// ===========================================================================
// 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 = 'Color Schemes: DRuMS';

  // 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\
<span class="aboutJTAT"> \n\
Careful selection of colors can help your structural views communicate \n\
effectively, and enhance their attractiveness. Except when there are \n\
compelling reasons to do otherwise, we recommend that you use the standard \n\
color schemes built into JTAT, which are based upon a standard named \n\
<a href="jtatdocs.htm#drums" \n\
target="_blank">DRuMS</a>. \n\
Below are examples illustrating these color schemes. \n\
</span> \n\
</p><p> \n\
<span class="forAuthors"> \n\
JTAT makes it easy to use these color schemes by providing scripts to \n\
color your molecules, ready-made color keys to explain your molecular \n\
views, and style sheets so you can apply the standard colors to text by \n\
naming them. For details on how to use these, please see the \n\
<a href="../../_docs/jtatdocs.htm#drums" \n\
target="_blank">Instructions for Authors</a>. \n\
</span> \n\
	<\/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_spin/chapter.htm";

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


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

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1s0v_2.mmol", // ATOMIC COORDINATE FILE
		"script view01.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningStart); // SPINNING (spinningStart/On/Same/Off)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Composition: '
+ composition_key(".") +
'<br> \n\
<p class="forAuthors" style="margin-left: 50px;"> \n\
Script: script ../../_drums/composition.spt \n\
<br> \n\
Color Key: composition_key(".") \n\
</p> \n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = 'What Is This?';
	buttons[buttonNumber][iDetailsText] =
'Not very many molecules in the \n\
<a href="http://proteopedia.org/wiki/index.php/Protein_Data_Bank" \n\
target="_blank">Protein Data Bank</a> \n\
have all five of protein, DNA, RNA, ligand, and solvent. This one \n\
is bacteriophage \n\
<a href="http://proteopedia.org/wiki/index.php/1s0v" \n\
target="_blank">T7 DNA-dependent RNA polymerase</a>. \n\
In this crystal structure, the \n\
<a href="http://proteopedia.org/wiki/index.php/Asymmetric_Unit" \n\
target="_blank">asymmetric unit</a> \n\
contained four copies. Shown here is \n\
<a href="http://www.ebi.ac.uk/msd-srv/pqs/pqs-bin/macmol.pl?filename=1S0V" \n\
target="_blank">copy 2</a>, \n\
separated by \n\
<a href="http://www.ebi.ac.uk/" \n\
target="_blank">EBI\'s Probable Quaternary Structure Server</a>. \n\
';

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1acf.pdb.gz", // ATOMIC COORDINATE FILE
		"script view02.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame); // SPINNING (spinningStart/On/Same/Off)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Secondary Structure: '
+ sst_key(".") +
'<p class="forAuthors" style="margin-left: 50px;"> \n\
Script: color structure \n\
<br> \n\
Color Key (with <q>Turn</q>): sst_key(".") \n\
<br> \n\
Color Key (witout <q>Turn</q>): ss_key(".") \n\
</p> \n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = 'Profilin; Turns?';
	buttons[buttonNumber][iDetailsText] =
'The molecule shown here is profilin \n\
(<a href="http://proteopedia.org/wiki/index.php/1acf" \n\
target="_blank">1acf</a>), \n\
an actin-binding protein involved in microfilament dyanamics. \n\
It is unusual that the authors of this model designated the \n\
<span class="turn">turns</span>. While it is routine for authors \n\
of protein models to designate <span class="helix">alpha helices</span>\n\
and <span class="strand">beta strands</span>, <span class="turn">turns</span> \n\
are specified in only about 4% of models in the PDB. Jmol shows \n\
secondary structure according to the HELIX, SHEET, and TURN records \n\
placed in the PDB file header by its authors. As of summer, 2008, \n\
Jmol\'s internal calculation of secondary structure is flawed. The best \n\
way to color turns in models lacking TURN records is to add such records. \n\
';

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1r3j_opm.pdb", // ATOMIC COORDINATE FILE
		"script view03.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame); // SPINNING (spinningStart/On/Same/Off)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Potassium channel (1r3j): \n\
<br><p style="margin-left: 25px;"> \n\ '
+ polarity2_key(".") +
'</p><p class="forAuthors" style="margin-left: 50px;"> \n\
Script: script ../../_drums/polarity2.spt \n\
<br> \n\
Color Key: polarity2_key(".") \n\
</p> \n\
';

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

	setupButton(1,  // NUMBER OF MOLECULES
		"../molecules4all/1r3j_opm.pdb", // ATOMIC COORDINATE FILE
		"script view04.spt;", // VIEW SCRIPT
		blackBackground, // BACKGROUND (blackBackground or whiteBackground)
		spinningSame); // SPINNING (spinningStart/On/Same/Off)

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'Potassium channel (1r3j) showing how the extensive hydrophobic \n\
region encircling the molecule fits between the predicted \n\
<span class="o">extracellular</span> and \n\
<span class="n">intracellular</span> lipid membrane/water boundaries. \n\
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = 'Membrane Planes';
	buttons[buttonNumber][iDetailsText] =
'Prediction of the membrane planes was done by the <i>Orientations \n\
of Proteins in Membranes (OPM) Server</i>, courtesy of the University \n\
of Michigan. This model, containing pseudo-atoms representing the \n\
predicted membrane planes, was downloaded from \n\
<a href="http://opm.phar.umich.edu/protein.php?pdbid=1r3j" \n\
target="_blank">OPM\'s page on the potassium channel</a>. \n\
';

	// TEXT AFTER MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iPostButtonText] =
	'<br> \n\
For instructions on how to apply \n\
<span class="o">arbitrary</span> \n\
<span class="n">colors</span> \n\
to text, please see the \n\
<a href="../../_docs/jtatdocs.htm#drumskeys" \n\
target="_blank">Instructions for Authors</a>. \n\
';

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

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

	// MOLECULAR VIEW DESCRIPTION
	buttons[buttonNumber][iButtonText] =
'<font color="red">This view</font> will always start out NOT spinning. \
This is useful when the author wants to show a particular perspective. \
In the perspective shown here, the major and minor grooves in the DNA \
double helix can be distinguished along the top of the DNA. \
';

	// MOLECULAR VIEW DETAILS
	buttons[buttonNumber][iDetailsTitle] = "Implementation..";
	buttons[buttonNumber][iDetailsText] =
'<span class="forAuthors">The initial spinning status for each View \
button is specified with a parameter \
in the setupButton() function call. The parameter must be one of \
three options: <i>spinningStart, spinningOn, spinningSame</i>, or \
<i>spinningOff</i>. '
+ noIdea +
'</span>\
';


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

	// CHAPTER CONCLUSION
	chapterConclusion =
	'<p> \n\
	<span class="forAuthors"> \n\
You should never put a <i>spin on</i> or <i>spin off</i> command in a \n\
Jmol command script (.spt file). Doing so would interfere with JTAT\'s \n\
spin controls. \n\
	</span> \n\
	<\/p> \n\
';

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