Marvin Beans 4.1.1 problem

User 870ab5b546

28-09-2006 12:36:10

Paste the file below into Marvin 4.1.1 (standalone version for Mac). Then press the O button, put an O on the left, press the H button, add an H to the newly drawn O. Note how the + sign disappears. Try to change the map number of the newly added O and see how the O-H disappears as you hover over the O. Press the Select button and watch the newly drawn O-H disappear for good.





There is a workaround -- use the bond tool to draw CH3-CH3, then change the two C atoms -- but the behavior I describe shouldn't occur.





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


<MDocument>


  <MChemicalStruct>


    <reaction>


      <propertyList>


        <property dictRef="NAME" title="NAME">


          <scalar><![CDATA[alkyne halogenation]]></scalar>


        </property>


        <property dictRef="REAGENTS" title="REAGENTS">


          <scalar>X2</scalar>


        </property>


        <property dictRef="EXAMPLE" title="EXAMPLE">


          <scalar><![CDATA[


CO.BrBr.CCCC#CCCC>>CCC\\C(OC)=C(\\CCC)Br


CC(O)=O.ClCl.CCCC#C>>CCC\\C(OC(=O)C)=C/Cl


              ]]></scalar>


        </property>


      </propertyList>


      <reactantList>


        <molecule molID="m1">


          <atomArray


              atomID="a1 a2"


              elementType="Cl Cl"


              mrvMap="4 3"


              mrvQueryProps="L,Cl,Br,I: L,Cl,Br,I:"


              x2="-0.48999977111816406 -2.029999771118164"


              y2="0.9099996089935303 0.9099996089935303"


              />


          <bondArray>


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


          </bondArray>


        </molecule>


        <molecule molID="m2">


          <atomArray


              atomID="a1 a2 a3 a4"


              elementType="C C H H"


              mrvMap="1 2 7 6"


              mrvQueryProps="0 0 L,H,C,N,O,F,Si,P,S,Cl,As,Se,Br,Te,I: L,H,C,N,O,F,Si,P,S,Cl,As,Se,Br,Te,I:"


              x2="-0.5946522186930512 -1.5502175856892757 -2.665554038886023 0.8123506230153543"


              y2="6.091981930527467 7.299706727154989 8.651030211403928 4.448991700139001"


              />


          <bondArray>


            <bond atomRefs2="a1 a4" order="1" />


            <bond atomRefs2="a1 a2" order="3" />


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


          </bondArray>


        </molecule>


      </reactantList>


      <productList>


        <molecule molID="m3">


          <atomArray


              atomID="a1 a2 a3 a4 a5 a6"


              elementType="C C O Cl H H"


              mrvMap="1 2 5 3 7 6"


              mrvQueryProps="0 0 0 L,Cl,Br,I: L,H,C,N,O,F,Si,P,S,Cl,As,Se,Br,Te,I: L,H,C,N,O,F,Si,P,S,Cl,As,Se,Br,Te,I:"


              x2="11.144979334936806 9.905588404898904 11.215390449350036 9.74537852439284 8.494273272571021 12.568497476483518"


              y2="5.983660748340629 6.897780257776567 4.445271241431833 8.645933529947857 6.281509540264906 6.571194662840371"


              />


          <bondArray>


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


            <bond atomRefs2="a1 a3" order="1" />


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


            <bond atomRefs2="a2 a4" order="1" />


            <bond atomRefs2="a2 a5" order="1" />


          </bondArray>


        </molecule>


        <molecule molID="m4">


          <atomArray


              atomID="a1 a2"


              elementType="Cl H"


              mrvMap="4 8"


              mrvQueryProps="L,Cl,Br,I: 0"


              x2="13.311666984558105 11.771666984558104"


              y2="1.6333333253860474 1.6333333253860474"


              />


          <bondArray>


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


          </bondArray>


        </molecule>


      </productList>


    </reaction>


  </MChemicalStruct>


</MDocument>


ChemAxon 7c2d26e5cf

28-09-2006 16:04:46

We will check it.

ChemAxon 7c2d26e5cf

03-10-2006 17:12:31

Thanks for the bug report. We have fixed this bug. The next Marvin release are going to include the bugfix.