// ===========================================================================
// 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 = 'Comparing Molecules Side-by-Side';

  // CHAPTER SUBTITLE IS OPTIONAL
chapterSubtitle = '';

  // OPTIONAL INTRODUCTION FOR THIS CHAPTER
// Be sure to include paragraphs within <p></p> tags. This gives them margins.
chapterIntro =
	'<p><span class="aboutJTAT"> \n\
JTAT allows a view button to show 1, 2, 3, or 4 molecular views \n\
(Jmols). Contents pages can also have multiple molecules (not \n\
illustrated in this Demo). You can compare different views of the \n\
same molecule, or different molecules. When not spinning, \n\
rotation or zooming with the mouse is <i>synchronized</i> for all \n\
Jmols. \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 = false; // ignored when isContents.

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

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


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

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

	setupButton(2,  // NUMBER OF MOLECULES

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01a.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOn, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01b.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOn); // SPINNING (spinningOn, spinningSame, or spinningOff)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Two views of the same molecule. \
<center><table class="tnice" border="1" cellpadding="4"><tr><td class="tdnice"> \
1A. Cartoon view with each chain a distinct color. \
</td></tr><tr><td class="tdnice"> \
1B. Spacefilling: \
' + protein_key(", ") + dna_key(".") +
'</td></tr></table></center> \
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Synchronization..";
	buttons[buttonNumber][iDetailsText] =
'This view starts with the molecules spinning. Toggle spinning off \
(using the <i>toggle spinning</i> button beneath the molecules) \
and you will see that the <i>Synchronize</i> checkbox is automatically \
checked. Now, when you rotate or zoom either molecule with the mouse, \
the other one follows. \
<br><br> \
<span class="aboutJTAT"> \
Why are spinning and synchronization mutually exclusive in JTAT? \
Because the initial alignment is lost when synchronized mouse \
rotations are done while spinning. \
In fact, in order to maintain the initial alignment perfectly, \
it is best to leave spinning off at the outset of a view. \
</span> \
';

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

	setupButton(3,  // NUMBER OF MOLECULES

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01a.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01b.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view02c.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff); // SPINNING (spinningOn, spinningSame, or spinningOff)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Three views of the same molecule. \
<center><table class="tnice" border="1" cellpadding="4"> \
	<tr><td class="tdnice"> \
2A. Cartoon view with each chain a distinct color. \
	</td></tr><tr><td class="tdnice"> \
2B. Spacefilling: \
' + protein_key(", ") + dna_key(".") +
'</td></tr><tr><td class="tdnice"> \
2C. \
<span class="dna"> \
	DNA \
</span>\
decorated with \
<span class="protein"> \
	protein \
</span>\
and \
<span class="solvent"> \
	water \
</span>\
atoms within 4.0 &Aring;. \
	</td></tr> \
</table></center> \
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "More on Synchronization..";
	buttons[buttonNumber][iDetailsText] =
'Here, the molecules are NOT spinning at the start, so synchronization \
is checked. \
';

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

	setupButton(4,  // NUMBER OF MOLECULES

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01a.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view01b.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view02c.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view03d.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff); // SPINNING (spinningOn, spinningSame, or spinningOff)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Four views of the same molecule. \
<center><table class="tnice" border="1" cellpadding="4"> \
	<tr><td class="tdnice"> \
3A. Cartoon view with each chain a distinct color. \
	</td><td class="tdnice"> \
3B. Spacefilling: \
<span class="protein"> \
	Protein\
</span>, \
<span class="dna"> \
	DNA\
</span>. \
	</td></tr><tr><td class="tdnice"> \
3C. \
<span class="dna"> \
	DNA \
</span>, \
decorated with \
<span class="protein"> \
	protein \
</span> \
and \
<span class="solvent"> \
	water \
</span> \
atoms within 4.0 &Aring;. \
	</td><td class="tdnice"> \
3D. \
<span class="protein"> \
	Protein \
</span> \
decorated with \
<span class="dna"> \
	DNA\
</span> \
and \
<span class="solvent"> \
	water \
</span> \
atoms within 4.0 &Aring;. \
	</td></tr> \
</table></center> \
';

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

	setupButton(1,  // NUMBER OF MOLECULES

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view03d.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff); // SPINNING (spinningOn, spinningSame, or spinningOff)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Single molecule, to emphasize that single- and multiple-molecule \
views can co-exist on the same page. \
(<span class="protein">\
Protein \
</span> \
decorated with \
<span class="dna">\
	DNA\
</span> \
and \
<span class="solvent">\
	water \
</span> \
atoms within 4.0 &Aring;.) \
';

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

	setupButton(2,  // NUMBER OF MOLECULES

		"../molecules4all/1d66.pdb", // ATOMIC COORDINATE FILE
		"script view05.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff, // SPINNING (spinningOn, spinningSame, or spinningOff)

		"../molecules4all/1pyi.pdb", // ATOMIC COORDINATE FILE
		"script view05.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningOff); // SPINNING (spinningOn, spinningSame, or spinningOff)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'<span class="aboutJTAT">Jmol\'s synchronization works not only \
for different views of the same molecule, \
but also for views of different molecules (not aligned in their coordinate \
systems).</span> \
<center><table class="tnice" border="1" cellpadding="4"><tr><td class="tdnice"> \
1A. Gal4:DNA cartoon (1D66). \
</td></tr><tr><td class="tdnice"> \
1B. PPR1:DNA cartoon (1PYI). \
</td></tr></table></center> \
';

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

	// CHAPTER CONCLUSION
	chapterConclusion = 
	'<p><span class="aboutJTAT"> \n\
Note that this Chapter lacks <i>Replay/Reset Initial View</i> buttons. \n\
</span><span class="forAuthors"> \n\
(<tt><big>provideResetButton</big></tt> is false in chapter.js.) \n\
</span></p> \n\
';

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