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

buggy behavior

User 870ab5b546

17-01-2007 02:44:36

Marvin 4.1.5. Load the file below. Hover over the Bu3Sn-H bond on the upper right, hold down the option key, click and hold, and drag the Bu3SnH molecule to the empty space in the topmost box. Now press the B key and place a B atom near the copy of the new Bu3SnH molecule. Now press the H key and draw a B-H bond. Repeat the B-H bond drawing. You will see the B turn into HH and you will see Marvin freeze up.





I think the problem has to do with copying and dragging the molecule that contains the shortcut group, but I'm not sure.








Code:
<?xml version="1.0" ?>


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  <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"


          elementType="C C C C C C I C C R R H C C C C C C C C R C C C C C C C C C C C C C C R Sn R R R C C R C C R R H"


          radical="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 monovalent 0 0 0 0 0 monovalent 0 0 0 0 0 0 0 0 0 0 monovalent 0 0 0 0 0 0 monovalent monovalent 0 0 0"


          sgroupRef="0 0 0 0 0 0 0 0 0 sg1 sg2 0 0 0 0 0 0 0 0 0 sg3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 sg4 0 sg5 sg6 sg7 0 0 sg8 0 0 sg9 sg10 0"


          x2="-8.75874948501587 -10.092418826064128 -10.092418826064128 -8.75874948501587 -7.425080143967611 -7.425080143967611 -6.091401022139575 -1.6362496614456177 -0.30257053961758196 1.0311085822104538 5.775000035762787 7.315000035762787 3.180200190978871 1.8465308499306126 1.8465308499306126 3.180200190978871 4.51386953202713 4.51386953202713 5.847548653855165 7.181227775683201 8.514906897511237 -6.641250133514404 -7.974919474562663 -7.974919474562663 -6.641250133514404 -5.307580792466146 -5.307580792466146 1.1688241360477045 -0.164845205000554 -0.164845205000554 1.1688241360477045 2.502493477095963 2.502493477095963 3.8361725989239988 5.1698517207520345 6.50353084258007 -4.235000133514404 -3.836418804056522 -2.6950001335144043 -3.836418804056522 4.269297598923997 5.602976720752033 6.936655842580069 -3.8157024392229753 -2.4820233173949395 -1.1483441955669038 -7.26687479019165 -5.72687479019165"


          y2="1.7325339359543541 0.9625169953953137 -0.5775168857227673 -1.3475338262818077 -0.5775168857227673 0.9625169953953137 -1.3475168857227673 5.0531251430511475 5.823125143051147 5.0531251430511475 2.1175000369548798 2.1175000369548798 1.038161289277015 0.26814434871797443 -1.2718895324001065 -2.041906472959147 -1.2718895324001065 0.26814434871797443 -2.0418895324001065 -1.2718895324001065 -2.0418895324001065 8.085033957412026 7.315017016852986 5.774983135734905 5.004966195175864 5.774983135734905 7.315017016852986 -6.213433266455718 -6.983450207014759 -8.52348408813284 -9.29350102869188 -8.52348408813284 -6.983450207014759 -9.293484088132839 -8.52348408813284 -9.293484088132839 -3.224375009536743 -1.736849237051578 -3.224375009536743 -4.7119007820219085 -18.19660855407522 -17.426608554075223 -18.19660855407522 -18.148484240720727 -17.37848424072073 -18.148484240720727 -15.255624771118164 -15.255624771118164"


          />


      <bondArray>


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


        <bond atomRefs2="a1 a6" order="1" />


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


        <bond atomRefs2="a3 a4" order="1" />


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


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


        <bond atomRefs2="a5 a7" order="1" />


        <bond atomRefs2="a8 a9" order="2" />


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


        <bond atomRefs2="a13 a18" order="1" />


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


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


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


        <bond atomRefs2="a17 a19" order="1" />


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


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


        <bond atomRefs2="a22 a23" order="1" />


        <bond atomRefs2="a22 a27" order="1" />


        <bond atomRefs2="a23 a24" order="1" />


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


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


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


        <bond atomRefs2="a28 a29" order="1" />


        <bond atomRefs2="a28 a33" order="1" />


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


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


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


        <bond atomRefs2="a32 a34" order="1" />


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


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


        <bond atomRefs2="a41 a42" order="2" />


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


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


        <bond atomRefs2="a45 a46" order="1" />


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


        <bond atomRefs2="a37 a40" order="1" />


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


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


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


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


        <bond atomRefs2="a11 a12" order="1" />


        <bond atomRefs2="a9 a10" order="1" />


      </bondArray>


      <molecule id="sg1" role="SuperatomSgroup" title="CO2Me"


                leftName="MeO2C" molID="m2">


        <atomArray


            atomID="a49 a50 a51 a52"


            elementType="C O C O"


            attachmentPoint="1 0 0 0"


            x2="-1.0999642223596346 0.23371489946840107 1.5673940212964368 -2.4336433441876704"


            y2="6.30437518119812 5.53437518119812 6.304375181198121 5.53437518119812"


            />


        <bondArray>


          <bond atomRefs2="a50 a49" order="1" />


          <bond atomRefs2="a49 a52" order="2" />


          <bond atomRefs2="a51 a50" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg2" role="SuperatomSgroup" title="SnBu3"


                leftName="Bu3Sn" molID="m3">


        <atomArray


            atomID="a53 a54 a55 a56 a57 a58 a59 a60 a61 a62 a63 a64 a65"


            elementType="Sn C C C C C C C C C C C C"


            attachmentPoint="1 0 0 0 0 0 0 0 0 0 0 0 0"


            x2="6.1970193332892185 3.1170193332892193 3.887019333289219 5.427019333289219 1.5770193332892193 5.427019333289218 3.887019333289218 3.1170193332892175 1.5770193332892175 7.7370193332892185 8.507019333289218 10.047019333289217 10.817019333289217"


            y2="1.899637225470188 4.56699546912626 3.2333163472982234 3.2333163472982234 4.56699546912626 0.5659581036421524 0.5659581036421533 -0.7677210181858816 -0.7677210181858807 1.899637225470188 3.2333163472982234 3.2333163472982243 4.56699546912626"


            />


        <bondArray>


          <bond atomRefs2="a56 a53" order="1" />


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


          <bond atomRefs2="a53 a62" order="1" />


          <bond atomRefs2="a57 a54" order="1" />


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


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


          <bond atomRefs2="a58 a59" order="1" />


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


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


          <bond atomRefs2="a62 a63" order="1" />


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


          <bond atomRefs2="a64 a65" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg3" role="SuperatomSgroup" title="CO2Me"


                leftName="MeO2C" molID="m4">


        <atomArray


            atomID="a66 a67 a68 a69"


            elementType="C O C O"


            attachmentPoint="1 0 0 0"


            x2="6.359410324645065 7.693089446473101 9.026768568301136 5.025731202817029"


            y2="-0.9143750572204592 -1.6843750572204592 -0.9143750572204583 -1.6843750572204592"


            />


        <bondArray>


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


          <bond atomRefs2="a66 a69" order="2" />


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


        </bondArray>


      </molecule>


      <molecule id="sg4" role="SuperatomSgroup" title="CO2Me"


                leftName="MeO2C" molID="m5">


        <atomArray


            atomID="a70 a71 a72 a73"


            elementType="C O C O"


            attachmentPoint="1 0 0 0"


            x2="4.3480342697138985 5.681713391541934 7.015392513369971 3.014355147885863"


            y2="-8.165969612953191 -8.935969612953192 -8.165969612953191 -8.935969612953192"


            />


        <bondArray>


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


          <bond atomRefs2="a70 a73" order="2" />


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


        </bondArray>


      </molecule>


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


        <atomArray


            atomID="a74 a75 a76 a77"


            elementType="C C C C"


            attachmentPoint="1 0 0 0"


            x2="-2.5232311455965695 -3.8569102674246047 -5.19058938925264 -6.524268511080676"


            y2="-2.8393750095367425 -3.6093750095367434 -2.8393750095367434 -3.6093750095367434"


            />


        <bondArray>


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


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


          <bond atomRefs2="a76 a77" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg6" role="SuperatomSgroup" title="Bu" molID="m7">


        <atomArray


            atomID="a78 a79 a80 a81"


            elementType="C C C C"


            attachmentPoint="1 0 0 0"


            x2="-2.2344814507723507 -3.568160572600386 -4.901839694428421 -6.235518816256457"


            y2="-2.887500038146972 -3.657500038146973 -2.887500038146973 -3.657500038146973"


            />


        <bondArray>


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


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


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


        </bondArray>


      </molecule>


      <molecule id="sg7" role="SuperatomSgroup" title="Bu" molID="m8">


        <atomArray


            atomID="a82 a83 a84 a85"


            elementType="C C C C"


            attachmentPoint="1 0 0 0"


            x2="-2.090106126523083 -3.4237852483511184 -4.757464370179154 -6.091143492007189"


            y2="-2.7431249523162835 -3.5131249523162844 -2.7431249523162844 -3.5131249523162844"


            />


        <bondArray>


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


          <bond atomRefs2="a83 a84" order="1" />


          <bond atomRefs2="a84 a85" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg8" role="SuperatomSgroup" title="CO2Me"


                leftName="MeO2C" molID="m9">


        <atomArray


            atomID="a86 a87 a88 a89"


            elementType="C O C O"


            attachmentPoint="1 0 0 0"


            x2="4.781159269713897 6.114838391541933 7.4485175133699695 3.4474801478858614"


            y2="-17.069094078895574 -17.839094078895574 -17.069094078895574 -17.839094078895574"


            />


        <bondArray>


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


          <bond atomRefs2="a86 a89" order="2" />


          <bond atomRefs2="a88 a87" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg9" role="SuperatomSgroup" title="CO2Me"


                leftName="MeO2C" molID="m10">


        <atomArray


            atomID="a90 a91 a92 a93"


            elementType="C O C O"


            attachmentPoint="1 0 0 0"


            x2="-3.3038407684330755 -1.9701616466050398 -0.6364825247770032 -4.637519890261111"


            y2="-17.020969765541082 -17.79096976554108 -17.020969765541082 -17.79096976554108"


            />


        <bondArray>


          <bond atomRefs2="a91 a90" order="1" />


          <bond atomRefs2="a90 a93" order="2" />


          <bond atomRefs2="a92 a91" order="1" />


        </bondArray>


      </molecule>


      <molecule id="sg10" role="SuperatomSgroup" title="SnBu3"


                leftName="Bu3Sn" molID="m11">


        <atomArray


            atomID="a94 a95 a96 a97 a98 a99 a100 a101 a102 a103 a104 a105 a106"


            elementType="Sn C C C C C C C C C C C C"


            attachmentPoint="1 0 0 0 0 0 0 0 0 0 0 0 0"


            x2="-6.844855731083798 -9.924855731083797 -9.154855731083797 -7.614855731083797 -11.464855731083798 -7.614855731083798 -9.1548557310838 -9.924855731083799 -11.464855731083798 -5.304855731083798 -4.534855731083798 -2.994855731083798 -2.2248557310837986"


            y2="-15.810362425246593 -13.143004181590522 -14.476683303418557 -14.476683303418557 -13.143004181590522 -17.14404154707463 -17.14404154707463 -18.477720668902663 -18.477720668902663 -15.810362425246593 -14.476683303418557 -14.476683303418557 -13.143004181590522"


            />


        <bondArray>


          <bond atomRefs2="a97 a94" order="1" />


          <bond atomRefs2="a94 a99" order="1" />


          <bond atomRefs2="a94 a103" order="1" />


          <bond atomRefs2="a98 a95" order="1" />


          <bond atomRefs2="a95 a96" order="1" />


          <bond atomRefs2="a96 a97" order="1" />


          <bond atomRefs2="a99 a100" order="1" />


          <bond atomRefs2="a100 a101" order="1" />


          <bond atomRefs2="a101 a102" order="1" />


          <bond atomRefs2="a103 a104" order="1" />


          <bond atomRefs2="a104 a105" order="1" />


          <bond atomRefs2="a105 a106" order="1" />


        </bondArray>


      </molecule>


    </molecule>


  </MChemicalStruct>


</MDocument>

User f359e526a1

17-01-2007 18:50:33

Hm, are you also getting an exception with a message "Molecule@a37c6a[4a,2b] is not a parent of child S-group: SuperatomSgroup@13d21d6[Bu3Sn,C].parentMolecule=Molecule@7881db[2a,1b] " in the very first line? I am working on Linux, but my impression is that it is the same error (pressing the Ctrl key). But do nat have to use this big molecule, any sgroup - atom bond can do.

User 870ab5b546

17-01-2007 21:09:52

I did see that error at one point when I was playing around with the "damaged" file. But I don't remember exactly how I elicited it. Perhaps by undoing, then trying to repeat what I did.