// ===========================================================================
// 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 and Descriptions.';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = '(Chapter 1 with a white background.)';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
chapterIntro =
	'<p><span class="aboutJTATwb"> \
In order to demonstrat a white background, this Chapter \n\
is a copy of Chapter 1 (with the Details removed), presented. \n\
on a white background. \n\
The colors that JTAT provides for text color keys, such as for \n\
</span>\
<span class="protein"> \
protein \
</span>\
<span class="aboutJTATwb"> \
and \
</span>\
<span class="dna"> \
DNA\
</span>\
<span class="aboutJTATwb">, \
have, in some cases, been darkened slightly so as to be \
readable on either a black or a white background. \
In these cases, the corresponding colors applied to the molecule can be lighter \
because they are depth-shaded into darker values automatically by Jmol. \
	<\/span></p> \
';

  // ========== 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_bkg/contents.htm";

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


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

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

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

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

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

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

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'This molecule consists of two \
<span class="protein"> \
	protein chains \
<\/span> \
 \
and two \
 \
<span class="dna"> \
	DNA chains\
<\/span>\
. Each DNA sequence-recognizing domain is folded around two \
<span class="ligand"> \
	zinc ions<\/span>, \
and binds in the major groove of the DNA. \
';

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view03.spt;", // VIEW SCRIPT
		whiteBackground, // 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) \
diameters, the intimate contact between the \
<span class="protein"> \
	protein\
<\/span> \
 \
and \
 \
<span class="dna"> \
	DNA\
<\/span> \
is evident.\
';

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