Error Opening .mrv files on Mac OSX

I have been using the Mac OSX Marvinsketch 5.3.2 for a while and have been getting this problem when opening larger files.  Any help please?

Hi,

Is it a multimolecule file? Can you please cut the first e.g. 100 lines of the file and send us? In addition, please send the Stack Trace as well.

Thank you and best regards,

Akos

Yes this is a multimolecule file...however, I have other multimolecule files that open up ok.  It seems to be giving me this problem after I add the two headed electron movement arrow.  Here is the stack trace...  How do I send you the first 100 lines of the file?

java.lang.NullPointerException

at chemaxon.struc.MoleculeGraph.indexOf(Unknown Source)

at chemaxon.struc.MoleculeGraph.contains(Unknown Source)

at chemaxon.struc.Molecule.contains(Unknown Source)

at chemaxon.struc.RgMolecule.contains(Unknown Source)

at chemaxon.struc.graphics.MChemicalStruct.containsAtom(Unknown Source)

at chemaxon.struc.graphics.MEFlowBasePoint.checkValidity(Unknown Source)

at chemaxon.struc.graphics.MPolyline.checkValidity(Unknown Source)

at chemaxon.struc.MDocument.setMainMoleculeGraph(Unknown Source)

at chemaxon.marvin.io.formats.cml.MrvImport.readMDocument(Unknown Source)

at chemaxon.marvin.io.formats.cml.MrvImport.readMRV(Unknown Source)

at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc0(Unknown Source)

at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)

at chemaxon.marvin.common.swing.modules.FreeLoadSave.readDocument(Unknown Source)

at chemaxon.marvin.common.swing.modules.LoadSave.open(Unknown Source)

at chemaxon.marvin.common.swing.modules.LoadSave.run(Unknown Source)

at java.lang.Thread.run(Thread.java:637)

Hi Tyson,

Thanks for the Stack Trace and the hint to investigate the electron flow arrow. Actually, there were improvments in the electron flow arrow in version 5.3.3, which was released today. Could you please try to open your file with the new version as well?

Regarding cutting the first 100 lines: you can do that in a text editor for example. It would be even better if you could identify the molecule record where you added the electron flow arrow; if you managed to open your file in a text editor, please search for the text "MEFlow", and the go to the start of the corresponding molecule record (search for the previous "<MDocument>") select the lines until the end of the record (search for the next "</MDocument>"), then paste these files to another text file.

Thanks in advance.

Best regards,

Akos

Akos,

Thanks for the help.  I copied the beginning of the text file for you.  The file is a chemical reaction so there are multiple molecules with electron flow arrows.  These are small peptides so the structures are pretty big.  I downloaded 5.3.3 and tried to open the file, but that did not work.  I received the same message error.  Thanks again for the help.

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MPolyline id="o1">

    <MAtomSetPoint atomRefs="m1.a67" />

    <MPoint x="23.613338470458984" y="-5.115000009536743" />

  </MPolyline>

  <MEllipse id="o2" background="#cccc00" lineColor="#000000"

            toption="NOROT" tcenter="NW">

    <MPoint x="-14.5879551064102" y="-4.689069257024737" />

    <MPoint x="-12.827955354365523" y="-4.689069257024737" />

    <MPoint x="-12.827955354365523" y="-6.394069180730793" />

    <MPoint x="-14.5879551064102" y="-6.394069180730793" />

  </MEllipse>

  <MEllipse id="o3" background="#ffffff" lineColor="#ffffff">

    <MPoint x="-13.123262636823778" y="-5.17491063497764" />

    <MPoint x="-13.329312848226468" y="-5.5318000700374075" />

    <MPoint x="-13.957318318542278" y="-5.169220942698011" />

    <MPoint x="-13.751268107139605" y="-4.81233150763822" />

  </MEllipse>

  <MPolyline id="o4">

    <MPoint x="-13.046810192020827" y="-4.978963904385286" />

    <MPoint x="-12.3856650548976" y="-4.317818767262063" />

  </MPolyline>

  <MTextBox id="o5" toption="NOROT" fontScale="10.0" halign="LEFT"

            valign="TOP" autoSize="false">

    <Field name="text"><![CDATA[Fmoc-Rink Amide MBHA Resin

0.67 mmol/g]]></Field>

    <MPoint x="-9.130000591278076" y="-13.428358989105224" />

    <MPoint x="1.320000171661377" y="-13.428358989105224" />

    <MPoint x="1.320000171661377" y="-15.941638989105225" />

    <MPoint x="-9.130000591278076" y="-15.941638989105225" />

  </MTextBox>

  <MTextBox id="o6" toption="NOROT" fontScale="10.0" halign="LEFT"

            valign="TOP" autoSize="true">

    <Field name="text"></Field>

    <MPoint x="11.824999809265137" y="-10.835000038146973" />

    <MPoint x="11.824999809265137" y="-10.835000038146973" />

    <MPoint x="11.824999809265137" y="-11.635800038146972" />

    <MPoint x="11.824999809265666" y="-11.635800038146972" />

  </MTextBox>

  <MEFlow id="o7" arcAngle="-117.20302527817755" headSkip="0.25"

          headLength="0.5" headWidth="0.4" tailSkip="0.25">

    <MEFlowBasePoint atomRef="m1.a55" />

    <MAtomSetPoint atomRefs="m1.a61" />

  </MEFlow>

  <MEFlow id="o8" arcAngle="-275.0779585092203" headSkip="0.25"

          headLength="0.5" headWidth="0.4" tailSkip="0.15">

    <MAtomSetPoint atomRefs="m1.a42 m1.a61" />

    <MAtomSetPoint atomRefs="m1.a42" />

  </MEFlow>

  <MPolyline id="o9" headLength="0.8" headWidth="0.5">

    <MPoint x="14.850000381469727" y="-8.96500039100647" />

    <MPoint x="20.734999656677246" y="-8.96500039100647" />

  </MPolyline>

  <MEllipse id="o10" background="#cccc00" lineColor="#000000"

            toption="NOROT" tcenter="NW">

    <MPoint x="22.31950569833173" y="-4.708502258614331" />

    <MPoint x="24.07950545037641" y="-4.708502258614331" />

    <MPoint x="24.07950545037641" y="-6.413502182320389" />

    <MPoint x="22.31950569833173" y="-6.413502182320389" />

  </MEllipse>

  <MEllipse id="o11" background="#ffffff" lineColor="#ffffff">

    <MPoint x="23.784198167918152" y="-5.194343636567236" />

    <MPoint x="23.578147956515462" y="-5.551233071627003" />

    <MPoint x="22.950142486199653" y="-5.1886539442876085" />

    <MPoint x="23.156192697602325" y="-4.831764509227817" />

  </MEllipse>

  <MEFlow id="o12" arcAngle="-254.995522631729" headSkip="0.15"

          headLength="0.5" headWidth="0.4" tailSkip="0.25">

    <MEFlowBasePoint atomRef="m1.a103" />

    <MAtomSetPoint atomRefs="m1.a102 m1.a103" />

  </MEFlow>

  <MEFlow id="o13" arcAngle="282.777308921453" headSkip="0.25"

          headLength="0.5" headWidth="0.4" tailSkip="0.15">

    <MAtomSetPoint atomRefs="m1.a101 m1.a102" />

    <MAtomSetPoint atomRefs="m1.a101" />

  </MEFlow>

  <MTextBox id="o14" toption="NOROT" fontScale="10.0" halign="LEFT"

            valign="TOP" autoSize="false">

    <Field name="text"><![CDATA[Piperidine

C{subL=-1,scale=0.7,dy=-0.4}5{subL=0,scale=1.0}H{subL=-1,scale=0.7,dy=-0.4}11{subL=0,scale=1.0}N

Average mass: 85.15 g/mol]]></Field>

    <MPoint x="6.948332786560059" y="-13.556693511352538" />

I have attached the actual file that is giving me problems.  Can you open it?  Maybe this will help.

Thanks for the file, I get the same error message when trying to open it. I assigned this topic to the corresponding developer; she will investigate this issue and reply here soon.

Best regards,

Akos

Dear Tyson,



The NPE is fixed.

Unfortunately the latest release is just came out, so you have to wait
for the next one, which is coming out in the next 2 month, (or rather
earlier).



Thank you,

Regards,

Eva