// study panel -------------

var Mol1Settings="All,Atoms,0.25,Bonds,0.10,Dots,Element";
var ethanolScp="load ethanol.mol; select all; spacefill 20%; wireframe 0.1; moveto 0 { -51 978 -202 32.6}  100.0 0.1 0.0  {0.29884997 -0.23134995 -0.040749967} 2.7144809 {0.0 0.0 0.0} -3.8333237 -5.7416306 50.0;";
var ethanolMsg= "Ethanol";

var ureaScp="load urea.mol; select all; spacefill 20%; wireframe 0.1";
var ureaMsg= "Urea";

var cyanideScp="load cyanide.mol; spacefill 20%; wireframe 0.1; select all";
var cyanideMsg= "Cyanide";

var hexaneScp="load hexane.pdb; moveto 0 { 938 311 152 160.96} 100.0 0.0 0.12  {-1.423 -1.2985 0.00850001} 5.2174587 {0.0 0.0 0.0} 17.174017 1.2229321 50.0;select all; spacefill 20%; wireframe 0.1";
var hexaneMsg= "Hexane";

var etherScp="load ether.pdb; moveto 0 { 941 17 338 117.7}  130.17 -3.71 -2.23  {-0.78999996 0.77799994 -1.1495} 4.8419933 {0.0 0.0 0.0} 14.912022 2.5934029 50.0; spacefill 20%; wireframe 0.1; javascript showDipole(2,1,0.4,'gold',30), showDipole(3,1,0.4,'gold',30); select all; ";
var etherMsg= "Diethyl Ether";

var estrdPrpScp="load estrdPrp.mol; moveto 0 { 7 -77 997 107.52} 100.0 0.0 0.12  {0.24450004 -4.9535 -2.0939999} 8.784641  {0.0 0.0 0.0} -27.79048 13.445466 50.0; spacefill 20%; wireframe 0.1; javascript showDipole(3,4,0.4,'gold',0), showDipole(3,5,0.4,'gold',0), showDipole(6,5,0.4,'gold',0), showDipole(49,23,0.4,'gold',0), showDipole(21,23,0.4,'gold',0); select all";
var estrdPrpMsg= "Estradiol propionate";

var aceticScp="load acetic.mol; moveto 0 { -277 951 -138 175.32} 100.0 0.0 0.11  {0.28045 0.3965 -9.998679E-5} 2.9823442  {0.0 0.0 0.0} 7.4013233 3.2454765 50.0; spacefill 20%; wireframe 0.1; javascript showDipole(2,3,0.4,'gold',30), showDipole(8,3,0.4,'gold',30), showDipole(2,4,0.4,'gold',30); select all";
var aceticMsg= "Acetic Acid";

var glucoseScp="load glucose.pdb; moveto 0 { -158 -418 894 86.65}  100.0 0.0 0.12  {-0.288 -0.6279998 -0.2850001} 5.143904 {0.0 0.0 0.0} -6.3400087 -4.2206755 50.0; spacefill 20%; wireframe 0.1; javascript showDipole(1,12,0.4,'gold',0), showDipole(24,12,0.4,'gold',0), showDipole(2,7,0.4,'gold',0), showDipole(6,7,0.4,'gold',0), showDipole(6,8,0.4,'gold',0), showDipole(20,8,0.4,'gold',0), showDipole(5,9,0.4,'gold',0), showDipole(21,9,0.4,'gold',0), showDipole(4,10,0.4,'gold',0), showDipole(22,10,0.4,'gold',0), showDipole(3,11,0.4,'gold',0), showDipole(23,11,0.4,'gold',0); select all";
var glucoseMsg= "Glucose";

var hexanoicScp="load hexanoic.mol; moveto 0 { -704 710 -29 178.7} 100.0 0.0 0.12  {-1.4884 -1.9252999 0.008650005} 5.768177 {0.0 0.0 0.0} -16.68548 15.389116 50.0;spacefill 20%; wireframe 0.1; javascript showDipole(6,7,0.4,'gold',20), showDipole(6,8,0.4,'gold',20), showDipole(20,8,0.4,'gold',20); select all";
var hexanoicMsg= "Hexanoic acid";

var sterSulfScp="load sterSulf.mol; moveto 0 { -892 342 295 161.0} 100.0 0.0 0.12  {3.0424 -1.5581 -0.6269002} 8.439589  {0.0 0.0 0.0} -19.056118 -5.112307 50.0; spacefill 20%; wireframe 0.1; javascript showDipole(23,25,0.4,'gold',0), showDipole(23,24,0.4,'gold',0), showDipole(23,26,0.4,'gold',0), showDipole(23,22,0.4,'gold',0), showDipole(14,22,0.4,'gold',0), showDipole(47,26,0.4,'gold',0); select all";
var sterSulfMsg= "Steroidal sulfate";

var lactateScp="load lactic.mol; moveTo 0 {702 -712 14 49.32} 100.0 11.33 -5.68  {0.37500006 0.39810002 0.6496} 3.9831605 {0.0 0.0 0.0} 12.700057 -6.8953037 50.0; set labelOffset 0 0; color label [x101010]; select atomno=11; font label 20 serif bold; label H; delay 0.5; translateSelected {0 1 1}; select atomno=5; label O-; font label 20 serif bold; delay 0.5; connect(atomno=5)(atomno=11) delete;  select atomno=11; font label 20 serif bold; label H+; select atomno=11; for(var i = 0; i <= 1; i = i +1); delay 0.2; translateSelected {0 0.09 0.09}; delay 0.05; end for; select atomno=11 or atomno=5; dots 1.0"
var lactateMsg="Ionization of lactic acid"

var glcPO4Scp="load glcPO4.mol; moveto 0 { 211 -977 40 79.15} 100.0 0.0 0.11  {-0.58265 -0.32974982 -1.8653499} 6.1734657 {0.0 0.0 0.0} -14.142836 2.0699103 50.0; select atomno=10; set labelOffset 0 0; font label 50 serif bold; color label [x101010]; dots 1.0; label -; select all"
var glcPO4Msg="Glucose-1-phosphate"

var KClSettings="All,Atoms,0.4,Dots,1.0,Element"
var KClScp="load KCl.pdb; wireframe off; spacefill 0.4; dots 1.0; set labelOffset 0 0; font label 30 serif bold; color label black; select atomno=1; label Cl-; select atomno=2; label K+";
var KClMsg="Potassium Chloride"

var NalactSettings="All,Atoms,0.4,Dots,1.2,Element"
var NalactScp="load NaLactate.mol; moveto 0 { -632 739 233 75.05} 100.0 0.0 0.12  {0.37500006 0.39810002 0.6496} 5.0531607 {0.0 0.0 0.0} -3.706623 8.412054 50.0;set labelOffset 0 0; color label black; select atomno=11; label Na+; dots 1.0; font label 20 serif bold; select atomno=5; label -; font label 40 serif bold; dots 1.0; spacefill 27%"
var NaLactMsg= "Sodium Lactate"

var BPSettings="Atoms,0.4,Bonds,0.15,H-Bonds,0.15,Dots,|mol;Nucleotide;all|,Element,|col;Base;shapely|";
var ATBPScp= "load ATpair.pdb; select atomno=1 OR atomno=32; CONNECT (selected) single; moveto 0 { 162 338 927 59.2}  100.0 3.04 -4.09  {0.74799967 -0.1164999 0.13450003} 11.937467 {0.0 0.0 0.0} 0.8212401 -1.775078 50.0; select all; CONNECT (atomno=18) (atomno=70) partial magenta CREATE; CONNECT (atomno=31) (atomno=54) partial magenta CREATE; spacefill 0.4; wireframe 0.15; delay 1; moveto 3 { 152 331 931 61.06}  239.01 3.17 -4.09  {0.74799967 -0.1164999 0.13450003} 11.937467 {0.0 0.0 0.0} -2.0660017 2.249064 50.0; javascript showDipole(70,52,0.4,'gold',20), showDipole(31,17,0.4,'gold',20), showDipole(53,54,0.4,'gold',20), showDipole(16,18,0.4,'gold',20),showDipole(19,18,0.4,'gold',20);";
var ATBPMsg="Adenine-Thymine pair";

var DNASettings="Atoms,0.4,Bonds,H-Bonds,0.15,Dots,Trace,Ribbon,200,|mol;DNA;all|,Backbone,Sidechain,Element,|col;Base;shapely|";
var DNAScp="load bdna.pdb; moveto 0 { -843 -236 483 106.48} 100.0 0.0 0.0  {-0.07799959 -0.10200024 -0.0050001144} 25.542456  {0.0 0.0 0.0} 0.047034025 -0.07771263 50.0; ribbon 200; color ribbon green; hbonds calculate; hbonds 0.15; color hbonds magenta; set atomPicking True; set bondPicking False"
var DNAMsg="DNA double helix"

var LysozScp = "load 132l.pdb  FILTER \"![HOH]\"; spacefill off; Ribbons 150; wireframe off; color atoms white; color ribbons structure; moveto 0 {-389 -862 324 86.0} 100.0 0.0 0.0 {2.5635 15.175002 55.595497} 27.3; hbonds calculate; color hbonds magenta; hbonds 0.2; delay 2; moveto 3 {-297 -951 89 107.81} 220.8 -35.64 4.21  {2.5635 15.175002 55.595497} 27.3 {0.0 0.0 0.0} 218.11787 144.94574 50.0; set atomPicking True; set bondPicking False";
var LysozMsg ="Lysozyme";
var LysozSettings="Atoms,Bonds,H-Bonds,0.2,Ribbon,150,Trace,Dots,White,Magenta,4o Structure,Protein,Element,1o Structure,2o Structure";

var WaterScp="load water_cluster.pdb; spacefill 100; wireframe 20; connect 1.6 2.2 (hydrogen) (oxygen) HBOND CREATE; hbonds 20; color hbonds magenta";
var WaterMsg ="Water molecules";
var WaterSettings="All,Atoms,0.3,Bonds,0.15,Dots,Element";

var PlpdScp="load blyrSlice_wH.pdb; select [LIP].X; color atoms white; select all; spacefill 0.4; moveto 0 { -2 1000 -2 87.4}  100.0 0.0 0.11 {-0.17250013 -0.2074995 -17.719} 37.6835 {0.0 0.0 0.0} 23.460972 -0.3103217 50.0;"
var Plpd2Scp=PlpdScp+ " delay 1; connect 2.0 4.0 (_H)(_H and not within(molecule, _1)) HBOND magenta CREATE; delay 1; moveto /* time, axisAngle */ 2.0 { -2 1000 -2 87.4} /* zoom, translation */  360.45 0.59 52.64  /* center, rotationRadius */ {-0.17250013 -0.2074995 -17.719} 37.6835 /* navigation center, translation, depth */ {0.0 0.0 0.0} 85.680626 51.345146 50.0; "
var PlpdMsg="Phospholipid bilayer"
var PlpdSettings="Atoms,0.4,Bonds,0.2,|mol;Lipid;all|,Dots";

// inquiry panel -------------

var molviewScp="load nitrate_aqueous.mol"
var molviewMsg="Test"
var molviewSettings=""

var keratScp="load keratan_sulfate.mol; select atomno=62 or atomno=29; dots 0.8; moveto 0 { 0 0 -1000 1.0} 199.44 0.1 0.0  {0.0 0.0 10.065} 14.611496 {0.0 0.0 0.0} 0.0 0.0 50.0;";
var keratMsg="Keratin";
var keratSettings="All,Atoms,0.4,Bonds,0.075,Dots,Element";
var keratAns="33,26,32,2,4,4,8,0,2";

var KNaGlutScp="load K-Na-glutamate.sdf; select atomno=1 or atomno=2; dots 0.8;";
var KNaGlutMsg="Glutamate";
var KNaGlutSettings="All,Atoms,0.4,Bonds,0.075,Dots,Element";
var KNaGlutAns="7,5,4,1,0,0,2,0,2";

var NereisScp="load Nereistoxin-dicyanate.sdf";
var NereisMsg="Nereistoxin-dicyanate";
var NereisSettings="All,Atoms,0.4,Bonds,0.075,Dots,Element";
var NereisAns="11,7,0,3,2,0,0,2,0";

var addbondScp="load 2-propynyl-thiocyanate.pdb; select all; wireframe 0.075; spacefill 0.3; set bondPicking False; set atomPicking False";
var addbondMsg="2-propynyl thiocyanate";
var addbondSettings="All,Atoms,0.3,Bonds,0.075,Dots,Element";
var addbondAnswers="1,3;7"

var addbond2Scp="load Dodecenyne.pdb; select all; wireframe 0.075; spacefill 0.3; set bondPicking False; set atomPicking False";
var addbond2Msg="Dodecenyne";
var addbond2Settings="All,Atoms,0.3,Bonds,0.075,Dots,Element";
var addbond2Answers="24;31"

var addbond3Scp="load aminomethyl-thiocyanate.pdb; select all; wireframe 0.075; spacefill 0.3; set bondPicking False; set atomPicking False";
var addbond3Msg="Aminomethyl thiocyanate";
var addbond3Settings="All,Atoms,0.3,Bonds,0.075,Dots,Element";
var addbond3Answers=";6"

var hexnlScp="load hexanol.sdf; set bondPicking False; select all; wireframe 0.075; spacefill 0.4; set bondPicking True; set atomPicking False";
var hexnlMsg="Hexanol";                              
var hexnlAns="False,False,True,False";

var isocitrScp="load isocitric_acid.sdf; select all; wireframe 0.075; spacefill 0.4; set bondPicking True; set atomPicking False";
var isocitrMsg="Isocitric Acid"; 
var isocitrSettings="All,Atoms,0.4,Bonds,0.075,Dots,Element";  
var isocitrAns="True,False,False,False";

var serScp="load ser.pdb; select all; wireframe 0.075; spacefill 0.4; set bondPicking False; set atomPicking False";
var serMsg="Serine"; 
var serAns="True,False,False,False";
                                    
var alaScp="load alanine.mol; select all; wireframe 0.075; spacefill 0.4; set bondPicking True; set atomPicking False";
var alaMsg="Alanine";                
var alaAns="False,True,False,False";

var butScp="load butane.sdf; select all; wireframe 0.075; spacefill 0.4; set bondPicking False; set atomPicking False";
var butMsg="Butane"; 
var butAns="False,False,False,True";

var Hbnd1Scp="load Hexan-2-4-dione-enol.sdf; moveto 0 { 177 314 -933 166.49} 100.0 0.1 0.0  {4.1266856 0.14162987 0.01812309} 5.316017 {0.0 0.0 0.0} 36.482483 -6.5676317 50.0; select atomno=2 OR atomno=18;{selected}.property_BPIndx=1;"
var Hbnd1Msg="Hexane-2,4-dione-enol"
var Hbnd1Settings="All,Atoms,1.5,Bonds,0.075,Dots,Element"; 

var Hbnd2Settings="Atoms,0.4,Bonds,0.15,Dots,|mol;Nucleotide;all|,Element,|col;Base;shapely|";
var Hbnd2Scp= "load GCpair.pdb; select atomno=1 OR atomno=33; CONNECT (selected) single; moveto 0 { 162 338 927 59.2}  100.0 3.04 -4.09 {0.74799967 -0.1164999 0.13450003} 11.937467 {0.0 0.0 0.0} 0.8212401 -1.775078 50.0; select all; wireframe 0.15; select base AND [G]; {selected}.property_typeIndx=1; select base AND [C]; {selected}.property_typeIndx=2; select atomno=34 OR atomno=52;{selected}.property_BPIndx=1; select atomno=31 OR atomno=53;{selected}.property_BPIndx=2; select atomno=17 OR atomno=69;{selected}.property_BPIndx=3; select all; spacefill 0.4; wireframe 0.15; set bondPicking False; set atomPicking True"
var Hbnd2Msg="GC Base Pair"

var Hbnd3Settings="Atoms,0.4,Bonds,0.15,Dots,|mol;Nucleotide;all|,Element,|col;Base;shapely|";
var Hbnd3Scp= "load two_base_pairs.mol; select all; wireframe 0.15; select atomno=46 OR atomno=94;{selected}.property_BPIndx=1; select atomno=96 OR atomno=43;{selected}.property_BPIndx=2; select atomno=66 OR atomno=83;{selected}.property_BPIndx=3; select atomno=118 OR atomno=4;{selected}.property_BPIndx=4; select atomno=120 OR atomno=3;{selected}.property_BPIndx=5; select all; spacefill 0.4; wireframe 0.15; set bondPicking False; set atomPicking True";
var Hbnd2Msg="GC Base Pair";

var Hbnd4Scp="load pepHbnds.mol; select atomno=85 OR atomno=4;{selected}.property_BPIndx=1; select atomno=19 OR atomno=95;{selected}.property_BPIndx=2; select atomno=63 OR atomno=119;{selected}.property_BPIndx=3; select atomno=104 OR atomno=39;{selected}.property_BPIndx=4";
var Hbnd4Msg="A short chain of amino acids";
var Hbnd4Settings="All,Atoms,0.3,Bonds,0.075,Dots,Element"; 

var Hbnd5Scp="load trisulfapyradine.sdf; select atomno=85 OR atomno=9;{selected}.property_BPIndx=1; select atomno=81 OR atomno=14;{selected}.property_BPIndx=2; select atomno=4 OR atomno=66;{selected}.property_BPIndx=3"
var Hbnd5Msg="Sulfamerazine";
var Hbnd5Settings="All,Atoms,0.3,Bonds,0.075,Dots,Element"; 

var vdwScp="load cholesterol.mol; load APPEND linoleic.mol;frame *;display 1.1,2.1; moveto 0 { 919 -377 -112 132.34}  92.02 -4.75 9.85   {8.090133 4.251994 10.384647} 10.763325 {0.0 0.0 0.0} -1.2290671 -63.01729 50.0; set appendNew false"
var vdwMsg="Fatty acid and cholesterol";
var vdwSettings="All,Atoms,0.3,Bonds,0.15,Dots,Element";
var vdwAns="False,False,True";
var vdwScp2="connect 2.0 3.3 (_H)(_H and not within(molecule, _1)) HBOND magenta CREATE";

var NitrScp="load nitrate_aqueous.mol";
var NitrMsg="Fatty acid and cholesterol";
var NitrSettings="All,Atoms,0.3,Bonds,0.15,Dots,Element";
var NitrAns="True,False,False";
var NitrScp2="connect 1 2.4 (Hydrogen)(Oxygen) Partial magenta CREATE";
                                                        
var NaGlutScp="load Na-glutamate.mol";
var NaGlutMsg="Monosodium Glutamate";  
var NaGlutSettings="All,Atoms,0.3,Bonds,0.15,Dots,Element";
var NaGlutAns="False,True,False";
var NaGlutScp2="select atomno=1 or atomno=2; dots 1.2;; set labelOffset 0 0; font label 16 serif bold; color label black; select atomno=2; label O-; select atomno=1; label Na+";

var GCPairScp="load GCPair.pdb";
var GCPairMsg="Base Pair";     
var GCPairSettings="All,Atoms,0.3,Bonds,0.15,Dots,Element";
var GCPairAns="True,False,False";
var GCPairScp2="CONNECT (atomno=69) (atomno=17) partial magenta CREATE; CONNECT (atomno=31) (atomno=53) partial magenta CREATE; CONNECT (atomno=34) (atomno=52) partial magenta CREATE;";

function showDipole(num1,num2,dpOffSet,dpColor,lblFont){
jmolScriptWait("dipole (atomno="+num1+")(atomno="+num2+"); dipole bonds width 0.06; dipole offsetSide "+dpOffSet+"; color dipoles "+dpColor+"; set labelOffset 0 0; color label [x101010]; font label "+lblFont+" serif; select atomno="+num2+"; label \u03B4 -; select atomno="+num1+"; label \u03B4 +;"); 
}


function showCrbnNum(){
jmolScript("select {@isCarb AND carbon}; set labelOffset 0 0; set labelFront; color label gold; font label 20; label %a; select ALL");
}

var mtchAns="";
function setMtchAnswers(Ans){
	// type of bond type to be described by correct match
mtchAns=Ans;
}

function checkMatch(mtchVal,ctlID){
var corMat="false"
if (mtchVal == mtchAns){
	corMat = "True"
}
evalResponse(corMat,true,ctlID);
}

var inpAnswers=""
function setInpAnswers(inpAns){
inpAnswers=inpAns.split(",");
   //IE wants to send 'enter' keycode to applet which activates zoom
   // this turns off zoom only for IE
if(window.event){     
  runScript('zoom off')
  }
}



function checkInp(e,corAns,inpVal,ctlID) {
	// look for 'enter' key code (13)
var keynum="";
if(window.event){     //IE
  keynum = window.event.keyCode;
  }
else if(e.which) // Netscape/Firefox/Opera
  {
  keynum = e.which;
  }
if (keynum == 13) {
document.getElementById(tallyGroup+"Attempts").value= Number(document.getElementById(tallyGroup+"Attempts").value)+1;
if (inpVal+"" == inpAnswers[corAns-1]){
	document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
	showMsg("Well done! That is Correct");
	}
else{
	showMsg("Oops! That is incorrect. Try Again.")
	document.getElementById(ctlID).value="";
	}
}
}

function setPolAnswers(Ans){
	// for amino acid models set sidechain type checkbox values
var aAnswers = window[Ans].split(",");	
for (i=0;i<=aAnswers.length-1;i++){
	document.getElementById("qPol"+(i+5)).value=aAnswers[i];
	}
}

var addBondAnswers=""
function setAddBondAnswers(Ans){
	// for amino acid models set sidechain type checkbox values
addBondAnswers = Ans.split(";");
}

function setBPAnswers(BPType){
	// for base pair models set asnswer checkbox values
var aAnswers = window[BPType+'Ans'].split(",");	
for (i=0;i<=6;i++){
	document.getElementById("qBP"+i).value=aAnswers[i];
	}
for (i=7;i<=11;i++){
	document.getElementById("q2BP"+i).value=aAnswers[i];
	}	
}

function setMutAnswers(MutType){
	// for base pair models set answer checkbox values
var aAnswers = window[MutType+'Ans'].split(",");	
for (i=0;i<=8;i++){
	document.getElementById("qMut"+i).value=aAnswers[i];
	}
}

var btypScp=""
function setbtypAnswers(Ans,scrp){
	// for identifying bond types	
btypScp=scrp;	
	//btypScrp holds script that shows bonds
var aAnswers = window[Ans].split(",");	
for (i=0;i<=aAnswers.length-1;i++){
	document.getElementById("btyp"+(i+1)).value=aAnswers[i];
	}
}

function PreEvalResponse(ctlValue,isChecked,ctlID){
evalResponse(ctlValue, isChecked, ctlID)
if (ctlValue == "True"){
	runScript(btypScp)
	}
}

var atmCount=0
var frstAtmNm=0
var frstAtmIdx=0
function IsPickCorrect (id){
	// examine atom selected and determine if it is correct	
document.getElementById(tallyGroup+"Attempts").value= Number(document.getElementById(tallyGroup+"Attempts").value)+1;	
if (toSelect == 'tplB') {
	if (addBondAnswers[1].search(id) != -1){
		var scriptTxt="connect (atomno="+bndAtom1+") (atomno="+bndAtom2+") RADIUS 0.075 TRIPLE MODIFY";
			// for some reason, running jmolScriptwait for the next command causes an error in Mozilla 3.0
			// so it is not sent to the runScript function
		jmolScript(" echo ; "+scriptTxt);
		document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
		return("Correct! This is the location of a triple bond.");
		} 
	else{
		return("Oops! This is not the location of a triple bond. Try Again.");
		}
	}
if (toSelect == 'dblB') {
	if (addBondAnswers[0].search(id) != -1){
		var scriptTxt="connect (atomno="+bndAtom1+") (atomno="+bndAtom2+") RADIUS 0.075 DOUBLE MODIFY";
			// for some reason, running jmolScriptwait for the next command causes an error in Mozilla 3.0
			// so it is not sent to the runScript function
		jmolScript(" echo ; "+scriptTxt);
		document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
		return("Correct! This is the location of a double bond.");
		} 
	else{
		return("Oops! This is not the location of a double bond. Try Again.");
		}
	}
	
if (toSelect == 'hexnl') {
	if (id == "1"  || id == "2" ) {
		document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
		return("Correct! This is a polar bond.");
		} 
	else{
		return("Oops! This is the non-polar region. Try Again.");
		}
	}

if (toSelect == 'ala') {
	if (id == "1" || id == "6" ||id == "7" ||id == "8") {
		document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
		return("Correct! This is a nonpolar bond.");
		} 
	else{
		return("Oops! This is the polar region. Try Again.");
		}
	}	
	
if (toSelect == 'Hbnd'){

			// this is for nucleotide pairs where students click on the atoms forming H-bonds
			// get the custom typeIndx property of the atom
	var typeIndx=jmolEvaluate("{atomno="+atmNm+"}.property_BPIndx");
	if (typeIndx === 0) {
		return "This atom is not |involved in hydrogen bonding";
		}
	else {
		if (atmCount === 0){		
			atmCount=1;
			frstAtmNm=atmNm;		
			frstAtmIdx=typeIndx;		
			return "Good. Now click on the atom|to which it will bond.";
			}
		else{
			if (atmNm == frstAtmNm){
					return "Click on a different atom.";
				}
			else {
					if(frstAtmIdx == typeIndx){
						jmolScript("select atomno="+frstAtmNm+" OR atomno="+atmNm+"; CONNECT (selected) HBOND; hbond 0.2; color hbonds magenta");
						document.getElementById(tallyGroup+"Correct").value = Number(document.getElementById(tallyGroup+"Correct").value)+1;
						atmCount=0
						return "Correct! These atoms will hydrogen bond.";
						}
					else{
						atmCount=0
						return "Oops! These atoms do not|hydrogen bond.|Start again.";
					}
				}
			}
		}	
	}


}