// ===========================================================================
// 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 = 'Molecular Views, Descriptions, and Details.';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = '';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
chapterIntro =
'<p><span class="aboutJTAT"> \n\
As you can see illustrated below, \n\
each Chapter consists of a series of molecular <i><u>Views</u><\/i> designed by \n\
the author of the tutorial. Each view has a brief <i><u>Description</u><\/i>. \n\
Optionally, further <i><u>Details</u><\/i> can be provided for each view. \n\
<br><br> \n\
As you read this Chapter, please be sure to click each \n\
<i>Details..<\/i> link below! \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 = "";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../ch_view2/chapter.htm";


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

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
"This molecule consists of four chains. \n\
Each chain has a different pastel color. \n\
";

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view02.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'This molecule consists of two \n\
	<span class="protein"> \n\
protein chains \n\
	<\/span> \n\
 \n\
and two \n\
 \n\
	<span class="dna"> \n\
DNA chains\n\
	<\/span>. \n\n\
Each \n\
	<span class="protein"> \n\
protein chain \n\
	<\/span> \n\
recognizes a specific sequence of \n\
	<span class="dna"> \n\
DNA<\/span>. \n\n\
Small zinc-finger superfamily domains are inserted into the major groove of the \n\
	<span class="dna"> \n\
DNA\n\
	<\/span> \n\
where they perform sequence recognition. \n\n\
Each DNA sequence-recognizing domain is folded around two \n\
	<span class="ligand"> \n\
zinc ions \n\n\
	<\/span>. \n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsText] =
'In this experiment, \n\
<span class="ligand"> \n\
<b>cadmium ions<\/b><\/span> \n\
were substituted for zinc ions \n\
when the crystal was prepared. \n\
<br><br>\n\
<span class="aboutJTAT"> \n\
The use of color keys, text colored to match the corresponding \n\
molecular structures, is crucial for clarity. \n\
<span class="forAuthors">Methods for coloring text and adding \n\
standard color keys are explained in the \n\
<a href="../../_docs/jtatdocs.htm#drums" \n\
target="_blank">JTAT Tutorial Authoring Instructions</a>. \n\
</span><br><br>\n\
Optionally, details beyond the main description \n\
can be provided for each molecular view button. Notice that View 1 \n\
has no details. Details are intended for individuals studying \n\
the tutorial by themselves. Details would typically not be displayed \n\
by a lecturer showing the tutorial to an audience. Rather, the lecturer \n\
would explain the relevant details verbally. \n\
</span>';

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view03.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'When the atoms are shown in their spacefilling (van der Waals) \n\
diameters, the intimate contact between the \n\
<span class="protein"> \n\
	protein\n\
<\/span> \n\
 \n\
and \n\
 \n\
<span class="dna"> \n\
	DNA\n\
<\/span> \n\
is evident.\n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Standard Color Schemes..";
	buttons[buttonNumber][iDetailsText] =
	'<span class="aboutJTAT"> \n\
The color scheme used here is one of the standard color schemes \n\
supported by JTAT. These are displayed in the \n\
<a href="../ch_drums/chapter.htm">Chapter about Color Schemes</a> \n\
in this JTAT Demonstration Tutorial.\n\
	</span> \n\
	<span class="forAuthors">Methods for coloring text and adding \n\
standard color keys are explained in the \n\
<a href="../../_docs/jtatdocs.htm#drums" \n\
target="_blank">JTAT Tutorial Authoring Instructions</a>. \n\
	</span> \n\
	<br><br> \n\
<span class="aboutJTAT"> \n\
Each chapter in a JTAT tutorial can have as few or as many View buttons \n\
as needed. \n\
	</span> \n\
';


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