add lone pairs manually in Marvin 5.9?

User 870ab5b546

09-03-2012 14:15:28

I understand that Marvin 5.9 has a feature that allows the user to add up to four lone pairs to an atom manually.  At the version of MarvinSketch posted here, I looked in the Atom and Insert menus, and I right-clicked on an O atom, but I could not find how to add lone pairs.  Does this feature need to be explicitly activated by the configuration file?  I don't see any information about this feature in the User's Guide.

ChemAxon f052bdfe3c

11-03-2012 16:05:29

Yes, this feature needs to be activated by configuration.


The related documentation you can find here:


http://www.chemaxon.com/marvin/help/sketch/gui/customization.html#special

User 870ab5b546

12-03-2012 16:10:59

I downloaded MarvinSketch 5.9.0 to my desktop, and I customized the tool bar so that the Lone pairs group appeared (see screen shot).  I made sure that automatic lone pair display was turned off.  However, after selecting Increase Lone Pairs, clicking on the O of tetrahydrofuran had no effect; lone pairs did not appear.  The other choices in the Lone pairs group also had no effect.

ChemAxon f052bdfe3c

12-03-2012 16:37:11

The automatic lone pair calculation has to be turned off (Edit>Preferences panel) and the display on (View>Misc). (I have attached screenshots and the mrv file).


Best Regards,


Efi


<?xml version="1.0"?>
<cml version="ChemAxon file format v5.9.0, generated by v5.9.0">
<MDocument>
  <MChemicalStruct>
    <molecule molID="m1">
      <atomArray atomID="a1 a2 a3 a4 a5" elementType="O C C C C" lonePair="4 0 0 0 0" x2="-2.694999933242798 -3.9408662622598243 -3.465003844872605 -1.9249960216129907 -1.4491336042257696" y2="3.234992207093842 2.329775608581841 0.865228168661948 0.865228168661948 2.329775608581841"/>
      <bondArray>
        <bond atomRefs2="a1 a2" order="1"/>
        <bond atomRefs2="a1 a5" order="1"/>
        <bond atomRefs2="a2 a3" order="1"/>
        <bond atomRefs2="a3 a4" order="1"/>
        <bond atomRefs2="a4 a5" order="1"/>
      </bondArray>
    </molecule>
  </MChemicalStruct>
</MDocument>
</cml>

ChemAxon f052bdfe3c

12-03-2012 16:41:30

And the second attachment...

User 870ab5b546

12-03-2012 16:59:10

Thanks.  I see that the configuration file is not sufficient; one must also use MarvinSketch parameters to turn automatic calculation off and to turn lone pair visibility on.


msketch_param('lonePairsVisible', 'true');
msketch_param('lonePairsAutoCalc', 'false');

In your MarvinSketch parameter documentation, you say that the default value for lonePairsAutoCalc is false, but I believe it is true.  


Finally, I notice that if lone pair visibility is off or automatic calculation of lone pairs is on, then lone pairs added manually are not visible, but they still appear in the MRV.  See the attached screen shot.  I think it is a VERY bad idea to allow users to change the features of a structure without the user being aware that anything has changed unless he or she looks at the MRV.  So, if automatic lone pair calculation is on OR lone pair display is off, the lone pair buttons on a tool bar should be disabled automatically, so a user cannot change the number of lone pairs on any atom.  


There remains the question of what to do if a user pastes into Marvin a structure that already has manually added lone pairs.  My instinct is that the lone pairs should be stripped from the structure, but I am open to persuasion on this point.

ChemAxon f052bdfe3c

13-03-2012 22:29:43

I can see this is important and I will make a task to fix it, but unfortunately, I am afraid that we cannot do it for 5.10. 


Best Regards,


Efi