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disappearing charges in MarvinSketch 5.3.8
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Michiel

Joined: 23 Jan 2004
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Link to postPosted: Fri Sep 24, 2010 2:50 pmPost subject: disappearing charges in MarvinSketch 5.3.8 Reply with quote

I think this may be related to the topic "disappearing MEFlow object in MarvinSketch 5.3.8", but I can't be sure.

 

Let's start with what I'm seeing in 5.2.4 to establish what I'm expecting to see in 5.3.8.

Note that the structure at left has a (somewhat ill-positioned but otherwise correct) + charge on the bottom/left carbon atom.

The idea is that students have to figure out a more reasonable/stable resonance form.

So, they should move the lone pair on N into the adjacent bond, and kick the double bond one over ....




 Filename: 524 solution.gif    Filesize: 50.36 KB    Viewed: 5360 Time(s)
 Description:  expected solution to the question
524 solution.gif

 Filename: 524 template.gif    Filesize: 49.23 KB    Viewed: 5360 Time(s)
 Description:  template given to students
524 template.gif
Michiel

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Link to postPosted: Fri Sep 24, 2010 3:07 pmPost subject: Re: disappearing charges in MarvinSketch 5.3.8 Reply with quote

mvanrhee wrote:

I think this may be related to the topic "disappearing MEFlow object in MarvinSketch 5.3.8", but I can't be sure.

 

Let's start with what I'm seeing in 5.2.4 to establish what I'm expecting to see in 5.3.8.

Note that the structure at left has a (somewhat ill-positioned but otherwise correct) + charge on the bottom/left carbon atom.

The idea is that students have to figure out a more reasonable/stable resonance form.

So, they should move the lone pair on N into the adjacent bond, and kick the double bond one over ....

Now, if I load the exact same MRV file (see below) in 5.3.8, the "+" has gone missing.....

And it gets even weirder when I tried to replicate the electron movements I described above: one of the arrows goes missing (which is why I linked in to the case cited above), the lone pairs gets magically moved on top of a bond, and although the "+" charge is not shown, if you use the context-sensitive menu (right-click on the atom), it will show you that the charge is present and set to "+1".

If I export the MRV from 5.3.8, the file is nominally the same as the correct solution with 5.2.4, so I know that the student solved this correctly, but the display/presentation of the question and answer is completely at odds with what is being taught in class.

Here's the MRV template. The formalCharge array clearly has the "1" charge in the correct position.

<?xml version="1.0" ?>
<cml>
<MDocument>
<MPolyline id="o1" headLength="0.8" headWidth="0.5">
<MPoint x="-3.4833333492279053" y="1.1733332872390747" />
<MPoint x="-0.036666665226221085" y="1.1733332872390747" />
</MPolyline>
<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"
elementType="C C C C C C N C C C H C C C C C C N C C C H"
formalCharge="0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"
lonePair="0 0 0 0 0 0 1 0 0 0 -3 0 0 0 0 0 0 0 0 0 0 -3"
x2="-9.826666831970215 -9.826666831970215 -8.49298771014218 -7.159308588314143 -7.159308588314143 -8.49298771014218 -5.825629466486108 -4.491950344658072 -4.491950344658072 -5.825629466486108 -5.825629466486108 1.244731501358297 1.244731501358297 2.5784106231863326 3.9120897450143683 3.9120897450143683 2.5784106231863326 5.245768866842404 6.57944798867044 6.57944798867044 5.245768866842404 5.245768866842404"
y2="1.8333334028720856 0.29333340287208554 2.6033334028720856 1.8333334028720856 0.29333340287208554 -0.4766665971279149 2.6033334028720856 1.8333334028720856 0.29333340287208554 -0.4766665971279149 4.143333402872086 1.9199999475479126 0.37999994754791255 2.6899999475479124 1.9199999475479126 0.37999994754791255 -0.3900000524520879 2.6899999475479124 1.9199999475479126 0.37999994754791255 -0.3900000524520879 4.229999947547913" />
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a1 a3" order="1" />
<bond atomRefs2="a3 a4" order="1" />
<bond atomRefs2="a5 a6" order="1" />
<bond atomRefs2="a6 a2" order="1" />
<bond atomRefs2="a10 a5" order="1" />
<bond atomRefs2="a4 a5" order="2" />
<bond atomRefs2="a4 a7" order="1" />
<bond atomRefs2="a7 a8" order="1" />
<bond atomRefs2="a8 a9" order="1" />
<bond atomRefs2="a9 a10" order="1" />
<bond atomRefs2="a7 a11" order="1" />
<bond atomRefs2="a12 a13" order="1" />
<bond atomRefs2="a12 a14" order="1" />
<bond atomRefs2="a14 a15" order="1" />
<bond atomRefs2="a16 a17" order="1" />
<bond atomRefs2="a17 a13" order="1" />
<bond atomRefs2="a21 a16" order="1" />
<bond atomRefs2="a15 a16" order="2" />
<bond atomRefs2="a15 a18" order="1" />
<bond atomRefs2="a18 a19" order="1" />
<bond atomRefs2="a19 a20" order="1" />
<bond atomRefs2="a20 a21" order="1" />
<bond atomRefs2="a18 a22" order="1" />
</bondArray>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

My IS staff tells me rolling back to 5.2.x is not easy given all the integration issues, but 5.3.8. is not workable for this type of content at the moment. (One big sticking point being that MRV files generated with 5.3.8 contain the new MEFlow objects which cause errors when sent into 5.2.4.)

Please investigate.

Thanks,

   Michiel

 




 Filename: 538 hidden charge.gif    Filesize: 48.77 KB    Viewed: 5358 Time(s)
 Description:  hidden charge revealed
538 hidden charge.gif

 Filename: 538 malformed elements.gif    Filesize: 42.76 KB    Viewed: 5358 Time(s)
 Description:  students are stumped by what MarvinSketch does here
538 malformed elements.gif

 Filename: 538 template.gif    Filesize: 41.59 KB    Viewed: 5358 Time(s)
 Description:  the same MRV source file in 5.3.8
538 template.gif
Peter
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Link to postPosted: Mon Oct 18, 2010 10:15 amPost subject: Reply with quote

Sorry for not responding any sooner.

The charges are disappearing on carbon atoms if the Carbon Label Visibility is set to "Never" option and Lone Pair painting is turned off.

We are working on the solution until then we suggest to set the Carbon Label Visibility to "At straight angles and at implicit H atoms" option.

Michiel

Joined: 23 Jan 2004
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Link to postPosted: Mon Oct 18, 2010 3:40 pmPost subject: Reply with quote

gezapeti wrote:

Sorry for not responding any sooner.

The charges are disappearing on carbon atoms if the Carbon Label Visibility is set to "Never" option and Lone Pair painting is turned off.

We are working on the solution until then we suggest to set the Carbon Label Visibility to "At straight angles and at implicit H atoms" option.

Lone pairs are actually turned on in this case, unless I'm misunderstanding what you mean with "Lone Pair painting".

Can you clarify?

Thanks,

   Michiel

Peter
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Link to postPosted: Mon Oct 18, 2010 10:18 pmPost subject: Reply with quote

Yes, the problem is more complicated. If the carbon labels are turned off, the charge appears on the carbon atom only if it has a negative charge and Lone Pair painting is turned on. If the carbon has a positive charge with the same options it is missig.

We managed to fix the problem, it will be available in 5.4.

Until then use the "At straight angles and at implicit H atoms" carbon label visibility option, if it's acceptible.

Best regards, 

Peter

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