// Help for Molecule Information Tab (also much of it is in moltab.js)
// debug through # 6

/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeOccupanciesAltLoc()
{
	var oal = '';
	var oalmin = Math.round(100. * occAltLocMin);
	var oalmax = Math.round(100. * occAltLocMax);

	if (!altLocCount || occAll100) return ".";

	var occslink = '<a href="javascript: showOccupancyReport()">occupancies</a>';

	if (occAltLocConstant)
	{
		oal += ', all with ' + occslink + ' of ' + oalmin + "%.";
	}
	else
	{
		oal += ' with ' + occslink + ' of ' + oalmin + "-" +
		oalmax + "%.";
	}

	return oal;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeOccupanciesSummary()
{
	var occsum = "";
	var occlink = "<a href='javascript: showOccupancyReport()'>Occupancy</a>";

	// no atoms without altlocs
	if (!jmolEvaluate("{%}.count")) return occsum;

	// all atoms 100% occupancy
  if (occAll100)
	{
		occsum += occlink + " is 100% for all atoms.";
		return occsum;
	}

	var range; // NAL = Not AltLoc (We've already returned blank if NAL==0)
	if (occNALConstant)
		range = '(namely ' + Math.round(100. * occNALMin) + '%) ';
	else
		range = '(range ' + Math.round(100. * occNALMin) + '-' + Math.round(100. * occNALMax) + '%) ';

	// SOME OCC < 100%
	if (!altLocCount) // all atoms lack altLocs
	{
		occsum += occlink + " is &lt;100% " +
			range +
			"for " + numberWithCommas(occ0to991Loc) + " atoms (" +
			occ0to991LocPct + "% of " + numberWithCommas(allAtomM1C1Count) + " total atoms).";
	}
	else // for the remaining non-altlocs (all the single-location atoms)
	{
		var forRemaining = " for the remaining " +
				numberWithCommas(allAtomM1C1Count - altLocC1Count) + " atoms.";

		if (occNALConstant && (occNALMin == 1.0))
			occsum += occlink + " is 100% " + forRemaining;

		else
		{
			var orange;
			if (occNALConstant)
					orange = "" + Math.round(100. * occNALMin) + "%";
			else
					orange = "" + Math.round(100. * occNALMin) + "-" + (100. * occNALMax) + "%";

			occsum += occlink + ' is ' + orange + forRemaining;
		}
	}

	return (occsum);	
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeOccupancyReport()
{
	return(makeOccupancyReport2());

	// No longer necessary since I decided not to include the column with locations/atom.
	// See getLPA()
	/*
	if (!altLocCount) return(makeOccupancyReport2());

	if (!altLocFreqsGotten)
	{
		setTimeout("getAltLocFreqs('')", 50);
		return altLocOneMoment;
	}
	else return(makeOccupancyReport2());
	*/
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var POWALNonWater;
var POWALWater;

function makeOccupancyReport2()
{

	// INTRODUCTION

	var occrep = "<center><b>Occupancy</b><br>";

	var altloclink1 =
		"<a href='javascript: showAltLocHelp()'>alternate locations</a>.";
	var altloclink2 =
		"<a href='javascript: showAltLocHelp()'>alternate locations in this model</a>.";
	var atloc = 's'; // when no AltLocs 'atoms'
	if (altLocCount) atloc = ' <i>locations</i>'; 'atom locations'

	if (altLocCount)
		occrep += 'In the <i><b>Atom location</b></i> counts below, ' +
			'every location will be counted for atoms with ' +
			altloclink1 +
			' The location count will exceed the number of atoms in a single conformation.';

	//	else // there are no altlocs
	//		occrep += 'Since there are no atoms with alternate locations here, ' +
	//		'counts of <i>atom locations</i> are equal to counts of atoms.';

	occrep += "</center><br>";	

	if (occAll100)
		occrep += "<b>All atoms have 100% occupancy in this model.</b>";
	else
	{
		occrep += "<b>" + numberWithCommas(occ0to99) +
			" atom" + atloc + "</b> in this model (" +
			occ0to99Pct + "% of " + atomLocationsCount +
			" total atom" + atloc + ") have partial occupancies.";

		// List All
		occrep += ' <a href="javascript: listPartialOccupancy()">' +
			'<span style="background:yellow;border-style:solid;border-width:1px;border-radius:3px;\
padding:2px 4px 3px 4px;">' +
			'&nbsp;List&nbsp;all&nbsp;</span></a>.';
	}

	occrep += "<br><br>";

	if (match(expMethod, "nmr")) occrep +=
'This model was determined by NMR. The occupancy value has no standard meaning for \
NMR results, and is usually set uniformly to 1.0 (100%). \
<br><br> \
The following information applies to X-ray crystallographic models. \
<br><br> \
<font color="gray"> \
';

	occrep +=
'Sometimes the \
<a href="http://proteopedia.org/w/Electron_density_map" \n\
target="_href">electron density map</a> from \n\
<a href="http://proteopedia.org/w/X-ray_crystallography" \n\
target="_href">X-ray crystallography</a> \n\
resolves two (or more) locations for a single atom (or amino acid side chain). This means that \n\
the atom occupies alternate locations in \n\
different copies of the molecule in the crystal. In such a case, each location \n\
has partial occupancy, and the occupancies for all locations should sum to 1.0 (100%). \n\
<br><br> \n\
In some cases*, particularly for water oxygens, only one location may be given, \n\
but assigned partial occupancy based on the intensity of the electron density map. \n\
';

	if (altLocCount == 0)
		occrep += "<br><br>There are no atoms with " + altloclink2;
	else
		occrep += "<br><br>See also " + altloclink2;

	if (!occAll100) occrep += makeOccupanciesTables();


	// EXAMPLES

	occrep += "<br><br>Examples:<ul>" +
'<li><a href="fg.htm?mol=9ins" target="_blank">9ins</a>: ' +
'Water atoms with partial occupancy and no alternate locations.</li>' +
'<li><a href="fg.htm?mol=2fgl" target="_blank">2fgl</a>: ' +
'118 non-water atoms with occupancies of 50-80%, no \
alternate locations, and some with average temperatures.</li>' +
'<li><a href="fg.htm?mol=1evv" target="_blank">1evv</a>: ' +
'27 non-water atoms and 94 water atoms with occupancies of 1-99% with no ' +
'alternate locations.' +
'<li><a href="fg.htm?mol=1sjv" target="_blank">1sjv</a>: ' +
'Three atoms of Asp68 modeled with zero occupancy, temperature 32-36.</li>' +
'<li>See additional examples under ' +
'<a href="javascript: showAltLocHelp()">alternate locations</a>.' +
'</ul>';

	return occrep;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeOccupanciesTables()
{
	var occrep = '';

	// NON-WATER OCCUPANCY

	occrep += '<br><br><center><b>For ';
	if (altLocCount == 0)
		occrep += numberWithCommas(allAtomM1C1Count - waterCount) + ' non-water atoms';
	else
		occrep += numberWithCommas(nonWaterLocationsCount) + ' non-water atom <i>locations</i>';
	occrep += ":</b>\n</center>\n";

	var inModel1 = "";
		if (modelCount > 1)
			 inModel1 = " in model 1";
	//	occrep += inModel1 + "</b>";

	occVal.length = occCount.length = 0;
	//occList = jmolEvaluate("{model=1 and not water}.occupancy.all.sort"); ALPHAFolD
	occList = jmolEvaluate("{not water}.occupancy.all.sort");
	occList = fixJmolList(occList);
	countOccupancies();

	var clickocc = "";

	// We already know !occAll100, but one of the 2 tables may have only occ=1.0
	//	if (occVal[0] != "1.0")
	//	{
		clickocc +=
'1. Optional: \
<a href="javascript: occView(\'occNonWaterNoH\')"><b>Show</b> All** Non-Water Atoms</a>, ';

		clickocc += "then<br>\
2. <b>Click</b> on occupancy values below to <i>Find</i> the corresponding atoms. ";

		if (toFind != "")
		{
			clickocc += '<b>Scroll to the top of this panel to see the <i>Find</i> query.</b> ';
			clickocc += '<center><a href="javascript: clearOccupancy()">Clear Halos</a></center>';
		}
		//		else
		//			clickocc += '<br><br>';

		clickocc += "Touching or clicking on an atom will report its occupancy.";
		//	}

	occrep += makeOccTable("not water", clickocc); // <<<<< TABLE

	//	alert("help1.js #1 occVal[0] = " + occVal[0] + "\n occVal.length = " + occVal.length);
	//  alert("help1.js #1a typeof(occVal[0]) = " + typeof(occVal[0])); STRING

	// WATER OCCUPANCY

	var wml = "water molecules";
	var wlc = numberWithCommas(waterCount);
	if (altLocCount > 0)
	{
		wml = "water molecule <i>locations</i>";
		wlc = numberWithCommas(waterLocationsCount);
	}

	if (waterCount == 0)
			occrep += "<br><br>There is no water in this model.<br><br>";
	else
	{
		occrep += '<br><center><b>For ' + wlc +
			' ' + wml + inModel1 + "</b>";

		//		if (altLocWaterCount > 0)
		//			occrep += "<br>(including water in <a href='javascript: showAltLocHelp()'>alternate" +
		//		" locations</a>)";

		occrep += ":\n</center>\n"

		occVal.length = occCount.length = 0;
		//occList = jmolEvaluate("{model=1 and water}.occupancy.all.sort"); // alphafold
		occList = jmolEvaluate("{water}.occupancy.all.sort");
		occList = fixJmolList(occList);
		countOccupancies();

		clickocc = "";
		// We already know !occAll100, but one of the 2 tables may have only occ=1.0
		//		if (occVal[0] != "1.0")
		//		{
			clickocc +=
				'1. <a href="javascript: occView(\'occWater\')">Show All Atoms** Including Water</a>, ';	

			clickocc += "then<br>\
2. Click on occupancy values below to <i>Find</i> the corresponding atoms. ";

			clickocc += "Touching or clicking on an atom will report its occupancy.";
		}

		occrep += makeOccTable("water", clickocc);
		//	}

	// END WATER
	// BEGIN PARTIAL OCCUPANCY WITHOUT ALTLOC

	// POWAL: Partial Occupancy Without Alternate Locations

	occrep += '<br><br>';

	if (occAll100) occrep +=
	 '*No atoms in this model have partial occupancy.<br><br>';
	
	else if ((POWALNonWater + POWALWater) == 0) occrep +=
'*No atoms in this model have partial occupancy without alternate locations.<br><br>';
	else
	{
		if (POWALNonWater == 0)
		{
			occrep +=
'*<a href="javascript: findPOWALWater()">\
Find all ' + POWALWater + ' atoms</a> that have ' +
'partial occupancies without alternate locations.';

			occrep += " In this model, all of them are water atoms.<br><br>";
		}
		else
		{
			occrep += "*Find all atoms that have partial occupancy without alternate locations:" +
				'<ul><li><a href="javascript: findPOWALNonWater()">' + POWALNonWater +
					' non-water atoms</a>.</li>';
			if (POWALWater > 0) occrep +=
				'<li><a href="javascript: findPOWALWater()">' + POWALWater +
				' water atoms</a>.';
			occrep += '</li></ul>';
		}
	}

	if (match(expMethod, "nmr")) occrep += "</font>";

	if (occ0to99 > 0)
		occrep += '**The above &quot;Show All&quot; views are the same as \n\
<i>Vines/Sticks</i> in the <i>Views</i> tab, with <i>More detail</i> \n\
and <i>Hide Hydrogen</i>  checked.';

	return occrep;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function occView(mode)
{
		// mode: occNonWater, occNonWaterNoH, occWater,
		// ALNonWater, ALNonWaterNoH, ALWater (AL = AltLoc)
		var vv = mode;
		var hh = mode.charAt(0);

		if (hh == "A")		
		{
			if (match(mode, "noh"))
				mode = "occNonWaterNoH";
			else if (match(mode, "nonwater"))
				mode = "occNonWater";
			else
				mode = "occWater";
		}
		doViewNoHelp(mode); // mode must be occ...

		if (hh == "o")
			showOccupancyReport();
		else // AL
			showAltLocHelp();
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function findPOWALWater()
{
		findOccupancy("water and altloc='' and occupancy < 1.0"); // all models
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function findPOWALNonWater()
{
		findOccupancy("altloc='' and occupancy < 1.0 and not water");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var occTableColorKeyDone = false;
var allowOccCompress = true;
var occTableColorKey;

function makeOccTable(subset, clickhelp)
{
	var occrep = "";
	var col3 = "";
	var col3head = "";
	var rowcount = occVal.length;
	var lpa;
	var doFifths = false;
	if (rowcount > 8) doFifths = true;
	var compress = false;
	if (rowcount > 12 && allowOccCompress) compress = true;
	if (occVal.length > 1) rowcount++; // add row for "All < 1.0"

	getALCodes(); // array of altloc codes ALCodes[]

	occTableColorKeyDone = false;

	var colorkey =
			'<big><big><b>' +
			coloredElements1 +
			'</b></big>' +
			' <a href="http://jmol.sourceforge.net/jscolors/#Atoms" target="_blank"><font color="#c0c0c0">more elements..</font></a> ' +
			'</big>';

	if (match(currentView, "vine"))
	{
		col3head = "<td>Color Key</td>";
		col3 = '<td rowspan="' + rowcount + '" bgcolor="black" width="75" valign="top">';
		col3 += colorkey; // guarantee one
		var max = rowcount/5;
		if (compress) max = 1;
		for (var cki = 2; cki <= max; cki++)
		{
			if (cki > 1) col3 += "<br><br><br><br><br><br><br><br><br>";
			col3 += colorkey;
		}
		col3 += '</td>';
	}
	occTableColorKey = col3;

	var ac = "Atom Count";
	if (altLocCount > 0) ac = "Atom Location Count";

	// BEGIN TABLE
	occrep +=	'<center><table cellpadding="6" bgcolor="#e0e0e0" border="1" width="80%"><tr>' +
		'<td colspan="4">' + clickhelp + '</td></tr><tr>' +
		'<td>Occupancy</td>' +
			//		'<td>Locations<br>per Atom</td>' +
		'<td>AltLoc Codes</td>' +
		'<td><center>' + ac + '</center></td>' + col3head + '</tr>';

	var range0, range2, range4, range6, range8 = false;

	for (i=0; i < occVal.length; i++)
	{
		// Insert <1.0 before 1.0
		if (occVal[i] == 1.0 && occVal.length > 2)
		{
			if (compress)
			{
				if (!range0) // there are none in range0
					{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
				if (!range2)
					occrep += insertFifth(0.21, 0.40, subset); range2 = true;
				if (!range4)
					occrep += insertFifth(0.41, 0.60, subset); range4 = true;
				if (!range6)
					occrep += insertFifth(0.61, 0.80, subset); range6 = true;
				if (!range8)
					occrep += insertFifth(0.81, 0.99, subset); range8 = true;
			}

			allocc = occ0to99NonWater;
			if (subset == "water") allocc = occ0to99Water;

			occrep += '<tr><td><a href="javascript: findOccupancy(\'' + subset +
					' and occupancy<1.0\')"><b>All &lt; 1.0</b></a></td>';

			occrep += '<td><b>' + getOccAltLocs("occupancy<1.0", subset) + '</b></td>';

			occrep += '<td><center><b>' +
					numberWithCommas(allocc) + '</b></center></td></tr>';
		}

		// Insert ranges: Fifths
		if (compress)
		{
			if (occVal[i] >= 0.81 && !range8)
			{
				if (!range0) // there are none in range0
					{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
				if (!range2)
					occrep += insertFifth(0.21, 0.40, subset); range2 = true;
				if (!range4)
					occrep += insertFifth(0.41, 0.60, subset); range4 = true;
				if (!range6)
					occrep += insertFifth(0.61, 0.80, subset); range6 = true;
				occrep += insertFifth(0.81, 0.99, subset); range8 = true;
			}
			else if (occVal[i] >= 0.61 && !range6)
			{
				if (!range0) // there are none in range0
					{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
				if (!range2)
					occrep += insertFifth(0.21, 0.40, subset); range2 = true;
				if (!range4)
					occrep += insertFifth(0.41, 0.60, subset); range4 = true;
				occrep += insertFifth(0.61, 0.80, subset); range6 = true;
			}
			else if (occVal[i] >= 0.41 && !range4)
			{
				if (!range0) // there are none in range0
					{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
				if (!range2)
					occrep += insertFifth(0.21, 0.40, subset); range2 = true;
				occrep += insertFifth(0.41, 0.60, subset); range4 = true;
			}
			else if (occVal[i] >= 0.21 && !range2)
			{
				if (!range0) // there are none in range0
					{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
				occrep += insertFifth(0.21, 0.40, subset); range2 = true;
			}
			else if (occVal[i] >= 0.01 && !range0)
				{occrep += insertFifth(0.01, 0.20, subset); range0 = true;}
		}

		if (!compress || occVal[i] == 0.0 || occVal[i] == 1.0)
		{
			// Occupancy value linked
			occrep += '<tr><td><a href="javascript: findOccupancy(\'' + subset +
				' and occupancy=' + occVal[i] + '\')">' +
					occVal[i] + '</a></td>';

			// Locations/atom
			//		lpa = getLPA(occVal[i], subset);
			//		occrep += '<td align="center">' + lpa +'</td>';

			occrep += '<td>' + getOccAltLocs("occupancy=" + occVal[i], subset) + '</td>';

			// Count for this occupancy value
			occrep += '<td><center>' + numberWithCommas(occCount[i]) + '</center></td>';

			// Optional color key column 3
			if (i == 0) {occrep += col3; occTableColorKeyDone = true;}

			occrep += '</tr>';
		}
	}

	if (compress)
	{
		occrep += '<tr><td colspan=4><a href=' +
		'"javascript: allowOccCompress = false; showOccupancyReport();">' +
		'List all ' + occVal.length + ' individual occupancy values</a>.</td>';
		occrep += '</tr>';
	}
	if (!allowOccCompress)
	{
		occrep += '<tr><td colspan=4><a href=' +
		'"javascript: allowOccCompress = true; showOccupancyReport();">' +
		'List only five ranges of occupancy values</a>.</td>';
		occrep += '</tr>';
	}

	occrep += '</table></center>';

	return occrep;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function insertFifth(low, high, subset)
{
	var fif = '';

	var occrange = "occupancy >= " + low + " and occupancy <= " + high;

	fif += '<tr><td><a href="javascript: findOccupancy(\'' + subset +
			' and ' + occrange + '\')"><b>' + low + '-' + high.toFixed(2) + '</b></a></td>';

	fif += '<td><b>' + getOccAltLocs(occrange, subset) + '</b></td>';

	var orc = jmolAtomCountAllConfigs(subset + ' and ' + occrange);
	fif += '<td><b><center>' +
			numberWithCommas(orc) + '</center></b></td>';

	//	alert(occTableColorKeyDone);
	//	alert(occTableColorKey);
	if (!occTableColorKeyDone)
	{
		fif += occTableColorKey;
		occTableColorKeyDone = true;
	}

	fif += '</tr>';

	return fif;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function getOccAltLocs(occ, subset) // occval includes = or < + value
{
	var ovl = ''

	if (jmolAtomCountAllConfigs(occ + " and % and " + subset))
		ovl += 'None';

	//	alert("help1.js #4a: ALCodes.length=" + ALCodes.length + " ALCodes=" + ALCodes);
	

	if (altLocCount)
	{
		for (var alci = 0; alci < ALCodes.length; alci++)
		{
			var occal = occ + " and %" + ALCodes[alci] + " and " + subset;
			var occalcount = jmolAtomCountAllConfigs(occal);
			//		alert("help1.js #4: occal=" + occal + "\noccalcount=" + occalcount);
			if (occalcount)
			{
				if (ovl.length) ovl += ',';
				ovl += ALCodes[alci];
			}
		}
	}

	return ovl;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// I think this is working, tested for FGiJ 2.85, but
// I don't think its useful. Very confusing. Blank when no altloc codes.
/*
function getLPA(occval, subset)
{
	// subset is "water" or "not water"
	var lpa = '';
	var ocount = new Array();
	var oi = 0;

	var occsub = (jmolEvaluate("{!% and occupancy=" + occval + " and " + subset + "}.count"))
			//	alert("help1.js #3a: occval=" + occval + " subset=" + subset + " freq=" + occsub);
	if (occsub)
	{
		for (var xi = 1; xi <= 5; xi++)
		{
			ocount[xi] = jmolEvaluate("{occupancy=" + occval + " and ~altloc" + xi + "list and " +
				subset + "}.count");
			
			//			if (occval == 0.5)
			//						alert("help1.js #3: occval=" + occval + " lpa=" + xi + " ocount[xi]=" + ocount[xi]);

			if (ocount[xi])
			{
				if (oi) lpa += ",";
				lpa += xi;
				oi++;
			}
		}
	}

	return lpa;
}
*/
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function findOccupancy(query)
{
		//	findNoHelp(query + " #allconformations"); // in findOccupancy()
	findNoHelp(query); // in findOccupancy()
	showOccupancyReport(); // refresh help to add "Halos around:" at top.
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function clearOccupancy()
{
	clearFindNoHelp();
	showOccupancyReport(); // refresh help to remove "Halos around:" at top.
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function showOccupancyReport()
{
	cancelPendingAndShowHelp("makeOccupancyReport()");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
//- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
var occList = [];
var occVal = [];
var occCount = [];

function countOccupancies()
{
	var prev;
	var oi = -1;

	for (var i = 0; i < occList.length; i++)
	{
		if (occList[i] != prev)
		{
			oi++;
			//			occVal.push(occList[i]);
			occVal[oi] = occList[i];
			occCount.push(1);
		}
		else
		{
			occCount[occCount.length-1]++;
		}
		prev = occList[i];
	}
}
//- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
function fixJmolList(list)
{
	var newList = [];
	var ni = 0;
	newList [0] = "";
	for (i=0; i < list.length; i++)
	{
		if (list[i] != "\n")
			newList[ni] += list[i];
		else
		{
			ni++;
			newList[ni] = "";
		}
	}

	newList.length = newList.length - 1;

	return newList;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeElementsReport()
{
	var erep = "<center><b>Chemical Elements</b></center>";

	erep += "<br>This model contains the following chemical elements. The atom count " +
			"is given for each.";

	erep +=	'<center><br><table cellpadding="3" bgcolor="#e0e0e0"><tr>';

	gotSe = false;

	for (i=0; i < elementSymbols.length; i++)
	{
		var ees = elementSymbols[i];
		var b1 = b2 = "";
		if (ees != "C" && ees != "H" && ees != "O" && ees != "N" && ees != "P" && ees != "S")
		{
			b1 = "<b>";
			b2 = "</b>";
		}

		erep += '<td><a href="javascript: findIt(\'_' +
			elementSymbols[i] + '\')">' + b1 +
				elementSymbols[i] + b2;

		if (elementSymbols[i] == "Se")
		{
			erep += "*";
			gotSe = true;
		}

		erep += '</a></td><td align="right">' +
				numberWithCommas(elementCounts[i]) + '</td></tr><tr>';
	}

	erep += '</td></tr></table>';
	
	erep += "<br>Click on an element to <i>Find</i> it.</center><br>";

	if (gotSe)
		erep += '*For more about selenium, click on <i>Disulfides/S/Se..</i> ' +
			'in the <i>Tools</i> tab.';
	if (mseCount)
		erep += ' This model contains ' + mseLink + 'selenomethoinine (MSE)</a>.';
	if (gotSe || mseCount)
		erep += '<br><br>';

	erep += 'Examples with >10 elements: \
<a href="fg.htm?mol=4kav" target="_blank">4kav</a>, \
<a href="fg.htm?mol=3eqc" target="_blank">3eqc</a>, \
<a href="fg.htm?mol=1ihu" target="_blank">1ihu</a>. \
<br>Examples with unknown elements Unx: \
<a href="fg.htm?mol=2awp" target="_blank">2awp</a>, \
<a href="fg.htm?mol=2dyr" target="_blank">2dyr</a>. \
';

	erep +=
'<br><br><b>Related:</b> ' +
'<i>Composition</i> (Views tab), ' +
'<a href="javascript: showMWHelp()">Molecular Masses</a>, ' +
'and ' +
'<a href="javascript: showHydrogenHelp()">Hydrogen</a>. ';


	erep += showHNonHCounts();

	return erep;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function showElementsReport()
{
	cancelPendingAndShowHelp("makeElementsReport()");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var save4SpreadsheetSB =
"<br>This tab-delimited list, saved as a text file, can be \
<b><font color='red'>imported into a spreadsheet for sorting</font></b> \
(see details at bottom below).<br>\
Save the file as <b>text</b>. Drag and drop it onto the spreadsheet icon, or File, Import.<br>\
(To save this page so it can be viewed in a web browser, File, Save As, Web Page, Complete.)<br><br>";

var save4SpreadsheetOC =
"<br>This tab-delimited list, saved as a text file, can be \
<b><font color='red'>imported into a spreadsheet for sorting</font></b>.<br>\
Save the file as <b>text</b>. Drag and drop it onto the spreadsheet icon, or File, Import.<br>\
(To save this page so it can be viewed in a web browser, File, Save As, Web Page, Complete.)<br><br>";

function listPartialOccupancy()
{
	var pol = "ATOMS WITH PARTIAL OCCUPANCY IN ";

	//	alert("help1.js #2 modelCount = " + modelCount);

	if (modelCount > 1)
		pol += "MODEL 1 OF ";

	if (validPDBId != "")
		pol += validPDBId + ".";
	else
		pol += "<br>" + pdbURL;

	pol += save4SpreadsheetOC;

	pol += "SeqNo = Sequence Number.<br>";
	pol += "Ins = Insertion Code for sequence number (usually blank).<br>";
	pol += "AltLoc = Alternate Location ID.<br>";
	pol += "Occ = Occupancy.<br>";
	pol += "Temp = Temperature (B factor).<br>";

	pol += "<br><br>";

	//	pol += "x\ty"; // YES TABS WORK

	pol += "Count\tGroup\tSeqNo\tIns\tChain\tElement\tAtom\tAltLoc\tOcc\tTemp<br>";

	//	pol += jmolEvaluate('{occupancy<1.0}.label("%3n\t%4R\t%3E\t%3c\t%4e\t%a\t%3A\t%3.2Q\t%3.2t")');

	// The following script line run manually crashes Java applet 14.3.16_2014.08.21 in FGiJ,
	// but not JSmol in FGiJ. When "List All" is run in Java applet FGiJ, the report is ERROR.
	// but "List All" works in JSmol.
	// Script does not crash Jmol app. It does not crash Java applet at St Olaf.
	// Note added FGiJ 2.5: try this without WAIT!!

	//	jmolScriptWait('listAllPartialOccupancies=' +
	// can use runBareSpt if add test and don't use Wait
	jmolScript('listAllPartialOccupancies=' +
						 '{occupancy<1.0}.label("%3n\t%4R\t%3E\t%3c\t%4e\t%a\t%3A\t%3.2Q\t%3.2t")');

	pol += jmolEvaluate('{*}.atomIndex.all[1][listAllPartialOccupancies.length].' +
		'add(1).format("%5i").join(listAllPartialOccupancies).join("\t",true)');

	alert("Look for the report in a separate\nbrowser tab or window.\n" +
		"Pop-ups must not be blocked for this site.");

	showSptInWindow(pol)
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var listSBPart1;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function listSaltBridges()
{
	var pol1 = "PROTEIN-PROTEIN SALT BRIDGES IN ";

	if (modelCount > 1)
		pol1 += "MODEL 1 OF ";

	if (validPDBId != "")
		pol1 += validPDBId + ".";
	else
		pol1 += "<br>" + pdbURL;

	pol1 += '<br>Listing by <a href="http://firstglance.jmol.org" target="_blank">FirstGlance ' +
			'in Jmol</a>.';

	pol1 += "<br><b>LIGAND-PROTEIN AND NUCLEIC-PROTEIN SALT BRIDGES ARE NOT LISTED.";
	pol1 += "<br>ONLY PROTEIN-PROTEIN SALT BRIDGES ARE LISTED.";
	pol1 += "<br>Salt bridges involving ligands+ or nucleic acids can be visualized using " +
		"<i>Contacts & Non-Covalent Interactions..</i> or <i>Ends..</i> (Tools tab).";
	pol1 += "<br><br>";

	var pol3 = "";
	var missingCharged = parseInt(missingNeg) + parseInt(missingPos);
	if (missingCharged)
	{
		pol3 += missingCharged + " charged amino acids that were present in the " +
		"preparation whose structure was determined are " +
		'<a href="where.htm#m" target="_blank">missing in this model</a>. ';
	}
	if (incompleteChargedSidechainsProteinCount)
	{
		if (pol3.length) pol3 += "<br>";
		pol3 += incompleteChargedSidechainsProteinCount +
		" amino acids in this model with charged sidechains have atoms missing in their sidechains " +
		'(<a href="where.htm#s" target="_blank">Sidechains, incomplete</a>; marked S-). ';
	}
	if (pol3.length)
	{
		pol3 += "<br>Salt bridges involving these residues are absent from the list below. ";
		pol3 += "<br><br>";
		pol3 = '<span style="background-color:#ffffb0;">' + pol3 + '</span>';
	}
	pol1 += pol3;

	pol1 += "Salt bridges are defined here as oppositely charged atoms &le;4.0 &Aring; apart";
	pol1 += "</b><br>(Jeffrey, George A., <i>An introduction to hydrogen bonding</i>. ";
	pol1 += "Oxford Univ. Press, 1997. Page 192.)<br>";

	pol1 += save4SpreadsheetSB;
	
	pol1 += "Count = Number of nitrogen atoms engaged in salt bridges, including those " +
		"with alternate locations.<br>" +
		repeat("&nbsp;", 3) +
		"(The atom count in the lower left panel in FirstGlance " +
		"excludes atoms with alternate locations.)<br>";
	pol1 += "SeqNo = Sequence Number.<br>";
	pol1 += "Ins = Insertion Code for sequence number (usually blank).<br>";
	pol1 += "Chain: Oxygen anion chain is <b>Bold*</b> for between-chain bridges.<br>";
	pol1 += "Atom:<br>";
	pol1 += repeat("&nbsp;", 3) +
		"SIDECHAINS: OD = Oxygen Delta; NE, OE = Nitrogen or Oxygen Epsilon; NH = Nitrogen Eta; " +
		"NZ = Nitrogen Zeta.<br>";
	pol1 += repeat("&nbsp;", 3) +
		"CHAIN TERMINI: <font color='magenta'>N, O, OXT</font> are main chain atoms. " +
		'(<font color="magenta">C</font> for C-termini lacking 1 oxygen: ' +
		'<a href="http://firstglance.jmol.org/notes.htm#saltbr" target="_blank">' +
		'more information</a>.)<br>';
	pol1 += "AltLoc = Alternate Location ID (usually blank).<br>";
	pol1 += "DIST = Distance in &Aring; between salt-bridged atoms.<br>" +
		repeat("&nbsp;", 3) +
		"When the C-terminus lacks one oxygen: " +
		"distance between the cationic nitrogen and the terminal carboxy carbon.<br>";

	//	getHiddenTot();
	//alert(hiddenTot);
	if (hiddenTot > 0 || isolatedDescription != "")
	{
		pol1 += '<br><span style="background-color:#ffe0e0;">';
		pol1 += "Only salt bridges with <b>visible</b> nitrogen cations are listed.<br>" +
"Salt bridges are NOT listed for the portions of the model whose nitrogen cations<br>" +
"are not visible due to <i>Hide</i> or <i>Isolate</i> operations.<br>";
		pol1 += '</span>';
	}

	listSBPart1 = pol1;

	// GENERATE TABLE BODY AND STATS IN JMOL	
	jmolScript("listSB();listSBStats();");

	setTimeout("listSaltBridges2()", 100);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function listSaltBridges2()
{
	var pol2 = "";

	// TABLE HEADER 1
	pol2 += "<br>\t\tNITROGEN CATIONS\t\t\tDIST\t\t\tOXYGEN ANIONS\t\t\tNOTES<br>";

	// HORIZONTAL BARS
	pol2 += repeat("&horbar;", 54) + "\t\t" + repeat("&horbar;", 46);;

	// TABLE HEADER 2
	pol2 += "<br>Count\tGroup1\tSeqNo1\tIns1\tChain1\tAtom1\tAltLoc1\t" +
		"\tGroup2\tSeqNo2\tIns2\tChain2\tAtom2\tAltLoc2<br>";

	// TABLE BODY
	pol2 += jmolEvaluate("sblist + sbliststats");

	// FOOTNOTES BELOW TABLE
	if (pol2.indexOf("1 oxygen") != -1)
		pol2 +=
'For <font color="magenta">C-termini</font> lacking 1 oxygen, ' +
'distances &le; 5.2 &Aring; are between '  +
'<br>the C-terminal carboxy carbon, <font color="magenta">C</font>, and the cationic nitrogen, ' +
'<br>and are excluded from the above statistics.<br>';

	if (match(pol2, "*"))
		pol2 += "<br>* " + jmolEvaluate("sbintercount") +
			" atom pairs in salt bridges between chains (inter-chain salt bridges).";
	else
		pol2 += "<br>No salt bridges are between chains. All are within chains.";

	pol2 += "<br>" + jmolEvaluate("sbpaircount") + " total atom pairs in salt bridges.";
	pol2 += "<br>" + jmolEvaluate("sbtermcount") +
		' atom pairs in salt bridges containing charged protein ' +
		'<font color="magenta">chain terminus atoms</font>.';
	if (pol2.indexOf("1 oxygen") != -1)
		pol2 += '<br><br><font color="magenta">&sect; C-terminus</font> ' +
			'lacking one oxygen, with carboxy ' +
			'carbon &le; 5.2 &Aring; from a cation: ' +
			'<a href="http://firstglance.jmol.org/notes.htm#saltbr" ' +
			'target="_blank">More information</a>. ' +
'<br>Distances (carboxy carbon to cationic nitrogen) are excluded from the above average, ' +
				'minimum, and maximum. ';

	pol2 += "<br>" + repeat("&horbar;", 110) + "<br>" +
"EXCEL suggestions:<br>" +
" - Save this page as text. Drag and drop it onto the spreadsheet icon, or File, Import.<br>" +
" - Delete text above and below the table of columns.<br>" +
" - <b>Auto-set all column widths</b>: Select entire sheet (Ctrl-A or Cmd-A), double click on any <br>" +
"\tcolumn boundary in the row of column letters at the top.<br>" +
" - <b>Delete blank rows</b>: Select the Group1 column (click on column B at the top).<br>" +
"\tIn the <i>Home</i> tab, open <i>Find & Select</i>, click on <i>Go to Special...</i>,<br>" +
"\tcheck <i>Blanks</i>, OK. Right click on a selected cell, <i>Delete...</i>, <i>Entire row</i>.<br>" +
" - <b>Delete all asterisks (*)</b>: <i>Edit</i> menu at top, <i>Find...</i>, <i>Replace...</i>.<br>" +
"\tEnter ~* (tilde asterisk) in the Find slot, and nothing in the Replace slot. Replace all.";

	alert("Look for the report in a separate\nbrowser tab or window.\n" +
		"Pop-ups must not be blocked for this site.");

	showSptInWindow(listSBPart1 + pol2);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var dipeptideCount;

function alertUnusual(halou)
{

	reportElapsed("alertUnusual(halou) started (help1.js)");

	// going to consurf, back to fg controls should not alert every time
	if (unusualAlerted) return("");

	unusualAlerted = true;

	// ALERT unconditionally if alpha carbons only, nucleic P only
	var abbo = "";
	if (proteinAlphaCarbonsOnly)
		abbo += "Only alpha carbon atoms are\npresent in the protein in this model.";
	if (nucleicPhosphorusOnly)
	{
		if (abbo.length > 0) abbo += "\n\n";
		abbo += "Only backbone phosphorus atoms are\npresent in the nucleic acid chains here.";
	}
	if (abbo.length > 0) alert(abbo);

	// BEGIN LIST OF UNUSUALS
	// uu is alerted only if preferenceSayUnusual
	var uu = '';

	var daacount = jmolAtomCount("~d_aa_ca"); // alpha carbons of D amino acids
	if (daacount)
		uu += 'Model contains ' + daacount + ' D amino acids.\n';

	if (jmolAtomCount("T and RNA")) // for alert Unusual
		uu += 'Model contains ribo-T.\n';

	if (jmolAtomCount("U and DNA")) // for alert Unusual
		uu += 'Model contains deoxyribo-U.\n';

	if (jmolAtomCount("GLX,ASX")) // for alert Unusual
		uu += 'Model contains ASX or GLX.\n';

	if (jmolAtomCount("*.x??")) // for alert Unusual
		uu += 'Model contains unknown atoms X.\n';

	if (jmolAtomCount("unx,unk")) // for alert Unusual
		uu += 'Model contains unknown atoms or groups UNX or UNK.\n';

	if (jmolAtomCount("[n]")) // for alert Unusual
		uu += 'Model contains unknown nucleotides "N".\n';

	if (jmolAtomCount("[unl]")) // for alert Unusual
		uu += 'Model contains unknown ligands "UNL".\n';

	if (jmolAtomCount("~anomalous_atoms")) // for alert Unusual
		uu += 'Model contains anomalous atoms.\n';

	if (jmolAtomCount("~nobackbone_aas")) // for alert Unusual
		uu += 'Model contains amino acids missing alpha carbons.\n';

	if (jmolAtomCount("~unbondable_aas")) // for alert Unusual
		uu += 'Model contains amino acids missing peptide-bonding atoms.\n';

	if (jmolAtomCount("~nomainchaino_aas")) // for alert Unusual
		uu += 'Model contains amino acids missing main chain oxygens.\n';

	var saa;
	if (saa = jmolAtomCount("~unchained_aas and *.ca")) // for alert Unusual
	{
		var ss = "";
		if (saa > 1) ss = "s";
		uu += 'Model contains ' + saa + ' single amino acid' + ss + ', not peptide bonded, ' +
			'listed/clickable under\n' +
			'  Ligands+ and Non-Standard Residues (Molecule Information Tab).\n';
	}

	if (jmolAtomCount("~hydroxy_unchained_nucs")) // for alert Unusual
		uu += 'Model contains single nucleoSides, not in a chain of standard nucleotides,\n' +
			'  listed/clickable under\n' +
			'  Ligands+ and Non-Standard Residues (Molecule Information Tab).\n';

	if (jmolAtomCount("~unchained_nucs")) // for alert Unusual
		uu += 'Model contains single nucleoTides, not in a chain of standard nucleotides,\n' +
			'  listed/clickable under\n' +
			'  Ligands+ and Non-Standard Residues (Molecule Information Tab).\n';

	// ~unchained_x is not alerted as Unusual

	if (jmolAtomCount("~cyclic_nucs")) // for alert Unusual
		uu += 'Model contains cyclic nucleotides.\n';

	if (jmolAtomCount("^?")) // for alert Unusual
		uu += 'Model contains sequence insertion codes.\n';

	if (jmolAtomCount("resno<1")) // for alert Unusual
		uu += 'Model contains zero or negative sequence numbers.\n';

	if (dipeptideCount = jmolAtomCount("~dipeptides and *.ca")) // for alert Unusual
	{
		dipeptideCount /= 2;
		var ss = "";
		if (dipeptideCount > 1) ss = "s";
		uu += 'Model contains ' + dipeptideCount + ' dipeptide ligand' + ss +
			', listed/clickable under\n' +
			'  Ligands+ and Non-Standard Residues (Molecule Information Tab).\n';
	}

	uu += unusualIsopeptideMsg;
	uu += unusualThioesterMsg;
	uu += unusualThioetherMsg;
	uu += unusualEsterMsg;
	uu += unusualHisTyrMsg;
	uu += unusualNOSBMsg;

//	if (altLocCount) // see getAltLoc() for why can't use jmolAtomCount which already has config=1
//		uu += 'Model contains ' + altLocCount + ' atoms with alternate locations.\n';

	// COMPLETE THE REPORT
	if (uu)
	{
		// SHOW RED "U"
		document.getElementById("redu").src="imgs/20px-redu.png";

		if (preferenceSayUnusual)
		{
			uu = "UNUSUAL COMPONENTS OR FEATURES:\n\n" + uu;
			uu += "\nOK for explanation, or Cancel for none.";

			if (halou)
				uu += "\nALL UNUSUAL COMPONENTS OR FEATURES WILL BE HALOED.";
			else
				uu+= "\n\nCLICK THE RED \"U\" BELOW THE MOLECULE\nTO PUT HALOS ON THESE COMPONENTS/FEATURES.";

			if (reportElapsedTimes)
				reportElapsed("alertUnusual(halou) done (alert suppressed) (help1.js)");
			else if (confirm(uu))
				window.open("notes.htm#unusual");			
		}
		else // preferencesSayUnusual false
		{
			if (crosslinksExist)
			{
				clm =
"Unusual protein crosslinks are present.\n" +
"OK to list them. Cancel to explore them later.\n" +
"Later, click the red U below the molecular view.";
				if (confirm(clm))
				{
					showCrosslinkHelpList();
				}
			}
		}
	}
	else reportElapsed("alertUnusual(halou) done, help1.js (nothing unusual found)");

	return (uu); // return is only for if(alertUnusual())
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function reiterateUnusual() // called only when red U is clicked.
{
	oldpref = preferenceSayUnusual;
	preferenceSayUnusual = false; // preparation to toggle on
	unusualAlerted = false; // otherwise alertUnusual() does nothing.
	// true = halo ~all_unusual
	togglePreferenceSayUnusual(true); // toggles preference true, sets cookie, alertUnusual(), halos
	// false = don't find->halos
	if (!oldpref) togglePreferenceSayUnusual(false); // restores pref and cookie to false
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function showCrosslinkHelp()
{
	showHelp("makeCrosslinkHelp()"); // sets helpPanel to same as string.
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
var crosslinkType; // same as xtype.
var previousCrosslinkType = "";
var xCount; // Count of crosslink bonds.
var xName; // Name of crosslink, e.g. "Isopeptide".
var xPpda; // URL to Proeopedia article on this type of crosslink.
var xIffy; // putative or possible
var showCrosslinkLabels = true; // default
var xLinxCount = 0; // visible cross-links.
var xHiddenCount = 0; // hidden cross-links.

var crosslinkValidation =
'*The ' +
'<a href="notes.htm#crosslinks" target="_blank">distance-based detection methods</a>\n\
are intentionally broad. ' +
'Check for geometry, appropriateness and lengths (see above) of covalent bonds, ' +
'and how well the electron density map supports the atom positions. ' +
'PDB files do not specify most covalent bonds. Jmol draws covalent bond sticks \n\
wherever two atoms are close enough (&le;1.81 &Aring for C, N, O), \n\
and not when they are too far apart. ';

function makeCrosslinkHelp()
{
	xtype = crosslinkType;
	switch (xtype)
	{
		case "i":
			xName = "Isopeptide";
			xCount = isopeptideCount;
			xPpda = "https://proteopedia.org/w/Isopeptide_bond";
			xIffy = "Putative";
			xres = isopeptideResidues;
			xatoms = isopeptideAtoms;
			xdist = isopeptideDistances;
			break;

		case "t":
			xName = "Thioester";
			xCount = thioesterCount;
			xPpda = "https://proteopedia.org/w/Thioester_protein_crosslinks";
			xIffy = "Putative";
			xres = thioesterResidues;
			xatoms = thioesterAtoms;
			xdist = thioesterDistances;
			break;

		case "h":
			xName = "Thioether";
			xCount = thioetherCount;
			xPpda = "https://proteopedia.org/w/Thioether_protein_crosslinks";
			xIffy = "Putative";
			xres = thioetherResidues;
			xatoms = thioetherAtoms;
			xdist = thioetherDistances;
			break;

		case "e":
			xName = "Ester";
			xCount = esterCount;
			xPpda = "https://proteopedia.org/wiki/index.php/Ester_protein_crosslinks";
			xIffy = "Putative";
			xres = esterResidues;
			xatoms = esterAtoms;
			xdist = esterDistances;
			break;

		case "y":
			xName = "His-Tyr";
			xCount = histyrCount;
			xPpda = "https://proteopedia.org/wiki/index.php/Histidine-tyrosine_protein_crosslinks";
			xIffy = "Putative";
			xres = histyrResidues;
			xatoms = histyrAtoms;
			xdist = histyrDistances;
			break;

		case "n":
			xName = "Lys-Cys NOS";
			xCount = NOSBCount;
			xPpda = "https://proteopedia.org/w/Lysine-cysteine_NOS_bonds";
			xIffy = "Possible";
			xres = NOSBResidues;
			xatoms = NOSBAtoms;
			xdist = NOSBDistances;
			break;
	} // End switch

	// Crosslinks Title
	iph = "<center><b>" + xName + '(?) <a href="javascript: showCrosslinkHelpList()">' +
		'Crosslinks</a></b></center><br>';

	var xlinx = ""; // Collect individual bond links.
	var clinx = ""; // Bond cluster links.
	xLinxCount = 0; // Count of visible xlinks.
	var xvis = ""; // for "visible"
	xHiddenCount = 0; // count of hidden bonds

	// GENERATE BOND/BOND CLUSTER LINKS xlinx
	if (xCount)
	{
		// Generate xlinx
		for (iir = 1; iir <= xCount; iir++)
		{
			var atbond = xres[iir];
			// FORMAT [GLN]211:F, [SPD]1223:F
			var selbond = atbond;

			var isCluster = match(atbond, " or ");

			if (!isCluster)
			{
				// get atoms
				ipa = xatoms[iir];
				atom1 = ipa.substring(0, ipa.indexOf(" "));
				atom2 = ipa.substring(ipa.indexOf(" ") + 1);
				//alert("|" + atom1 + "|" + atom2 + "|");

				// atbond: Insert atoms BEFORE colons (NOT LEGAL JMOL SYNTAX)
				icolon = atbond.indexOf(":");
				atbond = atbond.substring(0, icolon) + "." +
				atom1 + atbond.substring(icolon);

				icolon = atbond.lastIndexOf(":");
				atbond = atbond.substring(0, icolon) + "." +
				atom2 + atbond.substring(icolon);
				//alert("help1.js #5: atbond=" + atbond);
				// atbond IS NOT LEGAL JMOL FORMAT [GLN]211.CD:F, [SPD]1223.N1:F

				// selbond: Insert atoms AFTER chains (LEGAL JMOL for selection)
				icomma = selbond.indexOf(",");
				selbond = selbond.substring(0, icomma) + "." +
				atom1 + selbond.substring(icomma);
				selbond = selbond + "." + atom2;
				// COMMA FAILS IN {...}, USE OR
				selbond = selbond.replace(/, /, " or ");
				//alert(selbond);

				// COUNT HIDDEN BONDS
				toeval = "{(" + selbond + ") and not ~hidden_jdef}.count";
				//alert("help1.js #6:\njmolEvaluate(" + toeval + ")\n" + jmolEvaluate(toeval));
				if (jmolEvaluate(toeval) < 2)
				{
					xHiddenCount++;
					continue; // DON'T ADD HIDDEN BONDS TO xlinx
				}

			// Change colons to " Chain ".
			atbond = atbond.replace(/:/g, " Chain ");
			if (!isCluster)
			{
				// Change ", " to " to ".
				atbond = atbond.replace(/, /, " &nbsp; to &nbsp; ");
			}

			// Single bond links in xlinx
			if (!isCluster)
			{
				xlinx += '<li><a href="javascript: showCrosslink(' + iir + ', `' + xtype + '`)">'
					+ atbond + '</a>: ' + xdist[iir] + ' &Aring;' +
					'</li>';
				xLinxCount ++;
			}
			else // isCluster
			{
				clinx += '<li><a href="javascript: showCrosslink(' + iir + ', `' + xtype + '`)">'
					+ atbond + '</a></li>';
				xLinxCount ++;
			}
		} // end for loop if xCount: xlinx & clinx now complete.

		if (clinx.length)
		{
			clinx = 'Bond Clusters&sect;<br>' + clinx;
		}

		if (xHiddenCount) xvis = "<b>Visible</b> ";

		// Add link for ALL
		if (xLinxCount > 1)
		{
			xlinx +=
'<li><a href="javascript: showCrosslink(0, `' + xtype +
	'`)">All ' + xvis + 'Putative ' + xName + ' Bonds</a></li>';
		}

		// Emphasize some hidden
		if (xHiddenCount)
			xlinx += "(<b>" + xHiddenCount + '</b> ' + ((xHiddenCount == 1) ? 'bond is':'bonds are')  +
			' HIDDEN.)<br>';

		// LABELS
		// If this is the first display of crosslinks, label them.
		if (currentView != "renderCrosslink") {showCrosslinkLabels = true;}

		// If we are already showing crosslinks, add checkboxes.
		if (xCount && currentView == "renderCrosslink" && xtype == previousCrosslinkType)
		{
			// If we're showing a single crosslink:
			if (currentCrosslinkIndex) // Not when showing "All" crosslinks.
			{
				// Slab toggle
				initbut = "up";
				if (toggleIsDown[slabIndex]) {initbut = "down";}
				toggleIndex = slabIndex + 200; // none for cptab 1, 10 for cptab 2, 100 for molinfo tab.
				xlinx +=
"<a href='javascript: doToggleButton(slabIndex)'>" +
"<img src='" + initbut + ".gif' border='0' name='toggle" + toggleIndex + "'" +
" id='crosslinkslab' " +
" title='" + SlabTT_txt + "'\/><\/a>&nbsp;" + "Slab to declutter." +

'&nbsp; <a href="javascript: showHelp(toggleHelpName[slabIndex])">Slab settings</a>.<br>';
				// End Slab toggle
			}

			// Hide labels checkbox even when all xlinks shown.
			cksil = " checked ";
			if (showCrosslinkLabels) {cksil = "";}
			xlinx +=
'<input type="checkbox" id="xLabels" name="xLabels" \
onClick="toggleCrosslinkLabels()" ' + cksil + '> \
Hide labels.';

			// If we're showing a single crosslink:
			if (currentCrosslinkIndex) // Not when showing "All" crosslinks.
			{
				// Neighbors toggle
				cksin = "";
				if (showCrosslinkNeighbors) {cksin = " checked ";}
				xlinx +=
'<br><input type="checkbox" name="xNeighbors" id="xNeighbors" \
onClick="toggleCrosslinkNeighbors()" ' + cksin + '> \
Show 4.0 &Aring; neighbors&dagger; of this bond.';

				// Electron density. cf. crosslinkType, currentCrosslinkIndex, xres[].
				// href="javascript: execution order is left to right.
				if (hasMap)
					xlinx +=
					'<br><img src="new.gif"><b>' +
						'<a href="javascript: edmTarget=`' + xres[currentCrosslinkIndex] +
						'`;edmTargetJmol=``;openEDM();">' +
						cap1only(mapName) + ' Density Map</a></b>.<img src="new.gif">';

				xlinx +=
'<br>This view shows only the crosslinking residues, <span style="color:red;"><b>not</b> ' +
'</span>their covalent and non-covalent interactions with neighbors. ' +
'For those, check &quot;4.0 &Aring; neighbors&quot; above, or go to <i>Contacts\n\
& Non-Covalent Interactions</i> (Tools tab), and check &quot;Atoms with halos&quot;. \n';

			} // End of showing a single crosslink
		} // End of "already showing crosslinks" checkboxes.
	} // End if xCount. xlinx is now COMPLETE.

	//alert(xlinx);

		/*
	// Report FAILURE if it occurred due to partner count mismatches.
	if ((xtype == "i" && failIsopeptides) || (xtype == "t" && failThioesters) ||
			(xtype == "h" && failThioethers) || (xtype == "e" && failEsters) ||
			(xtype == "y" && failHisTyr) || (xtype == "n" && failNOSB))
	{
		iph +=
'Detection of ' + xName + ' bonds <u>FAILED</u>. ' +
'This is usually due to clashes (atoms being impossibly close together) in the model.<br>';
	}
	else // Detection did not fail.
		*/
		//	{ @@@
		if (xLinxCount)
		{
			iph += xIffy +
'* ' +
'<a href="' + xPpda + '" target="_blank">' + xName + ' bonds</a> ' +
'are present in this model. ';

			if (match(getMethod(), "electron microscopy"))
			{
				iph +=
'CAUTION: Models determined by <b>electron microscopy</b> sometimes have many ' +
'clashes or bond lengths too long to be detected. ' +
'<a href="notes.htm#crosslinks" target="_blank">Examples</a>. ';
			}

			if (xHiddenCount)
				iph +=
					'<b>' + xLinxCount + '</b> ' + ((xLinxCount == 1) ? 'is':'are')  + ' visible. ' +
					'<b>' + xHiddenCount + '</b> ' + ((xHiddenCount == 1) ? 'is':'are')  + ' HIDDEN. ';

			iph +=
'Detection criteria are intentionally broad, and sometimes report \n\
<a href="https://proteopedia.org/wiki/index.php/Clashes" \n\
target="_blank">clashes</a>'; // period space below.

			if (xtype == "i" || // Isopeptide
				xtype == "t" || // thioester
				 // "h" thioether no clash example found.
				xtype == "e" || // ester
				xtype == "y" || // his-tyr
				xtype == "n") // NOS
					iph += ' (example below&Dagger;). ';

			if (xtype == "n") // NOS
				iph +=
'See <a href="https://proteopedia.org/w/Electron_density_maps#2Fo-Fc_Map" \n\
target="_blank">validation examples</a>. ';

			/*
			// CLASH examples at top of crosslinks help.
			if (xtype == "i") // Isopeptide
				iph +=
					' (example: <a href="fg.htm?mol=3ic8" target="_blank">3ic8</a>&Dagger;). ';
			else if (xtype == "t") // thioeSTer
				iph +=
					' (example: <a href="fg.htm?mol=5d12" target="_blank">5d12</a>&Dagger;). ';
			// "h" thioether no clash examples found.
			else if (xtype == "e") // Ester
				iph +=
					' (example: <a href="fg.htm?mol=1pq8" target="_blank">1pq8</a>&Dagger;). ';
			// "y" His-Tyr no clash examples found.
			else if (xtype == "n") // NOS
				iph +=
					' (example: <a href="fg.htm?mol=6arh" target="_blank">6arh</a>&Dagger;). ' +
'See <a href="https://proteopedia.org/w/Electron_density_maps#2Fo-Fc_Map" \n\
target="_blank">validation examples</a>. ';

			else iph += ". ";
			*/

			iph +=
'Click the following ' + xvis + ' possible bonds to inspect for validation: ';

			iph += '<ol>' + xlinx + clinx; // List of bonds + "All" + checkboxes/slab.

			iph += '</ol>';
		} // END if xlinksCount

		if (!xLinxCount && xCount)
		{
			iph += xIffy +
'* ' +
'<a href="' + xPpda + '" target="_blank">' + xName + ' bonds</a> ' +
'are present in this model, but ALL ARE CURRENTLY HIDDEN. ' +
'Please use the <i>Hide..</i> or <i>Isolate..</i> dialogs in the ' +
'<a href="where.htm#focusbox" target="_blank">Focus Box</a> ' +
'to unhide those that you wish to visualize. <br>';
		}

		if (!xCount) // none in the first place.
		{
			iph +=
'<b>No</b> ' + xIffy + '* ' +
'<a href="' + xPpda + '" target="_blank">' + xName + ' bonds</a> ' +
'are present in this model.<br>';
		}
	
		if (xLinxCount)
		{
			if (!xCount) iph += "<br>";

			if (xtype == "i")
			{
				iph +=
'1.3-1.5 &Aring; is the range of typical N-Carbonyl isopeptide bond lengths in X-ray models.\n\
However, bond lengths of 1.25\n\
(<a href="fg.htm?mol=6kl4" target="_blank">6KL4</a>)\n\
to 1.56 &Aring;\n\
(<a href="fg.htm?mol=1fma" target="_blank">1FMA</a>)\n\
occur in 19 models with\n\
<a href="https://proteopedia.org/w/Resolution" target="_blank">resolutions</a>\n\
of 0.9 to 2.9 &Aring;, each containing\n\
bona fide isopeptide bonds.\n' + isopeptideCutoff +
' &Aring; is the detection cutoff.<br><br>';

				iph += 'CD = carbon delta (distal sidechain carbon of Glu/Gln).<br>';
				iph += 'CG = carbon gamma (distal sidechain carbon of Asp/Asn).<br>';
				iph += 'NZ = nitrogen zeta (sidechain nitrogen of Lys).<br>';
			}
			else if (xtype == "t")
			{
				iph +=
'1.6-1.8 &Aring; is the range of typical S-Carbonyl thioester bond lengths in X-ray models.\n\
However, bond lengths up to\n\
2.15 &Aring;\n\
(<a href="fg.htm?mol=3hku" target="_blank">3HKU</a>)\n\
occur in 10 models with\n\
<a href="https://proteopedia.org/w/Resolution" target="_blank">resolutions</a>\n\
of 1.3 to 2.9 &Aring;, each containing\n\
bona fide thioester bonds.\n' + thioeeCutoff +
' &Aring; is the detection cutoff.<br><br>';

				iph += 'CD = carbon delta (distal sidechain carbon of Gln).<br>';
				iph += 'SG = sulfur gamma (sidechain sulfur of Cys).<br>';
			}
			else if (xtype == "h") // thioether
			{
				iph +=
'1.7-1.9 &Aring; is the range of typical S-C thioether bond lengths in X-ray models.\n\
However, bond lengths up to\n\
2.05 &Aring;\n\
(<a href="fg.htm?mol=3hku" target="_blank">3HKU</a>)\n\
occur in 9 X-ray models with\n\
<a href="https://proteopedia.org/w/Resolution" target="_blank">resolutions</a>\n\
of 1.3 to 2.5 &Aring;, each containing\n\
bona fide thioether bonds. In one\n\
<a href="https://proteopedia.org/w/Electron_cryomicroscopy"\n\
target="_blank">cryo-EM</a> structure\n\
(<a href="fg.htm?mol=6nef" target="_blank">6NEF</a>),\n\
cysteine-heme (HEC) thioether bonds are 1.78 to 1.86 &Aring; to heme.CAB, but\n\
2.54 to 2.87 &Aring; to heme.CAC. The latter are not reported by FirstGlance because its\n\
detection cutoff is '  + thioeeCutoff + ' &Aring.<br><br>';

				iph += 'CD = carbon delta.<br>';
				iph += 'CE = carbon epsilon.<br>';
				iph += 'SG = sulfur gamma (sidechain sulfur of Cys).<br>';
			}
			else if (xtype == "e") // Ester
			{
				iph +=
'1.3-1.4 &Aring; is the range of typical O-Carbonyl ester bond lengths in X-ray models.\n\
However, bond lengths up to\n\
1.59 &Aring;\n\
(<a href="fg.htm?mol=2pnl" target="_blank">2PNL</a>,\n\
<a href="fg.htm?mol=1gdq" target="_blank">1GDQ</a>)\n\
occur in 9 models with\n\
<a href="https://proteopedia.org/w/Resolution" target="_blank">resolutions</a>\n\
of 0.9 to 2.5 &Aring;, each containing\n\
bona fide ester bonds.\n' + esterCutoff +
' &Aring; is the detection cutoff.<br><br>';

				iph += 'OG = oxygen gamma (distal sidechain oxygen of Thr).<br>';
				iph += 'CD = carbon delta (distal sidechain carbon of Gln).<br>';
			}
			else if (xtype == "y") // His Tyr
			{
				iph +=
'1.3-1.5 &Aring; is the range of typical His-Tyr N-C bond lengths in X-ray models.\n\
However, bond lengths up to\n\
2.06 &Aring;\n\
(<a href="fg.htm?mol=1gge" target="_blank">1GGE</a>)\n\
occur in 6 models with\n\
<a href="https://proteopedia.org/w/Resolution" target="_blank">resolutions</a>\n\
of 1.3 to 2.9 &Aring;, each containing\n\
bona fide His-Tyr bonds.\n' + histyrCutoff +
' &Aring; is the detection cutoff.<br><br>';

				iph += 'NE2 = nitrogen epsilon position 2 (distal sidechain nitrogen of His).<br>';
				iph += 'CE2 = carbon epsilon position 2 in the ring of Tyr.<br>';
			}
			else if (xtype == "n")
			{
				iph +=
'2.67 to 2.94 &Aring; are the N-S distances for the 4 cases reported by\n\
<a href="https://pubmed.ncbi.nlm.nih.gov/33953398/" target="_blank">Wensien\n\
<i>et al.</i> (2021)</a> and listed below.\n' + NOSBCutoff +
' &Aring is the detection cutoff.<br><br>';

				iph += 'NZ = nitrogen zeta (sidechain nitrogen of Lys).<br>';
				iph += 'SG = sulfur gamma (sidechain sulfur of Cys).<br>';
			}

			iph +='<a href="notes.htm#ident" target="_blank">Other atoms</a>. ';
			iph += 'Scroll down for <i>Methods</i>.<br>';
		} // End if xlinxCount
		//	} // End of 'detection method did not fail'.

	// VALIDATION AND CLASHES
	if (xtype != "n")
	{
		iph += '<br>' + crosslinkValidation;

		iph +=
'Occasionally, a \n\
<a href="https://proteopedia.org/wiki/index.php/Clashes" \n\
target="_blank">clash</a> \n\
(atoms closer\n\
than is physically possible) will be reported as a <i>putative</i> ' + xName + ' bond. ';

		iph +=
'Such clashes are sometimes removed when an X-ray model is automatically\n\
re-refined and rebuilt by\n\
<a href="https://pdb-redo.eu/" target="_blank">PDB-REDO</a>.\n';

		// CLASHES in double-dagger footnote.
		if (xtype == "i")
		{
			iph +=
'<br><br>&Dagger;Clash example: <a href="fg.htm?mol=3ic8" target="_blank">3ic8</a>.\n\
The atoms at the ends of the sidechains are too close together (see bond lengths above).\n\
Jmol draws spurious "bonds" between them.\n\
The two residues are modeled with two independent sidechains, not as an isopeptide bond.\n\
There is poor electron density for the end of the Lysine sidechain, and the difference\n\
map suggests that the sidechain nitrogen is misplaced.\n';
		}
		else if (xtype == "t") iph +=
'<br><br>&Dagger;Clash example: <a href="fg.htm?mol=5d12" target="_blank">5d12</a>.\n\
Atoms are too close together (see bond lengths above).\n\
Jmol draws spurious "bonds" between them.\n\
The two residues are modeled with two independent sidechains, not as a thioester bond.\n\
The electron density difference map is consistent with the sidechain of the Aspartic acid\n\
being misplaced.';

		else if (xtype == "h") // thioether
			iph +=
'<br><br>No example of a putative thioether bond actually being a clash is known to us.\n\
If you find one, please send the PDB ID code to ' +
make_contact_address("Ester crosslink examples", ".");

		else if (xtype == "e") // ester
		{
			iph +=
'<br><br>&Dagger;Clash example: <a href="fg.htm?mol=1pq8" target="_blank">1pq8</a>.\n\
In this extremely high resolution model of trypsin catalysis,\n\
the clash occurs between the sidechain oxygen of Ser195 vs. the main chain N and C-alpha\n\
of Lys403. The occupancies of those 3 atoms are 80%, 0%, and 14% respectively.\n\
(If you click "Show More Details" in the\n\
<a href="where.htm#mit" target="_blank">Molecule Information Tab</a>,\n\
touching an atom reports its occupancy.)\n\
Atoms are too close together (see bond lengths above).\n\
Jmol draws spurious "bonds" between them.\n\
The electron density map underscores the uncertainty in the position of Lys403, which\n\
is in the same space as (clashing with) two alternate locations of Arg3 of chain C (substrate).\n\
The average occupancies for Lys403, Arg3 altloc A, and Arg3 altloc B are 18%, 27%, and 23%\n\
respectively.\n\
';
		}

		//		else if (xtype == "y") // His-Tyr Clash: 4rea needs SONOS fix.

		// NOS Clash is below

		iph += "<br>";

	}
	else // NOSB
	{
		iph +=
'<br>*Since Lys-Cys NOS bonds were\n\
<a href="https://pubmed.ncbi.nlm.nih.gov/33953398/" target="_blank">\
not widely recognized until 2021</a>,\n\
earlier investigators\n\
may have overlooked them, omitting the O atom.\n\
When FirstGlance suggests such a bond (scroll down for methods), confirmation\n\
of the missing O atom will be crucial, based in part on examination of the electron\n\
density map.<br>';

		iph += '<br>' + crosslinkValidation + '<br>';

		iph +=
'<br>&Dagger;Clash example: <a href="fg.htm?mol=6arh" target="_blank">6arh</a>.\n\
The sidechains are too close together. Jmol draws spurious "bonds" between them.\n\
There is no room for an oxygen between the N and S. Both sidechains have two\n\
<a href="https://proteopedia.org/wiki/index.php/Alternate_locations"\n\
target="_blank">alternate locations with 50% occupancy each</a>.\n\
There is weak electron density for the Lysine rotamer that clashes with Cysteine.\n\
The difference map suggests a rotamer position that would not clash, a blue density\n\
(which, upon checking, is not occupied by a crystal contact).\n\
There are 4 sequence-identical chains, but Lys228 and Cys250 clash only in chain A.\n\
Other "NOS" clash examples are\n\
<a href="fg.htm?mol=7ns5" target="_blank">7ns5</a> and\n\
<a href="fg.htm?mol=5r67" target="_blank">5r67</a>.\n\
<br>';
	} // End NOSB

	iph += '<br><b>' + xName + ' Examples:</b>\n';

	if (xtype == "n")
		iph += '<br>See <a href="https://proteopedia.org/w/Electron_density_maps"' +
'target="_blank">electron density map (EDM) snapshots</a>.';

	iph += '<ul>\n';

	if (xtype == "i")
	{
		iph +=
'<li><a href="fg.htm?mol=3htl" target="_blank"><tt>3HTL</tt></a>:\n\
Lys-Asn (Pilin)\n\
</li>\n\
<li><a href="fg.htm?mol=4mli" target="_blank"><tt>4MLi</tt></a>:\n\
Lys-Asp (SpyTag/SpyCatcher).\n\
</li>\n\
<li><a href="fg.htm?mol=1n73" target="_blank"><tt>1N73</tt></a>:\n\
Lys-Gln (Fibrin with peptide ligand).\n\
</li>\n\
<li><a href="fg.htm?mol=6vzx" target="_blank"><tt>6VZX</tt></a>:\n\
Lys-Glu (Collagen peptides, engineered).\n\
</li>\n\
<li><a href="fg.htm?mol=7cap" target="_blank"><tt>7CAP</tt></a>:\n\
Lys-C-terminus (Ubiquitin homotrimer).\n\
</li>\n\
<li><a href="fg.htm?mol=5jqf" target="_blank"><tt>5JQF</tt></a>:\n\
N-terminus-Asp (Lasso peptide sphingopyxin I).\n\
</li>\n\
<li><a href="fg.htm?mol=5ein" target="_blank"><tt>5ein</tt></a>:\n\
Substrate-Glu (Lysine synthesis enzymes).\n\
</li>\n\
<li><a href="fg.htm?mol=4c0z" target="_blank"><tt>4c0z</tt></a>:\n\
Ligand-Gln (Pilus tip adhesin Cpa, spermidine cross-link).\n\
</li>\n';
	}

	if (xtype == "t")
	{
		iph +=
'<li><a href="fg.htm?mol=2b39" target="_blank"><tt>2B39</tt></a> (2006):\n\
Complement C3.\n\
<li><a href="fg.htm?mol=3khu" target="_blank"><tt>3KHU</tt></a> (2009):\n\
Human UDP-glucose dehydrogenase in complex with thiohemiacetal catalytic intermediate.\n\
<li><a href="fg.htm?mol=2xi9" target="_blank"><tt>2xi9</tt></a> (2010):\n\
Pilus-presented adhesin having both thioester and isopeptide crosslinks.</li>\n\
<li><a href="fg.htm?mol=6fwy" target="_blank"><tt>6FWY</tt></a> (2018):\n\
Bacterial adhesion thioester domain (TED).</li>\n\
';
	}

	if (xtype == "h")
	{
		iph +=
'<i>Cys-Tyr:</i><br>\n\
<li><a href="fg.htm?mol=1gof" target="_blank"><tt>1gof</tt></a> (1991):\n\
Galactose oxidase.</li>\n\
<li><a href="fg.htm?mol=1sy7" target="_blank"><tt>1sy7</tt></a> (2004):\n\
Catalase.</li>\n\
<li><a href="fg.htm?mol=4ysf" target="_blank"><tt>4ysf</tt></a> (2016):\n\
Cysteine dioxygenase.</li>\n\
<li><a href="fg.htm?mol=6e87" target="_blank"><tt>6e87</tt></a> (2019):\n\
Cysteine dioxygenase.</li><br>\n\
<i>Cys-Ligand:</i><br>\n\
<li><a href="fg.htm?mol=5nf0" target="_blank"><tt>5nf0</tt></a> (2017):\n\
Lectin:peptide with D-Cys:xylene.</li>\n\
<li><a href="fg.htm?mol=6o83" target="_blank"><tt>6o83</tt></a> (2019):\n\
Ubiquitin-activating enzyme E1, Cys-substrate.</li>\n\
<li><a href="fg.htm?mol=6vdq" target="_blank"><tt>6vdq</tt></a> (2021):\n\
Strep. peroxygenase, Cys-heme.</li>\n';
	}

	if (xtype == "e")
	{
		iph +=
'<li><a href="fg.htm?mol=4ni6" target="_blank"><tt>4ni6</tt></a>:\n\
<i>Clostridium perfringens</i> pilus repeat domain.</li>\n\
<li><a href="fg.htm?	mol=4mkm" target="_blank"><tt>4MKM</tt></a>:\n\
<i>Clostridium perfringens</i> pilus repeat domains.</li>\n\
<li><a href="fg.htm?	mol=3p06" target="_blank"><tt>3p06</tt></a>:\n\
Tellina virus 1 protease VP4, intrachain.</li>\n\
<li><a href="fg.htm?	mol=2pnl" target="_blank"><tt>2PNL</tt></a>:\n\
Infectious pancreatic necrosis virus protease VP4, interchain. \n\
Ester catalytic intermediate trapped by mutation.</li>\n\
<li><a href="fg.htm?	mol=1gdq" target="_blank"><tt>1GDQ</tt></a>:\n\
Interchain. Trypsin, ester catalytic intermediate trapped.</li>\n';
	}

	if (xtype == "y")
	{
		iph +=
'<li><a href="fg.htm?mol=1gge" target="_blank"><tt>1gge</tt></a> (2000):\n\
<i>E. coli</i> catalase HPII.\n\
His.N-delta to Tyr.C-beta.</li>\n\
\n\
<li><a href="fg.htm?mol=1v54" target="_blank"><tt>1v54</tt></a> (2003):\n\
Bovine heart cytochrome c oxidase.\n\
His.N-epsilon to Tyr.C-epsilon.</li>\n\
\n\
<li><a href="fg.htm?mol=2yev" target="_blank"><tt>2yev</tt></a> (2012):\n\
<i>Thermus thermophilus</i> cytochrome caa3 oxidase (also has thioethers).</li>\n\
His.N-epsilon to Tyr.C-epsilon.</li>\n\
\n\
<li><a href="fg.htm?mol=7coh" target="_blank"><tt>7coh</tt></a> (2021):\n\
Bovine heart cytochrome c oxidase.</li>\n\
His.N-epsilon to Tyr.C-epsilon.</li>\n\
';
	}

	if (xtype == "n")
	{
		iph +=
'<li><a href="fg.htm?mol=6zx4" target="_blank">6ZX4</a> (the first documented case). In this\n\
model, S-hydroxycysteine (the OS of NOS) has residue code\n\
<a href="https://www.rcsb.org/ligand/CSO" target="_blank">CSO</a>.\n\
</li>\n\
<li>Proposed by \n\
<a href="https://pubmed.ncbi.nlm.nih.gov/33953398/" target="_blank">Wensien\n\
<i>et al.</i> (2021)</a>:<ul>\n\
<li><a href="fg.htm?mol=1m3q" target="_blank">1M3Q</a>: \
EDM consistent with NOS.</li>\n\
<li><a href="fg.htm?mol=5y72" target="_blank">5Y72</a>: \
EDM consistent with NOS.</li>\n\
<li><a href="fg.htm?mol=6t3x" target="_blank">6T3X</a>: \
EDM consistent with NOS.</li>\n\
</ul>\n\
<li><a href="fg.htm?mol=3u7z" target="_blank">3u7z</a> (2011): \
EDM consistent with NOS.</li>\n\
<li><a href="fg.htm?mol=3wvb" target="_blank">3wvb</a> (2015): \
EDM consistent with NOS.</li>\n\
<li><a href="fg.htm?mol=6vb2" target="_blank">6vb2</a> (2020): \
EDM <u>rules out</u> NOS.</li>\n\
<li>\n\
<a href="http://doi.org/10.21203/rs.3.rs-635771/v1"\n\
target="_blank">Numerous additional examples</a>.\n\
</ul>';
	}
	iph += '</ul>';

	iph += 'Thanks to Amr A. Alhossary for some examples above.<br><br>';

	iph += 
			'<b>See <a href="notes.htm#crosslinks" target="_blank">Detailed Methods</a>.</b><br>';

	iph +=
'<br>When ' +
'<a href="javascript showAltLocHelp()">alternate locations</a> ' +
			' are present, only conformation 1 is queried. ';

	if (xtype != "n")
	{
		iph +=
'Possibly not all types of ' + xName + ' bonds will be detected ' +
'(see <a href="notes.htm#crosslinks" target="_blank">Methods</a>). ' +
'Please report PDB codes for any undetected or incorrect ' + xName + ' bonds to ' +
make_contact_address("Problematic " + xName + " bonds in FirstGlance", ".");
	}
	else // NOSB
	{
		iph +=
'Examples involving conformation 2 (alternate location B), not detected by FirstGlance, include\n\
<a href="fg.htm?mol=1nme" target="_blank">1nme</a>\n\
and\n\
<a href="fg.htm?mol=1jpu" target="_blank">1jpu</a>.\n\
In 2021, there were roughly 50 such cases in the PDB. See\n\
<a href="http://doi.org/10.21203/rs.3.rs-635771/v1"\n\
target="_blank">von Pappenheim <i>et al.</i>, 2021</a>.';
	}

	// If we are already showing crosslinks, additional help:
	if (xCount && currentView == "renderCrosslink")
	{
		iph += "<br><br>" +
'&dagger; Thick sticks represent the ' + xName + '-bonded residues. Medium sticks represent\n\
&quot;neighboring&quot; atoms (within 4.0 &Aring;). Thin sticks represent more distant\n\
portions of the residues containing neighboring atoms.\n';

	}

	previousCrosslinkType = xtype;

	return iph;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function showCrosslinkHelpList()
{
	showHelp("makeCrosslinkHelpList()");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// Displays list of all crosslink bond types with counts.

function makeCrosslinkHelpList()
{
	if (resfloat > 4.0)
	{
		chl = '<center><b>Protein Crosslinks</b></center><br>\n\
FirstGlance did not scan this model for protein crosslinks because its\n\
<a href="https://proteopedia.org/wiki/index.php/Resolution"\n\
target="_blank">resolution</a>\n\
(' + resfloat + ' &Aring) is too low.\n\
Models with resolutions worse than 4.0 &Aring; are not scanned because\n\
they have too many clashes and inaccuracies in inter-atomic distances.';

		return chl;
	}

		// TEST:
		//		failIsopeptides = true;

	grayzero = '<span style="color:#808080">0</span>';
	ic = (isopeptideCount ? "<b>" + isopeptideCount + "</b>":grayzero);
	tc = (thioesterCount ? "<b>" + thioesterCount + "</b>":grayzero);
	hc = (thioetherCount ? "<b>" + thioetherCount + "</b>":grayzero);
	ec = (esterCount ? "<b>" + esterCount + "</b>":grayzero);
	yc = (histyrCount ? "<b>" + histyrCount + "</b>":grayzero);
	nc = (NOSBCount ? "<b>" + NOSBCount + "</b>":grayzero);

	chl = '<center><b>Protein Crosslinks</b></center><br>\n\
Choose a type below to list the protein crosslinks present, view and analyze them:\n\
<ul>\n' +

	'<li>' + (disulfideCount ? "<b>" + disulfideCount + "</b>":grayzero) + " " +

	makeViewLink("makeSSBondsSpt()",
	 "Disulfide crosslinks", "makeSSBondsHelp()",
	 ssBondsLinkTT_txt) + "." +

'<li>' + (failIsopeptides ? "*":ic) +
' <a href="javascript: crosslinkType=\'i\';showCrosslinkHelp()">Isopeptide crosslinks</a> ' +
'(putative).\n' +

'<li>' + (failThioesters ? "*":tc) +
' <a href="javascript: crosslinkType=\'t\';showCrosslinkHelp()">Thioester crosslinks</a> ' +
'(putative).\n' +

'<li>' + (failThioethers ? "*":hc) +
' <a href="javascript: crosslinkType=\'h\';showCrosslinkHelp()">Thioether crosslinks</a> ' +
'(putative).\n' +

'<li>' + (failEsters ? "*":ec) +
' <a href="javascript: crosslinkType=\'e\';showCrosslinkHelp()">Ester crosslinks</a> ' +
'(putative).\n' +

'<li>' + (failHisTyr ? "*":yc) +
' <a href="javascript: crosslinkType=\'y\';showCrosslinkHelp()">His-Tyr crosslinks</a> ' +
'(putative).\n' +

'<li>' + (failNOSB ? "*":nc) +
' <a href="javascript: crosslinkType=\'n\';showCrosslinkHelp()">Lys-Cys NOS crosslinks</a> ' +
'(possible).\n' +
'</ul>\n';

	if (failIsopeptides || failThioesters || failThioethers || failEsters || failHisTyr || failNOSB)
		chl +=
'* Detection failed. This is usually due to clashes (atoms impossibly close to each other).<br>';

	chl +=
'Types of crosslinks not listed above are not detected. Fluorophores in green fluorescent\n\
protein and its family members are not detected.\n\
';

	return chl;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function showMapHelp()
{
	showHelp("makeMapHelp()");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
function makeMapHelp()
{
	dmh = "<center><b>" + cap1only(mapName) + ' Density Map</b></center><br>';

	mtd = expMethod;
	if (!expMethod.length) mtd = "(unknown)";
	if (pdbIsSwissModel) mtd = "homology modeling (Swiss Model server)";
	if (pdbIsMakeMultimer) mtd = "symmetry operations (MakeMultimer server)";
	if (pdbIsOPM) mtd = "the Orientations of Membranes in Proteins server";
	if (pdbIsAlphaFold || pdbIsAFColab) mtd = "AlphaFold";
	if (pdbIsRosettafold) mtd = "RoseTTAFold";

	var dtb = "determined by";
	if (pdbIsSwissModel || pdbIsOPM || pdbIsAlphaFold || pdbIsAFColab || pdbIsRosettafold)
		dtb = "predicted by";
	if (pdbIsMakeMultimer) dtb = "generated by";

	if (!hasMap)
	{
		dmh += '<i><b>No</b> ' + mapName +
' density map is available for this model. Maps are available only for ' +
'models determined by X-ray diffraction or electron microscopy. ' +
'This model was ' + dtb + ' ' + mtd + '.</i><br><br>';

		return dmh;
	}

	dmh +=
'Use the <u>' + cap1only(mapName) + ' Density Map</u> links in these locations:' +
'<ul>' +
'<li>' +
'<b>Find..</b> (in the ' +
'<a href="where.htm#focusbox" target="_blank">Focus Box</a>). ' +
'The link appears after residues you specify have been identified with yellow halos.' +
'</li><li>' +
'<b>Ends..</b> of protein chains (Tools Tab), after displaying one ' +
'end of a chain.' +
'</li><li>' +
'<b>Protein Crosslinks</b> (Tools Tab), after displaying a single ' +
'protein crosslink (when present; example ' +
'<a href="fg.htm?mol=6zx4" target="_blank">6zx4</a>).' +
'</li></ul>';

	dmh +=
'Examining the ' + mapName + ' density map reveals how well the atomic model ' +
'fits the experimental data. For an explanation, see ' +
'<a href="https://proteopedia.org/w/Electron_density_maps" target="_blank">' +
'Electron Density Maps</a>.';

	return dmh;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */