ChemAxon Forum Archive » Drawing & visualization: Marvin/Sketch /View /Space

too many dots

User 870ab5b546

11-03-2014 16:23:34

Please look at the figure below. The image above the MarvinSketch window shows too many dots for the number of electrons around O and Br. I am using JChem/Marvin 6.2.1. I create the image using this method:


    private static String getImage(String format, String molStr, long qFlags) {

        final String SELF = "MolString.getImage: ";

        String imageData = "";

        if (!Utils.isEmpty(molStr)) try {

            final boolean isLewis = molStr.contains("Lewis ");

            final Molecule mol = MolImporter.importMol(molStr);

            final int[] dims = getBestAppletSize(mol, isLewis);

            final String opts =

                    getImageOptsString(format, dims, qFlags, isLewis);

            // workaround for bug in displaying lone pairs in JChem 6.1

            MDocument mDoc = mol.getDocument();

            if (mDoc == null) mDoc = new MDocument(mol);

            if (Question.showLonePairs(qFlags)) toBinFormat(mDoc, opts);

                    // generates the lone pairs for printing later

            if (PNG.equals(format)) {

                final StringBuilder imageDataBld = new StringBuilder();

                imageDataBld.append("data:image/");

                imageDataBld.append(PNG).append(";base64,");

                imageDataBld.append(Base64Coder.encode(

                        toBinFormat(mDoc, opts)));

                imageData = imageDataBld.toString();

            } else {

                imageData = Utils.bytesToString(toBinFormat(mDoc, opts))

                        .replaceAll("\"clipPath1\"", "\"clipPath2\"");

            } // if format

            debugPrint(SELF + "generated image src URI with options ", opts,

                    "; isLewis = ", isLewis);

            debugPrintMRV(SELF + "image data:\n", imageData);

        } catch (MolFormatException e) {

            System.out.println(SELF + "caught MolFormatException: ");

            e.printStackTrace();

        } // try

        return imageData;

    } // getImage(String, String, long)

In this case, the format is SVG, and qFlags has the value to show lone pairs.

ChemAxon d26931946c

12-03-2014 08:13:42

Hi Bob,


 


Thanks for reporting this issue.


My colleges will respond to you when they find a solution.


BRs,


Peter

ChemAxon 2c555f5717

13-03-2014 16:35:55

Dear Bob!


   We have came across this issue recently, but we could not find the solution yet, because we can not reproduce it constantly. I have run your code several times (with Marvin 6.2.1) and it has never resulted the picture that has been given by you. However you can find an Applet based image export here. This solution might can simplify your process. 


   I have tried to gave molStr the painted reaction in MRV and CXSMARTS both worked correctly. Could you provide me with the exact source that was used by you?


Regards:
Balázs 

User 870ab5b546

13-03-2014 17:54:08

reactants:


<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_1_0.xsd" version="ChemAxon file format v6.1, generated by v6.1.3">

<MDocument><MElectronContainer id="o1" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.6107300330129286 -0.08040414651015215 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.488705650188229 -0.37499704995386285 0.0"></MElectron></MElectronContainer><MElectronContainer id="o2" occupation="1 1" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.04028832151531869 -0.6146810971141692 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="0.2724498386489831 -0.5524736060846189 0.0"></MElectron></MElectronContainer><MElectronContainer id="o3" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.1980067279655584 0.5833089538832512 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.4631333334800338 0.4061570083350414 0.0"></MElectron></MElectronContainer><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3" elementType="O R Br" formalCharge="-1 0 0" sgroupRef="0 sg1 0" x2="-5.919374942779541 -3.1762499809265137 -1.2993748998641967" y2="2.0693750381469727 -0.8181250095367432 0.28874996304512024"></atomArray><bondArray><bond id="b1" atomRefs2="a2 a3" order="1"></bond></bondArray><molecule id="sg1" role="SuperatomSgroup" title="Me" molID="m2"><atomArray atomID="a4" elementType="C" attachmentPoint="1" sgroupAttachmentPoint="1" x2="-3.1762499809265137" y2="-0.8181250095367432"></atomArray><bondArray></bondArray><AttachmentPointArray><attachmentPoint atom="a4" order="1" bond="b1"></attachmentPoint></AttachmentPointArray></molecule></molecule></MChemicalStruct><MElectronContainer id="o5" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.5935109350714045 0.16492655926401767 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.4315322675636848 0.43958605761710157 0.0"></MElectron></MElectronContainer><MElectronContainer id="o6" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.16492655926401856 -0.5935109350714036 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.43958605761710157 -0.4315322675636839 0.0"></MElectron></MElectronContainer><MElectronContainer id="o7" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="-0.16492655926401678 0.5935109350714054 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="-0.4395860576170998 0.4315322675636848 0.0"></MElectron></MElectronContainer><MEFlow id="o8" arcAngle="-140.0" headSkip="0.08" headLength="0.5" headWidth="0.4" tailSkip="0.08" baseElectronContainerIndex="1" baseElectronIndexInContainer="-1"><MEFlowBasePoint atomRef="m1.a1"></MEFlowBasePoint><MAtomSetPoint atomRefs="m1.a1 m1.a2" weights="0.25 0.75"></MAtomSetPoint></MEFlow><MEFlow id="o9" arcAngle="254.77468199999998" headSkip="0.85" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="0"><MAtomSetPoint atomRefs="m1.a2 m1.a3"></MAtomSetPoint><MAtomSetPoint atomRefs="m1.a3"></MAtomSetPoint></MEFlow></MDocument>

</cml>

products:


<?xml version="1.0" encoding="UTF-8"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument>

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

    <MElectron atomRefs="m1.a1" difLoc="-0.6107300330129286 -0.08040414651015215 0.0"/>

    <MElectron atomRefs="m1.a1" difLoc="-0.488705650188229 -0.37499704995386285 0.0"/>

  </MElectronContainer>

  <MElectronContainer id="o2" occupation="1 1" radical="0">

    <MElectron atomRefs="m1.a1" difLoc="-0.04028832151531869 -0.6146810971141692 0.0"/>

    <MElectron atomRefs="m1.a1" difLoc="0.2724498386489831 -0.5524736060846189 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a1" difLoc="-0.1980067279655584 0.5833089538832512 0.0"/>

    <MElectron atomRefs="m1.a1" difLoc="-0.4631333334800338 0.4061570083350414 0.0"/>

  </MElectronContainer>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3" elementType="O C Br" formalCharge="0 0 -1" x2="-6.99608234089173 -4.252957379038703 -0.22266750175200767" y2="1.4343937952346486 -1.4531062524490672 0.9237312059574443"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="1"/>

      </bondArray>

    </molecule>

  </MChemicalStruct>

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

    <MElectron atomRefs="m1.a3" difLoc="0.5935109350714045 0.16492655926401767 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="0.4315322675636848 0.43958605761710157 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a3" difLoc="0.16492655926401856 -0.5935109350714036 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="0.43958605761710157 -0.4315322675636839 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a3" difLoc="-0.16492655926401678 0.5935109350714054 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="-0.4395860576170998 0.4315322675636848 0.0"/>

  </MElectronContainer>

</MDocument>

</cml>

And here is the SVG generated by Marvin for reactants:


<svg fill-opacity="1" xmlns:xlink="http://www.w3.org/1999/xlink" color-rendering="auto" color-interpolation="auto" stroke="black" text-rendering="auto" stroke-linecap="square" width="164" stroke-miterlimit="10" stroke-opacity="1" shape-rendering="auto" fill="black" stroke-dasharray="none" font-weight="normal" stroke-width="1" height="122" xmlns="http://www.w3.org/2000/svg" font-family="&apos;Dialog&apos;" font-style="normal" stroke-linejoin="miter" font-size="12" stroke-dashoffset="0" image-rendering="auto">

  <!--Generated by Marvin with Batik SVG Generator

MolSource:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument><MElectronContainer id="o1" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.6107300330129286 -0.08040414651015215 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.488705650188229 -0.37499704995386285 0.0"></MElectron></MElectronContainer><MElectronContainer id="o2" occupation="1 1" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.04028832151531869 -0.6146810971141692 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="0.2724498386489831 -0.5524736060846189 0.0"></MElectron></MElectronContainer><MElectronContainer id="o3" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.1980067279655584 0.5833089538832512 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.4631333334800338 0.4061570083350414 0.0"></MElectron></MElectronContainer><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3" elementType="O R Br" formalCharge="-1 0 0" sgroupRef="0 sg1 0" x2="-5.919374942779541 -3.1762499809265137 -1.2993748998641967" y2="2.0693750381469727 -0.8181250095367432 0.28874996304512024"></atomArray><bondArray><bond id="b1" atomRefs2="a2 a3" order="1"></bond></bondArray><molecule id="sg1" role="SuperatomSgroup" title="Me" molID="m2"><atomArray atomID="a4" elementType="C" attachmentPoint="1" sgroupAttachmentPoint="1" x2="-3.1762499809265137" y2="-0.8181250095367432"></atomArray><bondArray></bondArray><AttachmentPointArray><attachmentPoint atom="a4" order="1" bond="b1"></attachmentPoint></AttachmentPointArray></molecule></molecule></MChemicalStruct><MElectronContainer id="o5" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.5935109350714045 0.16492655926401767 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.4315322675636848 0.43958605761710157 0.0"></MElectron></MElectronContainer><MElectronContainer id="o6" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.16492655926401856 -0.5935109350714036 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.43958605761710157 -0.4315322675636839 0.0"></MElectron></MElectronContainer><MElectronContainer id="o7" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="-0.16492655926401678 0.5935109350714054 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="-0.4395860576170998 0.4315322675636848 0.0"></MElectron></MElectronContainer><MEFlow id="o8" arcAngle="-140.0" headSkip="0.08" headLength="0.5" headWidth="0.4" tailSkip="0.08" baseElectronContainerIndex="1" baseElectronIndexInContainer="-1"><MEFlowBasePoint atomRef="m1.a1"></MEFlowBasePoint><MAtomSetPoint atomRefs="m1.a1 m1.a2" weights="0.25 0.75"></MAtomSetPoint></MEFlow><MEFlow id="o9" arcAngle="254.77468199999998" headSkip="0.85" headLength="0.5" headWidth="0.4" tailSkip="0.25" baseElectronContainerIndex="1" baseElectronIndexInContainer="0"><MAtomSetPoint atomRefs="m1.a2 m1.a3"></MAtomSetPoint><MAtomSetPoint atomRefs="m1.a3"></MAtomSetPoint></MEFlow></MDocument>

</cml>-->

  <defs id="genericDefs" />

  <g>

    <defs id="defs1">

      <clipPath clipPathUnits="userSpaceOnUse" id="clipPath2">

        <path d="M0 0 L164 0 L164 122 L0 122 L0 0 Z" />

      </clipPath>

    </defs>

    <g font-size="16" stroke-linecap="round" text-rendering="optimizeLegibility" font-family="sans-serif" stroke-linejoin="bevel" shape-rendering="geometricPrecision" stroke-width="1.6171553134918213">

      <line clip-path="url(#clipPath1)" fill="none" x1="104.03680506513672" x2="118.61312841730171" y1="94.82311432581531" y2="86.22682165105721" />

      <line clip-path="url(#clipPath1)" fill="none" x1="118.61312841730171" x2="133.1894517694667" y1="86.22682165105721" y2="77.6305289762991" stroke="rgb(102,51,51)" />

    </g>

    <g font-size="16" fill="red" text-rendering="optimizeLegibility" font-family="sans-serif" shape-rendering="geometricPrecision" stroke="red">

      <text xml:space="preserve" x="19" y="33" clip-path="url(#clipPath1)" stroke="none">OH

      </text>

      <text font-size="12" x="32" y="21" clip-path="url(#clipPath1)" stroke="none" xml:space="preserve">&#8211;

      </text>

      <rect x="84" y="91" clip-path="url(#clipPath1)" fill="white" width="24" rx="8" ry="5.5" height="19" stroke="none" />

      <text x="84" y="106" clip-path="url(#clipPath1)" fill="black" stroke="none" xml:space="preserve">Me

      </text>

      <rect x="133" y="63" clip-path="url(#clipPath1)" fill="white" width="19" rx="6.5" ry="5.5" height="19" stroke="none" />

      <text x="133" y="78" clip-path="url(#clipPath1)" fill="rgb(102,51,51)" stroke="none" xml:space="preserve">Br

      </text>

      <circle r="1.5" clip-path="url(#clipPath1)" cx="9.5" cy="26.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="11.5" cy="34.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="22.5" cy="42.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="30.5" cy="41.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="23.5" cy="11.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="16.5" cy="13.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="156.5" cy="67.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="152.5" cy="60.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="145.5" cy="86.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="152.5" cy="82.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="137.5" cy="56.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="130.5" cy="60.5" stroke="none" />

    </g>

    <g font-size="16" stroke-linecap="butt" text-rendering="optimizeLegibility" font-family="sans-serif" shape-rendering="geometricPrecision" stroke-width="1.5792531967163086">

      <path d="M75.85092163085938 83.02994537353516 L62.2481803894043 83.38070678710938 L66.24256134033203 92.6651382446289" clip-path="url(#clipPath1)" stroke="none" />

      <path fill="none" d="M75.85092163085938 83.02994537353516 L62.2481803894043 83.38070678710938 L66.24256134033203 92.6651382446289 L75.85092163085938 83.02994537353516 Z" clip-path="url(#clipPath1)" />

      <path fill="none" d="M64.24536895751953 88.0229263305664 C52.45564651489258 90.56639862060547 40.221153259277344 86.43419647216797 32.388023376464844 77.26309967041016 C24.55489730834961 68.09200286865234 22.38702964782715 55.36178970336914 26.743125915527344 44.11495590209961" clip-path="url(#clipPath1)" />

      <path d="M142.66799926757812 57.43607711791992 L137.7775421142578 44.73801040649414 L130.3693389892578 51.61366271972656" clip-path="url(#clipPath1)" stroke="none" />

      <path fill="none" d="M142.66799926757812 57.43607711791992 L137.7775421142578 44.73801040649414 L130.3693389892578 51.61366271972656 L142.66799926757812 57.43607711791992 Z" clip-path="url(#clipPath1)" />

      <path fill="none" d="M134.0734405517578 48.17583465576172 C125.2214584350586 43.341339111328125 114.15275573730469 45.8881721496582 108.30384063720703 54.10523986816406 C102.4549331665039 62.32230758666992 103.67284393310547 73.61475372314453 111.13931274414062 80.39573669433594" clip-path="url(#clipPath1)" />

    </g>

  </g>

</svg>

and products:


<svg fill-opacity="1" xmlns:xlink="http://www.w3.org/1999/xlink" color-rendering="auto" color-interpolation="auto" stroke="black" text-rendering="auto" stroke-linecap="square" width="219" stroke-miterlimit="10" stroke-opacity="1" shape-rendering="auto" fill="black" stroke-dasharray="none" font-weight="normal" stroke-width="1" height="109" xmlns="http://www.w3.org/2000/svg" font-family="&apos;Dialog&apos;" font-style="normal" stroke-linejoin="miter" font-size="12" stroke-dashoffset="0" image-rendering="auto">

  <!--Generated by Marvin with Batik SVG Generator

MolSource:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

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ChemAxon 2c555f5717

02-04-2014 09:54:11

Dear Bob!


   We were still unlucky with these files. We are still investigating this issue, but unfortunately we can not give you any solution. 


Regards:
Balázs 

User 870ab5b546

28-04-2014 15:03:06

Maybe this log output will help you diagnose the problem.  Image is below.


Apr 28, 2014 10:53:26 AM org.apache.catalina.core.StandardWrapperValve invoke

INFO: MolString.getImage: molStr:

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MolString.getImage: generated image src URI with options svg:headless,w117,h110,valenceErrorVisible,H_heteroterm,cv_inChain,lp; isLewis = false

MolString.getImage: image data:

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MolSource:

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      <path d="M95.276123046875 54.76686096191406 L86.94058227539062 43.83354949951172 L81.69982147216797 52.59828186035156" clip-path="url(#clipPath1)" stroke="none" />

      <path fill="none" d="M95.276123046875 54.76686096191406 L86.94058227539062 43.83354949951172 L81.69982147216797 52.59828186035156 L95.276123046875 54.76686096191406 Z" clip-path="url(#clipPath1)" />

      <path fill="none" d="M84.32020568847656 48.21591567993164 C78.3105239868164 47.63402557373047 72.5431900024414 50.73410415649414 69.71315002441406 56.06755447387695 C66.88311004638672 61.40100860595703 67.54914093017578 67.91476440429688 71.4000244140625 72.5650863647461" clip-path="url(#clipPath1)" />

    </g>

    <g font-size="16" fill="red" text-rendering="optimizeLegibility" font-family="sans-serif" shape-rendering="geometricPrecision" stroke="red">

      <circle r="1.5" clip-path="url(#clipPath1)" cx="3.5" cy="27.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="6.5" cy="35.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="17.5" cy="41.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="25.5" cy="39.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="13.5" cy="10.5" stroke="none" />

      <circle r="1.5" clip-path="url(#clipPath1)" cx="7.5" cy="15.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="109.5" cy="64.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="105.5" cy="57.5" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="98.5" cy="84.5" stroke="none" />

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      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1.5" cx="90.5" cy="53.5" stroke="none" />

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MolString.getImage: molStr:

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<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument>

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

    <MElectron atomRefs="m1.a1" difLoc="-0.610208952460928 -0.08426763516639824 0.0"/>

    <MElectron atomRefs="m1.a1" difLoc="-0.4863226368646556 -0.37808238900140356 0.0"/>

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  <MElectronContainer id="o2" occupation="1 1" radical="0">

    <MElectron atomRefs="m1.a1" difLoc="-0.038343058193889945 -0.6148055057401001 0.0"/>

    <MElectron atomRefs="m1.a1" difLoc="0.27419669041535677 -0.551608715454412 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a3" difLoc="0.5950103089940679 0.15943253178315242 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="0.4355777772109146 0.43557777721091284 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a3" difLoc="0.1594325317831533 -0.5950103089940662 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="0.4355777772109146 -0.43557777721091373 0.0"/>

  </MElectronContainer>

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

    <MElectron atomRefs="m1.a3" difLoc="-0.15943253178314976 0.5950103089940662 0.0"/>

    <MElectron atomRefs="m1.a3" difLoc="-0.43557777721091284 0.43557777721091284 0.0"/>

  </MElectronContainer>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3" elementType="O C Br" formalCharge="0 0 -1" x2="6.569343264342938 8.205593283416423 11.704335914705556" y2="-4.0899999141693115 -6.544374942779541 -4.524374942779541"/>

      <bondArray>

        <bond id="b1" atomRefs2="a1 a2" order="1"/>

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

    <MElectron atomRefs="m1.a1" difLoc="-0.2035351003463841 0.5814030124853033 0.0"/>

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  </MElectronContainer>

</MDocument>

</cml>

MolString.getImage: generated image src URI with options svg:headless,w176,h99,valenceErrorVisible,H_heteroterm,cv_inChain,lp; isLewis = false

MolString.getImage: image data:

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MolSource:

<?xml version="1.0" encoding="UTF-8"?><cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/help/formats/schema/mrvSchema_6_2_0.xsd" version="ChemAxon file format v6.2, generated by v6.2.1">

<MDocument><MElectronContainer id="o1" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.610208952460928 -0.08426763516639824 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.4863226368646556 -0.37808238900140356 0.0"></MElectron></MElectronContainer><MElectronContainer id="o2" occupation="1 1" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.038343058193889945 -0.6148055057401001 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="0.27419669041535677 -0.551608715454412 0.0"></MElectron></MElectronContainer><MElectronContainer id="o3" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.5950103089940679 0.15943253178315242 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.4355777772109146 0.43557777721091284 0.0"></MElectron></MElectronContainer><MElectronContainer id="o4" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.1594325317831533 -0.5950103089940662 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.4355777772109146 -0.43557777721091373 0.0"></MElectron></MElectronContainer><MElectronContainer id="o5" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="-0.15943253178314976 0.5950103089940662 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="-0.43557777721091284 0.43557777721091284 0.0"></MElectron></MElectronContainer><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3" elementType="O C Br" formalCharge="0 0 -1" x2="6.569343264342938 8.205593283416423 11.704335914705556" y2="-4.0899999141693115 -6.544374942779541 -4.524374942779541"></atomArray><bondArray><bond id="b1" atomRefs2="a1 a2" order="1"></bond></bondArray></molecule></MChemicalStruct><MElectronContainer id="o7" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="-0.2035351003463841 0.5814030124853033 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.46696807370443505 0.40174222847588226 0.0"></MElectron></MElectronContainer><MElectronContainer id="o8" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="0.6106241524709253 0.0799570377361718 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="0.4888375093360784 0.37455690212633863 0.0"></MElectron></MElectronContainer><MElectronContainer id="o9" occupation="0 0" radical="0"><MElectron atomRefs="m1.a1" difLoc="0.04049191830951582 0.6145041806334564 0.0"></MElectron><MElectron atomRefs="m1.a1" difLoc="-0.27218506041272317 0.552422190315073 0.0"></MElectron></MElectronContainer><MElectronContainer id="o10" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.4127159322024472 -0.45707826766391424 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.5859616156658518 -0.1894834252135098 0.0"></MElectron></MElectronContainer><MElectronContainer id="o11" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="0.45707826766391335 0.4127159322024472 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="0.1894834252135098 0.5859616156658527 0.0"></MElectron></MElectronContainer><MElectronContainer id="o12" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="-0.4127159322024454 0.4570782676639151 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="-0.5859616156658518 0.1894834252135098 0.0"></MElectron></MElectronContainer><MElectronContainer id="o13" occupation="0 0" radical="0"><MElectron atomRefs="m1.a3" difLoc="-0.4570782676639151 -0.4127159322024463 0.0"></MElectron><MElectron atomRefs="m1.a3" difLoc="-0.1894834252135098 -0.5859616156658518 0.0"></MElectron></MElectronContainer></MDocument>

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  <defs id="genericDefs" />

  <g>

    <defs id="defs1">

      <clipPath clipPathUnits="userSpaceOnUse" id="clipPath2">

        <path d="M0 0 L176 0 L176 99 L0 99 L0 0 Z" />

      </clipPath>

    </defs>

    <g font-size="14" stroke-linecap="round" fill="red" text-rendering="optimizeLegibility" font-family="sans-serif" stroke-linejoin="bevel" shape-rendering="geometricPrecision" stroke="red" stroke-width="1.5048142671585083">

      <line clip-path="url(#clipPath1)" fill="none" x1="37.34687623062357" x2="51.091970565977334" y1="31.423043181675585" y2="52.040684684706235" />

      <line clip-path="url(#clipPath1)" fill="none" x1="51.091970565977334" x2="64.8370649013311" y1="52.040684684706235" y2="72.65832618773689" stroke="black" />

    </g>

    <g font-size="14" fill="white" text-rendering="optimizeLegibility" font-family="sans-serif" shape-rendering="geometricPrecision" stroke="white">

      <rect x="16" y="15" clip-path="url(#clipPath1)" width="23" rx="7.5" ry="5" height="18" stroke="none" />

      <text x="16" y="29" clip-path="url(#clipPath1)" fill="red" stroke="none" xml:space="preserve">HO

      </text>

      <rect x="65" y="73" clip-path="url(#clipPath1)" width="22" rx="7.5" ry="5" height="18" stroke="none" />

      <rect x="85" y="81" clip-path="url(#clipPath1)" width="7" rx="2.5" ry="4" height="14" stroke="none" />

      <text x="65" y="87" clip-path="url(#clipPath1)" fill="black" stroke="none" xml:space="preserve">CH

      </text>

      <text font-size="11" x="85" y="92" clip-path="url(#clipPath1)" fill="black" stroke="none" xml:space="preserve">3

      </text>

      <text x="145" y="39" clip-path="url(#clipPath1)" fill="rgb(102,51,51)" stroke="none" xml:space="preserve">Br

      </text>

      <text font-size="11" x="159" y="27" clip-path="url(#clipPath1)" fill="rgb(102,51,51)" stroke="none" xml:space="preserve">&#8211;

      </text>

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="17" cy="25" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="20" cy="32" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="30" cy="37" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="38" cy="36" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="166" cy="29" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="162" cy="23" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="156" cy="47" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="162" cy="43" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="148" cy="19" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="142" cy="23" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="27" cy="9" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="20" cy="13" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="45" cy="20" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="42" cy="13" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="32" cy="8" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="red" r="1" cx="25" cy="9" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="166" cy="36" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="166" cy="29" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="155" cy="18" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="148" cy="18" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="138" cy="29" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="138" cy="36" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="148" cy="46" stroke="none" />

      <circle clip-path="url(#clipPath1)" fill="rgb(102,51,51)" r="1" cx="155" cy="46" stroke="none" />

    </g>

  </g>

</svg>

ChemAxon 2c555f5717

29-04-2014 15:12:39

Thank you very much, we are investigating it.

User 870ab5b546

12-05-2014 12:49:58

Hi, any progress?

ChemAxon 2c555f5717

16-05-2014 14:09:08

Dear Bob,


   I could not find a solution for this case yet, but we really appreciate your help on this.


Regards:
Balázs