are called\n\
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC42241/"\n\
target="_blank">anchor residues</a>.\n\
</li></ol> \n\
</span> \n\
';

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

	setupButton(2,                 // NUMBER OF MOLECULES

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

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

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Comparison of the two epitopes. ' + custom_polarity();

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
	buttons[buttonNumber][iPostButtonText] =
'<span class="lightGreenText"> \n\
<br><br><center>What do you see?</center> \n\
<ol start="16"> \n\
<li> \n\
How could a T lymphocyte distinguish these two peptides, \n\
from their exposed sidechains, as presented by MHC class I? \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 ============
