// ===========================================================================
// 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 = '2. Peptides and Backbones';

  // 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> \n\
Element colors: ' + element_key("c n o h") +
'	<\/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 = "../chapter01/chapter.htm";

  // Leave blank if this is the last chapter.
nextChapterButtonGoesTo = "../chapter03/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 = false; // 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/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view01.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// TEXT BEFORE MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPreButtonText] = '';

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'This is the backbone (main chain) of 1 amino acid (AA).';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "";
	buttons[buttonNumber][iDetailsText] = '';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION AND DETAILS
	buttons[buttonNumber][iPostButtonText] = '';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view02.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Adding an AA to each end of the first AA gives a tripeptide (3 AAs). \n\
Atoms forming peptide bonds are marked with translucent spheres. \n\
(No sidechains are shown, and most hydrogens are omitted.) \n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view03.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Now each AA has a <font color="yellow">1-carbon sidechain (yellow halos)\n\
</font>, so we have Ala-Ala-Ala (tri-alanine, AAA in\n\
<a href="http://firstglance.jmol.org/notes.htm#aanames"\n\
target="_blank">one-letter code</a>).\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view04.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Adding a <font color="yellow">lysine sidechain</font> to the\n\
1st AA gives Lys-Ala-Ala (KAA). \n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view05.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Adding <font color="yellow">3 carbons</font> to the\n\
3rd AA gives isoleucine, Lys-Ala-Ile (KAI). \n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view06.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Adding <font color="yellow">threonine</font> to the\n\
N terminus gives the tetrapeptide Lys-Ala-Ile-Thr (KAIT). \n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view07.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Here is the shape of the tetrapeptide.\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view08.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'The stick representation has too much detail for larger polypeptides\n\
(proteins), so the <font color="yellow">alpha-carbons</font> are connected\n\
with a schematic line called a\n\
<font color="#00ff00">BACKBONE</font> trace.\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/pepb27_4.pdb", // ATOMIC COORDINATE FILE
		"script view09.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Showing only the <font color="#00ff00">backbone</font> trace\n\
looks silly for a tetrapeptide, but that is the level of simplification\n\
needed to understand the structure of a protein.\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1pgb.pdb.gz", // ATOMIC COORDINATE FILE
		"script view10.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'For comparison, here is a very small protein (56 AAs, 6 kD) as sticks.\n\
460 non-hydrogen atoms are shown. Hydrogens are almost exactly half of the\n\
atoms in proteins, so with hydrogens, there would be about 900 atoms.\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1pgb.pdb.gz", // ATOMIC COORDINATE FILE
		"script view11.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Here is the <font color="#00ff00">backbone</font> trace\n\
for the 56 AA protein.\n\
';

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1pgb.pdb.gz", // ATOMIC COORDINATE FILE
		"script view12.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Now the backbone trace is colored by secondary structure:\n\
' + ss_key();

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

	setupButton(1,                 // NUMBER OF MOLECULES
		"../molecules4all/1pgb.pdb.gz", // ATOMIC COORDINATE FILE
		"script view13.spt;",        // VIEW SCRIPT
		blackBackground, // blackBackground or whiteBackground
		spinningStart);  // spinningStart, spinningOn, spinningSame, or spinningOff

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Here, the backbone trace is represented as a smoothed, secondary\n\
structure ribbon schematic. Arrowheads point towards the C terminus.\n\
';

// ===== ===== ===== ===== ===== ===== ===== ===== =====
// YOU MAY ADD BELOW AS MANY VIEW BUTTONS AS YOU WISH SIMPLY BY COPYING THE
// Molecular View Button BLOCK FOR EACH ONE.
// ===== ===== ===== ===== ===== ===== ===== ===== =====

// Insert additional molecular view buttons here, as needed.


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

	// CHAPTER CONCLUSION
	chapterConclusion =
	'<p> \n\
[Optionally, conclusion text can go here.] \n\
	<\/p> \n\
';

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