Reference numbers to S-groups does not match number of S-gro

The code:

    private Molecule getMolResponse(String responseMRV) {

        try {

            return MolImporter.importMol(responseMRV); // line 420

        } catch (MolFormatException e) {

            Utils.alwaysPrint("Response.getMolResponse: error in "

                    + "importing Molecule from response string:\n",

                    responseMRV);

            e.printStackTrace();

            initializationErrorResult.grade = 0;

            final String[] feedback = new String[] {

                    CANNOT + "response.",

                    "Please report this error to the programmers."};

            translate(feedback);

            final StringBuilder fdbck = new StringBuilder();

            fdbck.append(feedback[0]).append(' ');

            fdbck.append(feedback[1]).append(BR);

            fdbck.append(e.getMessage());

            initializationErrorResult.feedback = fdbck.toString();

            return null;

        } // try importing Molecule

    } // getMolResponse(String)

The substrate:

<?xml version="1.0" encoding="windows-1252"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generated by v14.9.8.0">

<MDocument>

  <MElectronContainer id="o1" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a6" difLoc="4.440892098500626E-16 0.4375799999999983 0.0"/>

    <MElectron atomRefs="m1.a6" difLoc="-0.21878999999999982 0.37895539618799257 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o2" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a6" difLoc="4.440892098500626E-16 -0.43758000000000097 0.0"/>

    <MElectron atomRefs="m1.a6" difLoc="0.2187900000000007 -0.37895539618799523 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o3" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="-0.4226698230675705 -0.11325403775596321 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="-0.30941578531160907 -0.30941578531161085 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o4" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="0.11325403775596143 -0.4226698230675723 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="0.30941578531160907 -0.30941578531161085 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o5" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="-0.11325403775596143 0.42266982306756873 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="-0.30941578531160907 0.3094157853116073 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o6" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a13" difLoc="-0.2181247840915903 -0.3793386810819559 0.0"/>

    <MElectron atomRefs="m1.a13" difLoc="7.677363226639145E-4 -0.4375793265008525 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o7" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a13" difLoc="0.3104996218185372 -0.3083281389210937 0.0"/>

    <MElectron atomRefs="m1.a13" difLoc="0.42306462982086135 -0.11177019009797551 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o8" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a13" difLoc="-0.05825720501160969 0.4336846255797342 0.0"/>

    <MElectron atomRefs="m1.a13" difLoc="-0.26729453228340017 0.34645330047698675 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o9" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a21" difLoc="-0.23833151184560464 0.3669800360528982 0.0"/>

    <MElectron atomRefs="m1.a21" difLoc="-0.3898911618070944 0.19864827798073648 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o10" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a21" difLoc="-0.3898821939175967 -0.19866587846431927 0.0"/>

    <MElectron atomRefs="m1.a21" difLoc="-0.23831494518369034 -0.3669907945740515 0.0"/>

  </MElectronContainer>

  <MRectangle id="o11">

    <MPoint x="-8.711999893188477" y="2.815999984741211"/>

    <MPoint x="4.004000186920166" y="2.815999984741211"/>

    <MPoint x="4.004000186920166" y="-3.4760000705718994"/>

    <MPoint x="-8.711999893188477" y="-3.4760000705718994"/>

  </MRectangle>

  <MRectangle id="o12">

    <MPoint x="4.400000095367432" y="3.4760000705718994"/>

    <MPoint x="11.307999610900879" y="3.4760000705718994"/>

    <MPoint x="11.307999610900879" y="-3.0799999237060547"/>

    <MPoint x="4.400000095367432" y="-3.0799999237060547"/>

  </MRectangle>

  <MElectronContainer id="o13" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a31" difLoc="0.21879000000000115 0.3789553961879939 0.0"/>

    <MElectron atomRefs="m1.a31" difLoc="8.881784197001252E-16 0.4375800000000005 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o14" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a31" difLoc="-0.3094157853116082 0.30941578531160907 0.0"/>

    <MElectron atomRefs="m1.a31" difLoc="-0.4226698230675696 0.11325403775596143 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o15" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a36" difLoc="-0.3094157853116095 0.30941578531160907 0.0"/>

    <MElectron atomRefs="m1.a36" difLoc="-0.42266982306757095 0.11325403775595966 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o16" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a36" difLoc="0.3094157853116104 0.3094157853116055 0.0"/>

    <MElectron atomRefs="m1.a36" difLoc="0.11325403775596099 0.42266982306756695 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o17" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a36" difLoc="-0.3094157853116095 -0.30941578531160907 0.0"/>

    <MElectron atomRefs="m1.a36" difLoc="-0.1132540377559601 -0.4226698230675705 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o18" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a43" difLoc="0.11325403775596232 0.42266982306756695 0.0"/>

    <MElectron atomRefs="m1.a43" difLoc="-0.11325403775596055 0.42266982306756695 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o19" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a43" difLoc="-0.11325403775596055 -0.4226698230675723 0.0"/>

    <MElectron atomRefs="m1.a43" difLoc="0.11325403775596232 -0.4226698230675723 0.0"/>

  </MElectronContainer>

  <MEFlow id="o20" arcAngle="-140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0">

    <MAtomSetPoint atomRefs="m1.a34 m1.a36"/>

    <MAtomSetPoint atomRefs="m1.a34 m1.a43" weights="0.25 0.75"/>

  </MEFlow>

  <MRectangle id="o21">

    <MPoint x="-7.435999870300293" y="-4.927999973297119"/>

    <MPoint x="4.664000034332275" y="-4.927999973297119"/>

    <MPoint x="4.664000034332275" y="-12.319999694824219"/>

    <MPoint x="-7.435999870300293" y="-12.319999694824219"/>

  </MRectangle>

  <MPolyline id="o22" headLength="0.6" headWidth="0.4">

    <MPoint x="0.8360000252723694" y="-2.2880001068115234"/>

    <MPoint x="-1.4274352997245146" y="-6.208385089352299"/>

  </MPolyline>

  <MElectronContainer id="o23" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a49" difLoc="0.4226698230675723 0.11325403775595966 0.0"/>

    <MElectron atomRefs="m1.a49" difLoc="0.30941578531161085 0.3094157853116055 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o24" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a49" difLoc="0.0 0.43757999999999875 0.0"/>

    <MElectron atomRefs="m1.a49" difLoc="-0.21878999999999849 0.3789553961879921 0.0"/>

  </MElectronContainer>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="C" x2="-7.363124847412109" y2="1.1549999713897705"/>

        <atom id="a2" elementType="C" x2="-6.029445725584074" y2="1.9249999713897705"/>

        <atom id="a3" elementType="C" x2="-4.695766603756038" y2="1.1549999713897705"/>

        <atom id="a4" elementType="C" x2="-3.3620874819280027" y2="1.9249999713897705"/>

        <atom id="a5" elementType="C" x2="-2.028408360099967" y2="1.1549999713897705"/>

        <atom id="a6" elementType="O" x2="-0.6947292382719312" y2="1.9249999713897705"/>

        <atom id="a7" elementType="Br" x2="-6.641250133514404" y2="-2.1656250953674316"/>

        <atom id="a8" elementType="C" x2="-5.307571011686369" y2="-1.3956250953674316"/>

        <atom id="a9" elementType="C" x2="-3.973891889858333" y2="-2.1656250953674316"/>

        <atom id="a10" elementType="C" x2="-2.640212768030297" y2="-1.3956250953674316"/>

        <atom id="a11" elementType="R" sgroupRef="sg1" x2="-1.3065336462022616" y2="-2.1656250953674316"/>

        <atom id="a12" elementType="R" sgroupRef="sg2" x2="1.588125228881836" y2="0.5293750166893005"/>

        <atom id="a13" elementType="O" formalCharge="-1" x2="3.128125228881836" y2="0.5293750166893005"/>

        <atom id="a14" elementType="C" x2="8.806876182556152" y2="1.2512838882706385"/>

        <atom id="a15" elementType="C" x2="7.473206841507894" y2="0.48126694771159795"/>

        <atom id="a16" elementType="C" x2="7.473206841507894" y2="-1.058766933406483"/>

        <atom id="a17" elementType="C" x2="8.806876182556152" y2="-1.8287838739655238"/>

        <atom id="a18" elementType="C" x2="10.140545523604410" y2="-1.058766933406483"/>

        <atom id="a19" elementType="C" x2="10.140545523604410" y2="0.48126694771159795"/>

        <atom id="a20" elementType="C" x2="6.008668593799296" y2="-1.534623759337988"/>

        <atom id="a21" elementType="O" x2="5.103447396751934" y2="-0.2887511012717824"/>

        <atom id="a22" elementType="C" x2="6.008558944685262" y2="0.957088908462719"/>

        <atom id="a23" elementType="H" x2="7.473206841507894" y2="2.021266947711598"/>

        <atom id="a24" elementType="H" x2="7.473206841507894" y2="-2.598766933406483"/>

        <atom id="a25" elementType="R" sgroupRef="sg3" x2="8.806876182556152" y2="2.791283888270639"/>

        <atom id="a26" elementType="C" x2="-5.5879998207092285" y2="-10.472000122070312"/>

        <atom id="a27" elementType="C" x2="-5.618321019315763" y2="-8.734000186920166"/>

        <atom id="a28" elementType="C" x2="-4.284641897487727" y2="-7.964000186920167"/>

        <atom id="a29" elementType="C" x2="-4.254320698881193" y2="-11.242000122070312"/>

        <atom id="a30" elementType="C" x2="-5.373586340515010" y2="-6.875055743892884"/>

        <atom id="a31" elementType="O" x2="-4.284641897487727" y2="-5.786111300865601"/>

        <atom id="a32" elementType="H" x2="-6.462530783542293" y2="-5.786111300865601"/>

        <atom id="a33" elementType="H" x2="-6.707265462343045" y2="-7.645055743892884"/>

        <atom id="a34" elementType="C" x2="1.6720000505447388" y2="-9.460000038146973"/>

        <atom id="a35" elementType="C" x2="3.0056791723727745" y2="-8.690000038146973"/>

        <atom id="a36" elementType="Br" x2="0.3383209287167035" y2="-8.690000038146971"/>

        <atom id="a37" elementType="C" x2="3.0056791723727745" y2="-7.150000038146973"/>

        <atom id="a38" elementType="H" sgroupRef="sg4" x2="1.9167347293454913" y2="-6.061055595119690"/>

        <atom id="a39" elementType="H" x2="4.0946236154000575" y2="-6.061055595119690"/>

        <atom id="a40" elementType="H" x2="2.7609444935720218" y2="-10.548944481174257"/>

        <atom id="a41" elementType="H" x2="0.5830556075174556" y2="-10.548944481174257"/>

        <atom id="a42" elementType="R" sgroupRef="sg5" x2="-2.552000045776367" y2="-7.611999988555908"/>

        <atom id="a43" elementType="O" x2="-1.0120000457763672" y2="-7.611999988555908"/>

        <atom id="a44" elementType="C" x2="13.022468831725515" y2="-11.361154166553290"/>

        <atom id="a45" elementType="C" x2="11.284468896575369" y2="-11.391475365159822"/>

        <atom id="a46" elementType="C" x2="10.514468896575370" y2="-10.057796243331788"/>

        <atom id="a47" elementType="C" x2="13.792468831725515" y2="-10.027475044725257"/>

        <atom id="a48" elementType="C" x2="9.425524453548086" y2="-11.146740686359072"/>

        <atom id="a49" elementType="O" x2="8.336580010520805" y2="-10.057796243331788"/>

        <atom id="a50" elementType="H" x2="8.336580010520802" y2="-12.235685129386356"/>

        <atom id="a51" elementType="H" x2="10.195524453548089" y2="-12.480419808187110"/>

        <atom id="a52" elementType="C" x2="13.755765302711936" y2="-7.315433241273910"/>

        <atom id="a53" elementType="C" x2="12.666820859684652" y2="-6.226488798246626"/>

        <atom id="a54" elementType="C" x2="11.179295087199490" y2="-6.625070127704505"/>

        <atom id="a55" elementType="R" sgroupRef="sg7" x2="10.409295087199487" y2="-7.958749249532542"/>

        <atom id="a56" elementType="H" x2="9.845615965371453" y2="-5.855070127704509"/>

        <atom id="a57" elementType="H" x2="14.525765302711935" y2="-5.981754119445873"/>

        <atom id="a58" elementType="H" x2="15.089444424539970" y2="-8.085433241273911"/>

      </atomArray>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="2"/>

        <bond id="b2" atomRefs2="a2 a3" order="1"/>

        <bond id="b3" atomRefs2="a3 a4" order="2"/>

        <bond id="b4" atomRefs2="a4 a5" order="1"/>

        <bond id="b5" atomRefs2="a5 a6" order="1"/>

        <bond id="b6" atomRefs2="a7 a8" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="2"/>

        <bond id="b9" atomRefs2="a12 a13" order="1"/>

        <bond id="b10" atomRefs2="a10 a11" order="1"/>

        <bond id="b11" atomRefs2="a14 a15" order="1"/>

        <bond id="b12" atomRefs2="a16 a17" order="1"/>

        <bond id="b13" atomRefs2="a17 a18" order="1"/>

        <bond id="b14" atomRefs2="a18 a19" order="1"/>

        <bond id="b15" atomRefs2="a14 a19" order="1"/>

        <bond id="b16" atomRefs2="a15 a22" order="1"/>

        <bond id="b17" atomRefs2="a15 a16" order="1"/>

        <bond id="b18" atomRefs2="a16 a20" order="1"/>

        <bond id="b19" atomRefs2="a20 a21" order="1"/>

        <bond id="b20" atomRefs2="a21 a22" order="1"/>

        <bond id="b21" atomRefs2="a15 a23" order="1"/>

        <bond id="b22" atomRefs2="a16 a24" order="1"/>

        <bond id="b23" atomRefs2="a14 a25" order="1"/>

        <bond id="b24" atomRefs2="a26 a27" order="1"/>

        <bond id="b25" atomRefs2="a26 a29" order="2"/>

        <bond id="b26" atomRefs2="a27 a28" order="2"/>

        <bond id="b27" atomRefs2="a28 a30" order="1"/>

        <bond id="b28" atomRefs2="a30 a31" order="1"/>

        <bond id="b29" atomRefs2="a30 a32" order="1"/>

        <bond id="b30" atomRefs2="a30 a33" order="1"/>

        <bond id="b31" atomRefs2="a34 a35" order="1"/>

        <bond id="b32" atomRefs2="a34 a36" order="1"/>

        <bond id="b33" atomRefs2="a35 a37" order="2"/>

        <bond id="b34" atomRefs2="a37 a38" order="1"/>

        <bond id="b35" atomRefs2="a37 a39" order="1"/>

        <bond id="b36" atomRefs2="a34 a40" order="1"/>

        <bond id="b37" atomRefs2="a34 a41" order="1"/>

        <bond id="b38" atomRefs2="a42 a43" order="1"/>

        <bond id="b39" atomRefs2="a44 a45" order="1"/>

        <bond id="b40" atomRefs2="a44 a47" order="2"/>

        <bond id="b41" atomRefs2="a45 a46" order="2"/>

        <bond id="b42" atomRefs2="a46 a48" order="1"/>

        <bond id="b43" atomRefs2="a48 a49" order="1"/>

        <bond id="b44" atomRefs2="a48 a50" order="1"/>

        <bond id="b45" atomRefs2="a48 a51" order="1"/>

        <bond id="b46" atomRefs2="a52 a53" order="1"/>

        <bond id="b47" atomRefs2="a53 a54" order="2"/>

        <bond id="b48" atomRefs2="a54 a55" order="1"/>

        <bond id="b49" atomRefs2="a54 a56" order="1"/>

        <bond id="b50" atomRefs2="a52 a57" order="1"/>

        <bond id="b51" atomRefs2="a52 a58" order="1"/>

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m2">

        <atomArray atomID="a59 a60 a61 a62" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="-2.1105895847558753 -0.7769104629278396 0.5567686589001957 -3.4442687065839106" y2="-1.7806250953674316 -2.550625095367432 -1.7806250953674312 -2.550625095367432"/>

        <bondArray>

          <bond id="b52" atomRefs2="a60 a59" order="1"/>

          <bond id="b53" atomRefs2="a59 a62" order="2"/>

          <bond id="b54" atomRefs2="a61 a60" order="1"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a59" order="1" bond="b10"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="tBu" molID="m3">

        <atomArray atomID="a63 a64 a65 a66" elementType="C C C C" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="1.5400002002716064 0.7700002002716069 3.0800002002716065 0.770000200271606" y2="0.721875011920929 2.0555541337489647 0.721875011920929 -0.6118041099071063"/>

        <bondArray>

          <bond id="b55" atomRefs2="a63 a64" order="1"/>

          <bond id="b56" atomRefs2="a63 a65" order="1"/>

          <bond id="b57" atomRefs2="a63 a66" order="1"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a63" order="1" bond="b9"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg3" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m4">

        <atomArray atomID="a67 a68 a69 a70" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="22.041250076293945 22.811250076293945 24.351250076293944 20.501250076293946" y2="4.62691024835112 3.2932311265230823 3.2932311265230823 4.62691024835112"/>

        <bondArray>

          <bond id="b58" atomRefs2="a69 a68" order="1"/>

          <bond id="b59" atomRefs2="a68 a67" order="1"/>

          <bond id="b60" atomRefs2="a67 a70" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a67" order="1" bond="b23"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg4" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m5">

        <atomArray atomID="a71 a72 a73 a74" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="5.313000049591064 6.083000049591064 7.623000049591064 3.7730000495910643" y2="-6.694839438843705 -8.028518560671742 -8.028518560671742 -6.694839438843705"/>

        <bondArray>

          <bond id="b61" atomRefs2="a73 a72" order="1"/>

          <bond id="b62" atomRefs2="a72 a71" order="1"/>

          <bond id="b63" atomRefs2="a71 a74" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a71" order="1" bond="b34"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg5" role="SuperatomSgroup" title="tBu" molID="m6">

        <atomArray atomID="a75 a76 a77 a78" elementType="C C C C" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="0.35200007438659675 1.1220000743865963 1.1220000743865972 -1.1879999256134033" y2="-7.611999988555908 -6.2783208667278725 -8.945679110383944 -7.611999988555908"/>

        <bondArray>

          <bond id="b64" atomRefs2="a75 a76" order="1"/>

          <bond id="b65" atomRefs2="a75 a77" order="1"/>

          <bond id="b66" atomRefs2="a75 a78" order="1"/>

        </bondArray>

        <SgroupAtom>

          <scalar title="graphicalMarvinProperty::FormattedLabel" convention="atomprop" dataType="xsd:string">\i\St\n&#8201;Bu</scalar>

        </SgroupAtom>

        <AttachmentPointArray>

          <attachmentPoint atom="a75" order="1" bond="b38"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg6" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m7">

        <molecule id="sg7" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m8">

          <atomArray atomID="a79 a80 a81 a82" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="14.11299976348877 14.882999763488769 16.422999763488768 12.57299976348877" y2="-8.718839606690384 -10.052518728518422 -10.052518728518422 -8.718839606690384"/>

          <bondArray>

            <bond id="b67" atomRefs2="a81 a80" order="1"/>

            <bond id="b68" atomRefs2="a80 a79" order="1"/>

            <bond id="b69" atomRefs2="a79 a82" order="2"/>

          </bondArray>

          <AttachmentPointArray>

            <attachmentPoint atom="a79" order="1" bond="b48"/>

          </AttachmentPointArray>

        </molecule>

      </molecule>

    </molecule>

  </MChemicalStruct>

  <MEFlow id="o26" arcAngle="-140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0">

    <MEFlowBasePoint atomRef="m1.a46"/>

    <MAtomSetPoint atomRefs="m1.a46 m1.a54" weights="0.25 0.75"/>

  </MEFlow>

  <MEFlow id="o27" arcAngle="-140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="-1" baseElectronIndexInContainer="0">

    <MEFlowBasePoint atomRef="m1.a47"/>

    <MAtomSetPoint atomRefs="m1.a47 m1.a53" weights="0.25 0.75"/>

  </MEFlow>

  <MRectangle id="o28">

    <MPoint x="6.820000171661377" y="-4.5320000648498535"/>

    <MPoint x="16.41200065612793" y="-4.5320000648498535"/>

    <MPoint x="16.41200065612793" y="-12.847999572753906"/>

    <MPoint x="6.820000171661377" y="-12.847999572753906"/>

  </MRectangle>

  <MPolyline id="o29" headLength="0.6" headWidth="0.4">

    <MPoint x="8.184000015258789" y="-5.323999881744385"/>

    <MPoint x="6.448368718345446" y="-2.317798292283812"/>

  </MPolyline>

  <MPolyline id="o30" headLength="0.6" headWidth="0.4">

    <MPoint x="3.7839999198913574" y="-9.855999946594238"/>

    <MPoint x="7.831999778747559" y="-7.303999900817871"/>

  </MPolyline>

</MDocument>

</cml>

The exception:

chemaxon.formats.MolFormatException: Reference numbers to S-groups does not match number of S-groups.

	at chemaxon.marvin.io.formats.cml.MrvImport.readMDocument(MrvImport.java:286)

	at chemaxon.marvin.io.formats.cml.MrvImport.readMRV(MrvImport.java:139)

	at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(MrvImport.java:79)

	at chemaxon.marvin.io.formats.cml.CMLImport.readDocument(CMLImport.java:207)

	at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:715)

	at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:687)

	at chemaxon.marvin.io.MRecordImporter.readMol0(MRecordImporter.java:595)

	at chemaxon.marvin.io.MRecordImporter.readMol(MRecordImporter.java:512)

	at chemaxon.formats.MolImporter.readMol(MolImporter.java:883)

	at chemaxon.formats.MolImporter.read(MolImporter.java:766)

	at chemaxon.formats.MolImporter.importMol(MolImporter.java:1308)

	at chemaxon.formats.MolImporter.importMol(MolImporter.java:1499)

	at chemaxon.formats.MolImporter.importMol(MolImporter.java:1465)

	at com.epoch.responses.Response.getMolResponse(Response.java:420)

	at com.epoch.responses.Response.initializeResponse(Response.java:161)

	at com.epoch.responses.Response.<init>(Response.java:104)

	at com.epoch.qBank.Question.parseResponse(Question.java:1216)

	at com.epoch.session.HWSession.submitResponse(HWSession.java:928)

	at org.apache.jsp.homework.answerframe_jsp._jspService(answerframe_jsp.java:582)

What does this mean? JChem and MarvinSketch 14.9.8.0.

I see there is a weird construction of sg7 and sg8 in the MRV; maybe this is the root of the problem. But the question then becomes, how could a student have used MarvinSketch to generate such a structure? The structure would have come straight from a MarvinSketch applet.

Here's another response that elicited the same error.

<?xml version="1.0" encoding="windows-1252"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation

="http://www.chemaxon.com/marvin/schema/mrvSchema_14_8_4.xsd" version="ChemAxon file format v14.8.4, generate

d by v14.9.8.0">

<MDocument>

  <MElectronContainer id="o1" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a19" difLoc="-0.22916491523615434 0.35286541928163473 0.0"/>

    <MElectron atomRefs="m1.a19" difLoc="-0.37489534789143875 0.1910079595968628 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o2" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a19" difLoc="-0.37488672492076347 -0.19102488313876798 0.0"/>

    <MElectron atomRefs="m1.a19" difLoc="-0.2291489857535467 -0.35287576401351073 0.0"/>

  </MElectronContainer>

  <MRectangle id="o3">

    <MPoint x="-8.800000190734863" y="3.6519999504089355"/>

    <MPoint x="2.552000045776367" y="3.6519999504089355"/>

    <MPoint x="2.552000045776367" y="-6.248000144958496"/>

    <MPoint x="-8.800000190734863" y="-6.248000144958496"/>

  </MRectangle>

  <MRectangle id="o4">

    <MPoint x="1.7599999904632568" y="-6.424000263214111"/>

    <MPoint x="14.739999771118164" y="-6.424000263214111"/>

    <MPoint x="14.739999771118164" y="-15.576000213623047"/>

    <MPoint x="1.7599999904632568" y="-15.576000213623047"/>

  </MRectangle>

  <MRectangle id="o5">

    <MPoint x="6.116000175476074" y="3.388000011444092"/>

    <MPoint x="18.875999450683594" y="3.388000011444092"/>

    <MPoint x="18.875999450683594" y="-5.4120001792907715"/>

    <MPoint x="6.116000175476074" y="-5.4120001792907715"/>

  </MRectangle>

  <MElectronContainer id="o6" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a27" difLoc="0.21037500000000264 0.36438018864230237 0.0"/>

    <MElectron atomRefs="m1.a27" difLoc="3.552713678800501E-15 0.42074999999999996 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o7" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a27" difLoc="-0.29751517818423423 0.29751517818423956 0.0"/>

    <MElectron atomRefs="m1.a27" difLoc="-0.40641329141112337 0.10889811322688558 0.0"/>

  </MElectronContainer>

  <MPolyline id="o8" headLength="0.6" headWidth="0.4">

    <MPoint x="-3.0799999237060547" y="-6.248000144958496"/>

    <MRectanglePoint pos="7" rectRef="o4"/>

  </MPolyline>

  <MElectronContainer id="o9" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="-0.40641329141112337 -0.10889811322688558 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="-0.2975151781842378 -0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o10" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="0.10889811322688558 -0.40641329141112514 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="0.2975151781842449 -0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o11" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a7" difLoc="-0.10889811322688203 0.40641329141112514 0.0"/>

    <MElectron atomRefs="m1.a7" difLoc="-0.2975151781842378 0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o12" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a6" difLoc="-1.3322676295501878E-15 0.4207500000000004 0.0"/>

    <MElectron atomRefs="m1.a6" difLoc="-0.21037500000000042 0.3643801886423028 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o13" occupation="1 1" radical="0">

    <MElectron atomRefs="m1.a6" difLoc="-1.3322676295501878E-15 -0.42074999999999996 0.0"/>

    <MElectron atomRefs="m1.a6" difLoc="0.21037499999999776 -0.36438018864230237 0.0"/>

  </MElectronContainer>

  <MPolyline id="o14" headLength="0.6" headWidth="0.4">

    <MPoint x="6.335999965667725" y="-6.380000114440918"/>

    <MRectanglePoint pos="6" rectRef="o5"/>

  </MPolyline>

  <MElectronContainer id="o15" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a43" difLoc="0.4064132914111269 0.10889811322688558 0.0"/>

    <MElectron atomRefs="m1.a43" difLoc="0.29751517818424134 0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o16" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a43" difLoc="-0.10889811322688558 0.4064132914111256 0.0"/>

    <MElectron atomRefs="m1.a43" difLoc="-0.29751517818423956 0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MEFlow id="o17" arcAngle="140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="1">

    <MAtomSetPoint atomRefs="m1.a45 m1.a46"/>

    <MAtomSetPoint atomRefs="m1.a45 m1.a47" weights="0.25 0.75"/>

  </MEFlow>

  <MEFlow id="o18" arcAngle="140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="1">

    <MAtomSetPoint atomRefs="m1.a38 m1.a39"/>

    <MAtomSetPoint atomRefs="m1.a38 m1.a44" weights="0.25 0.75"/>

  </MEFlow>

  <MRectangle id="o19">

    <MPoint x="22.8799991607666" y="3.7839999198913574"/>

    <MPoint x="34.891998291015625" y="3.7839999198913574"/>

    <MPoint x="34.891998291015625" y="-4.136000156402588"/>

    <MPoint x="22.8799991607666" y="-4.136000156402588"/>

  </MRectangle>

  <MRectangle id="o20">

    <MPoint x="39.11600112915039" y="5.191999912261963"/>

    <MPoint x="50.64400100708008" y="5.191999912261963"/>

    <MPoint x="50.64400100708008" y="-5.5879998207092285"/>

    <MPoint x="39.11600112915039" y="-5.5879998207092285"/>

  </MRectangle>

  <MPolyline id="o21" headLength="0.6" headWidth="0.4">

    <MRectanglePoint pos="5" rectRef="o19"/>

    <MRectanglePoint pos="7" rectRef="o20"/>

  </MPolyline>

  <MElectronContainer id="o22" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a34" difLoc="-0.40641329141112514 -0.10889811322688736 0.0"/>

    <MElectron atomRefs="m1.a34" difLoc="-0.297515178184236 -0.29751517818424134 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o23" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a34" difLoc="0.10889811322688736 -0.40641329141112514 0.0"/>

    <MElectron atomRefs="m1.a34" difLoc="0.2975151781842431 -0.29751517818424134 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o24" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a60" difLoc="-0.2416139830424342 0.34446080429908155 0.0"/>

    <MElectron atomRefs="m1.a60" difLoc="-0.3814742493738308 0.17750481560980735 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o25" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a60" difLoc="0.2416139830424342 -0.34446080429908155 0.0"/>

    <MElectron atomRefs="m1.a60" difLoc="0.3814742493738308 -0.17750481560980824 0.0"/>

  </MElectronContainer>

  <MEFlow id="o26" arcAngle="140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="1">

    <MAtomSetPoint atomRefs="m1.a62 m1.a55"/>

    <MAtomSetPoint atomRefs="m1.a62 m1.a54" weights="0.25 0.75"/>

  </MEFlow>

  <MEFlow id="o27" arcAngle="140.0" headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="-1">

    <MEFlowBasePoint atomRef="m1.a6"/>

    <MAtomSetPoint atomRefs="m1.a6 m1.a26" weights="0.25 0.75"/>

  </MEFlow>

  <MElectronContainer id="o28" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a34" difLoc="-0.10889811322688736 0.40641329141112514 0.0"/>

    <MElectron atomRefs="m1.a34" difLoc="-0.29751517818423956 0.2975151781842378 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o29" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a33" difLoc="0.4064132914111269 0.10889811322688558 0.0"/>

    <MElectron atomRefs="m1.a33" difLoc="0.29751517818424134 0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o30" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a33" difLoc="-0.10889811322688381 0.40641329141112514 0.0"/>

    <MElectron atomRefs="m1.a33" difLoc="-0.2975151781842378 0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o31" occupation="0 0" radical="0">

    <MElectron atomRefs="m1.a66" difLoc="-0.40641329141112514 -0.10889811322688558 0.0"/>

    <MElectron atomRefs="m1.a66" difLoc="-0.29751517818423956 -0.29751517818423956 0.0"/>

  </MElectronContainer>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60 a61 a62 a63 a64 a65 a66 a67 a68" elementType="C C C C C O Br C C C C C C C C C C C O C H H R C C C O C C C C C O Br C C C C C C C C O C C C C C C R R C C C C C C R C O C C C C C O H H" formalCharge="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0" sgroupRef="0 0 0 0 0 0 0 0 0 0 sg1 0 0 0 0 0 0 0 0 0 0 0 sg2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 sg6 sg7 0 0 0 0 0 0 sg8 0 0 0 0 0 0 0 0 0 0" x2="-7.363124847412109 -6.029445725584074 -4.695766603756038 -3.3620874819280027 -2.028408360099967 -0.6947292382719312 -6.641250133514404 -5.307571011686369 -3.973891889858333 -2.640212768030297 -1.3065336462022616 46.69087600708008 45.35720666603182 45.35720666603182 46.69087600708008 48.024545348128335 48.024545348128335 43.892668418323225 42.98744722127586 43.89255876920919 45.35720666603182 45.35720666603182 46.69087600708008 -6.4679999351501465 -4.9279999351501464 -4.9279999351501464 -3.8390554921228635 3.900786445682799 5.234465567510833 6.568144689338871 7.901823811166905 9.23550293299494 10.569182054822976 4.622661159580504 5.956340281408538 7.290019403236575 8.623698525064611 9.004788444584165 10.338467566412199 11.672146688240236 13.00582581006827 14.339504931896307 15.673184053724341 11.060342280309904 12.394021402137941 13.727700523965975 16.44318405372434 17.98318405372434 16.841765383182224 9.855999946594238 14.828001022338867 -3.440474162664981 30.360000610351562 29.026331269303306 30.360000610351562 31.69366995139982 31.69366995139982 31.130000610351562 27.807998657226562 26.58705615206549 25.927000045776367 26.69952566567364 11.339182054822976 12.672861176651011 11.339182054822976 12.672861176651011 12.672861176651011 14.160386949136177" y2="1.1549999713897705 1.9249999713897705 1.1549999713897705 1.9249999713897705 1.1549999713897705 1.9249999713897705 -2.1656250953674316 -1.3956250953674316 -2.1656250953674316 -1.3956250953674316 -2.1656250953674316 2.2632838529846886 1.4932669124256481 -0.0467669686924328 -0.8167839092514735 -0.0467669686924328 1.4932669124256481 -0.5226237946239376 0.7232488634422678 1.9690888731767693 3.033266912425648 -1.5867669686924328 3.8032838529846895 -3.9600000381469727 -3.9600000381469727 -5.500000038146973 -2.8710555951196897 -8.124625366384333 -7.354625366384333 -8.124625366384333 -7.354625366384333 -8.124625366384333 -7.354625366384333 -11.445250433141535 -10.675250433141535 -11.445250433141535 -10.675250433141535 0.6533754652196713 1.4233754652196708 0.6533754652196713 1.4233754652196708 0.6533754652196713 1.4233754652196708 -1.8972496015375313 -2.667249601537531 -1.8972496015375313 0.08969634339163512 0.08969634339163512 -1.3978294290935303 -12.187999725341797 -2.8379993438720703 -4.358581367604854 1.936033878972314 1.1660169384132733 -1.1440338832638484 -0.37401694270480784 1.1660169384132733 3.2697130008003494 1.715999960899353 0.4950555781919703 -0.45088891776423745 -1.7023076240691424 -8.688304488212369 -7.918304488212369 -10.22830448821237 -9.458304488212368 -10.99830448821237 -9.85688581767025"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="2"/>

        <bond id="b2" atomRefs2="a2 a3" order="1"/>

        <bond id="b3" atomRefs2="a3 a4" order="2"/>

        <bond id="b4" atomRefs2="a4 a5" order="1"/>

        <bond id="b5" atomRefs2="a5 a6" order="1"/>

        <bond id="b6" atomRefs2="a7 a8" order="1"/>

        <bond id="b7" atomRefs2="a8 a9" order="1"/>

        <bond id="b8" atomRefs2="a9 a10" order="2"/>

        <bond id="b9" atomRefs2="a10 a11" order="1"/>

        <bond id="b10" atomRefs2="a12 a13" order="1"/>

        <bond id="b11" atomRefs2="a14 a15" order="1"/>

        <bond id="b12" atomRefs2="a15 a16" order="1"/>

        <bond id="b13" atomRefs2="a16 a17" order="1"/>

        <bond id="b14" atomRefs2="a12 a17" order="1"/>

        <bond id="b15" atomRefs2="a13 a20" order="1"/>

        <bond id="b16" atomRefs2="a13 a14" order="1"/>

        <bond id="b17" atomRefs2="a14 a18" order="1"/>

        <bond id="b18" atomRefs2="a18 a19" order="1"/>

        <bond id="b19" atomRefs2="a19 a20" order="1"/>

        <bond id="b20" atomRefs2="a13 a21" order="1"/>

        <bond id="b21" atomRefs2="a14 a22" order="1"/>

        <bond id="b22" atomRefs2="a12 a23" order="1"/>

        <bond id="b23" atomRefs2="a24 a25" order="1"/>

        <bond id="b24" atomRefs2="a25 a26" order="1"/>

        <bond id="b25" atomRefs2="a25 a27" order="1"/>

        <bond id="b26" atomRefs2="a28 a29" order="2"/>

        <bond id="b27" atomRefs2="a29 a30" order="1"/>

        <bond id="b28" atomRefs2="a30 a31" order="2"/>

        <bond id="b29" atomRefs2="a31 a32" order="1"/>

        <bond id="b30" atomRefs2="a32 a33" order="1"/>

        <bond id="b31" atomRefs2="a34 a35" order="1"/>

        <bond id="b32" atomRefs2="a35 a36" order="1"/>

        <bond id="b33" atomRefs2="a36 a37" order="2"/>

        <bond id="b34" atomRefs2="a38 a39" order="2"/>

        <bond id="b35" atomRefs2="a39 a40" order="1"/>

        <bond id="b36" atomRefs2="a40 a41" order="2"/>

        <bond id="b37" atomRefs2="a41 a42" order="1"/>

        <bond id="b38" atomRefs2="a42 a43" order="1"/>

        <bond id="b39" atomRefs2="a44 a45" order="1"/>

        <bond id="b40" atomRefs2="a45 a46" order="2"/>

        <bond id="b41" atomRefs2="a43 a47" order="1"/>

        <bond id="b42" atomRefs2="a47 a48" order="1"/>

        <bond id="b43" atomRefs2="a47 a49" order="1"/>

        <bond id="b44" atomRefs2="a37 a50" order="1"/>

        <bond id="b45" atomRefs2="a46 a51" order="1"/>

        <bond id="b46" atomRefs2="a25 a52" order="1"/>

        <bond id="b47" atomRefs2="a55 a56" order="1"/>

        <bond id="b48" atomRefs2="a56 a57" order="1"/>

        <bond id="b49" atomRefs2="a53 a57" order="1"/>

        <bond id="b50" atomRefs2="a53 a58" order="1"/>

        <bond id="b51" atomRefs2="a59 a60" order="1"/>

        <bond id="b52" atomRefs2="a60 a61" order="1"/>

        <bond id="b53" atomRefs2="a59 a54" order="1"/>

        <bond id="b54" atomRefs2="a54 a53" order="1"/>

        <bond id="b55" atomRefs2="a61 a62" order="1"/>

        <bond id="b56" atomRefs2="a62 a55" order="2"/>

        <bond id="b57" atomRefs2="a33 a63" order="1"/>

        <bond id="b58" atomRefs2="a63 a64" order="1"/>

        <bond id="b59" atomRefs2="a63 a65" order="1"/>

        <bond id="b60" atomRefs2="a63 a66" order="1"/>

        <bond id="b61" atomRefs2="a66 a67" order="1"/>

        <bond id="b62" atomRefs2="a66 a68" order="1"/>

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m2">

        <atomArray atomID="a69 a70 a71 a72" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="-2.1105895847558753 -0.7769104629278396 0.5567686589001957 -3.4442687065839106" y2="-1.7806250953674316 -2.550625095367432 -1.7806250953674312 -2.550625095367432"/>

        <bondArray>

          <bond id="b63" atomRefs2="a70 a69" order="1"/>

          <bond id="b64" atomRefs2="a69 a72" order="2"/>

          <bond id="b65" atomRefs2="a71 a70" order="1"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a69" order="1" bond="b9"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg2" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m3">

        <atomArray atomID="a73 a74 a75 a76" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="59.925249900817875 60.69524990081787 62.23524990081787 58.38524990081787" y2="5.63891021306517 4.3052310912371325 4.3052310912371325 5.63891021306517"/>

        <bondArray>

          <bond id="b66" atomRefs2="a75 a74" order="1"/>

          <bond id="b67" atomRefs2="a74 a73" order="1"/>

          <bond id="b68" atomRefs2="a73 a76" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a73" order="1" bond="b22"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg3" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m4"/>

      <molecule id="sg4" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m5"/>

      <molecule id="sg5" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m6"/>

      <molecule id="sg6" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m7">

        <atomArray atomID="a77 a78 a79 a80" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="13.320999946594238 14.090999946594238 15.630999946594237 11.780999946594239" y2="-12.854839286255814 -14.188518408083851 -14.188518408083851 -12.854839286255814"/>

        <bondArray>

          <bond id="b69" atomRefs2="a79 a78" order="1"/>

          <bond id="b70" atomRefs2="a78 a77" order="1"/>

          <bond id="b71" atomRefs2="a77 a80" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a77" order="1" bond="b44"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg7" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m8">

        <atomArray atomID="a81 a82 a83 a84" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="18.293001022338867 19.063001022338867 20.603001022338866 16.753001022338868" y2="-3.5048389047860873 -4.838518026614125 -4.838518026614125 -3.5048389047860873"/>

        <bondArray>

          <bond id="b72" atomRefs2="a83 a82" order="1"/>

          <bond id="b73" atomRefs2="a82 a81" order="1"/>

          <bond id="b74" atomRefs2="a81 a84" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a81" order="1" bond="b45"/>

        </AttachmentPointArray>

      </molecule>

      <molecule id="sg8" role="SuperatomSgroup" title="CO2Me" leftName="MeO2C" molID="m9">

        <atomArray atomID="a85 a86 a87 a88" elementType="C O C O" attachmentPoint="1 0 0 0" sgroupAttachmentPoint="1 0 0 0" x2="28.820000610351563 27.280000610351564 26.51000061035156 29.590000610351563" y2="0.6023547571442762 0.6023547571442798 -0.7313243646837613 1.9360338789723137"/>

        <bondArray>

          <bond id="b75" atomRefs2="a87 a86" order="1"/>

          <bond id="b76" atomRefs2="a86 a85" order="1"/>

          <bond id="b77" atomRefs2="a85 a88" order="2"/>

        </bondArray>

        <AttachmentPointArray>

          <attachmentPoint atom="a85" order="1" bond="b50"/>

        </AttachmentPointArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

  <MEFlow id="o33" arcAngle="254.77468199999998" headSkip="0.6" headLength="0.5" headWidth="0.4" tailSkip="0.38" baseElectronContainerIndex="1" baseElectronIndexInContainer="0">

    <MAtomSetPoint atomRefs="m1.a63 m1.a66"/>

    <MAtomSetPoint atomRefs="m1.a66"/>

  </MEFlow>

  <MEFlow id="o34" arcAngle="254.77468199999998" headSkip="0.6" headLength="0.5" headWidth="0.4" tailSkip="0.38" baseElectronContainerIndex="1" baseElectronIndexInContainer="0">

    <MAtomSetPoint atomRefs="m1.a34 m1.a35"/>

    <MAtomSetPoint atomRefs="m1.a34"/>

  </MEFlow>

  <MPolyline id="o35" headLength="0.6" headWidth="0.4">

    <MRectanglePoint pos="5" rectRef="o5"/>

    <MPoint x="22.8799991607666" y="0.054999999701976776"/>

  </MPolyline>

</MDocument>

</cml>

Here's a conversation about it with a student:

Me: I don’t suppose you remember doing anything unusual when you were drawing the response that couldn’t be interpreted?


Student: Something happened when I attempted to copy and paste the compound and the CO2Me did not copy as such it copied as CH3 however when I ran my mouse over the molecule some blue circles and brackets popped up saying CO2Me in blue as well like it was there but wasn't there. so I just changed the visible CH3 compound to CO2Me and that worked fine but the blue still popped up when I ran my  mouse over it. however if my mouse wasn't there I couldn't see it.

Note: This student submitted the first response I posted above. This would have been a mechanism problem, so automatic lone pair calculation would have been turned on. I've noted elsewhere in this forum a few bugs around shortcut groups when automatic lone pair calculation is turned on.

I've managed to reproduce this issue, it happens when there is an expanded abbreviation  on the canvas and the student creates an abbreviation of the exact same atoms. We'll prevent the creation of such Sgroups in the near future.

Thanks for persisting at discovering the root of the bug!

So imagine a user has drawn a CO₂Me shortcut group, then expands it. Your proposed solution is to prevent the user from drawing another CO₂Me group? I'm not sure this approach is best. My students won't understand why they're suddenly not permitted to draw a CO₂Me group; they won't make the connection to a previous expansion of a CO₂Me group. Then they'll start complaining to me that they can't draw a CO₂Me group.

Perhaps a better solution would be to automatically ungroup any expanded CO₂Me groups if a student draws a new CO₂Me group.

But an even better solution would be to fix the problem so that users can draw a new CO₂Me group in the presence of an expanded one.

Any progress on fixing this bug? I've had a number of these exceptions pop up again. Students find it extremely frustrating.

What is the status of this bug?

Hi Bob,

as we started work on the reproduction case that Peti found, we however fixed it, while fixing it we got to be unsure whether that was the real root cause of the issue.

After some more research we gave up the search for other possible causes, and released the fix in december. Unfortunatelly or intentionally (we do not remember) we left this out from the release notes, and apparently we forget to notify you about the fix. Sorry about that, and thank your patience.

Regards,
Istvan