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

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

  // These control whether this Contents 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: TITLE, INTRODUCTION, CONTENTS, DETAILS ============

  // CONTENTS TITLE IS REQUIRED
chapterTitle = 'MHC: Contents';

	// CONTENTS SUBTITLE IS OPTIONAL
chapterSubtitle = '';

	// OPTIONAL INTRODUCTION FOR CONTENTS
	// Be sure to enclose paragraphs in <p>...</p>, or you will lose margins.
chapterIntro =
'<p> \n\
\"MHC\" stands for \n\
<a href="http://proteopedia.org/wiki/index.php/Major_Histocompatibility_Complex_Class_I" \n\
target="_blank"><i>Major Histocompatibility Complex</i></a>, \n\
a complex of genes coding for a family of proteins, \n\
many of which function in the immune system. This tutorial \n\
deals with two members of the family, MHC classes I and II. \n\
</p> \n\
';

	// OPTIONAL TOP DETAILS (IF TEXT IS BLANK, DETAILS LINK WILL NOT APPEAR.)
topContentsDetailsTitle = 'Why <i>histocompatibility</i>?';

topContentsDetailsText =
'MHC was so-named when it was found to play a crucial role\n\
in the rejection of tissue grafts. Later, it was recognized to have\n\
a fundamental role in the immune system.';


	// REQUIRED: LINKS TO EACH CHAPTER IN THIS TUTORIAL
contentsText = 
'<ol class="contents">\n\
<small><font color="#808080">\n\
	Introduction to Protein Visualization\n\
<small>\n\
   	<li> <a href="../chapter01/chapter.htm">Glycine Representations</a></li>\n\
\n\
   	<li> <a href="../chapter02/chapter.htm">Peptides and Backbones</a></li>\n\
\n\
   	<li> <a href="../chapter03/chapter.htm">Disulfide Bonds</a></li>\n\
</small></font></small>\n\
</ol>\n\
<span class="lightGreenText"><p> \n\
QUESTIONS to challenge your understanding apper in this green color \n\
in the chapters below. They are also \n\
<a href="../MHC-Questions.doc" \n\
target="_blank">available separately for printing handouts,\n\
LESSON PLAN included</a>. \n\
</p></span>\n\
<ol class="contents" start="4">\n\
  Class I MHC\n\
   	<li> <a href="../chapter04/chapter.htm">Extracellular Domains</a></li>\n\
\n\
   	<li> <a href="../chapter05/chapter.htm">Peptide-Binding Cleft</a></li>\n\
\n\
   	<li> <a href="../chapter06/chapter.htm">Peptides, Their Contacts & Epitopes</a></li>\n\
\n\
<br>\n\
  Class II MHC\n\
   	<li> <a href="../chapter07/chapter.htm">Extracellular Domains & Epitope</a></li>\n\
</ol>\n\
';

	// OPTIONAL BOTTOM DETAILS (IF TEXT IS BLANK '', DETAILS LINK WILL NOT APPEAR.)
//bottomContentsDetailsTitle = '[Optional Bottom Details Title]';

//bottomContentsDetailsText =
//'Optionally, bottom details can be put here.';

	// OPTIONAL BOTTOM TEXT
//chapterConclusion =
//'<p> \n\
//Optionally, "conclusion" 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 contents.
  // The position and style of the navigation bar are set in config.js

  // Leave blank since this IS the Contents.
contentsButtonGoesTo = '';

  // Leave blank since this is Contents.
previousChapterButtonGoesTo = "";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../chapter01/chapter.htm";

// provideResetButton is ignored when isContents.

  // ========== SECTION IV: MOLECULAR VIEW FOR CONTENTS ============

// Molecular View Button ===== ===== ===== ===== ===== ===== ===== ===== =====
// Although no "View 1" button will appear when isContents is true, 
// the molecular view is nevertheless specified as though it were a button.
// The "single molecular view" in the Contents page may contain more than
// one molecule (side by side: more than one Jmol) if you wish. See the
// Demo chapter on Comparisons.

setupButton(
	1,  // NUMBER OF MOLECULES
	'../molecules4all/2vab.pdb.gz', // ATOMIC COORDINATE FILE
	'script initial-view.spt', // SCRIPT FOR MOLECULAR VIEW
	blackBackground, // BACKGROUND (blackBackground or whiteBackground)
	spinningStart); // spinningStart, spinningOn, spinningSame, or spinningOff

  // ========== END OF contents.js ============
