moving multiatom ligands

User 870ab5b546

05-04-2013 14:45:10

Consider this structure:


<?xml version="1.0" encoding="MacRoman"?>
<cml version="ChemAxon file format v5.10.0, generated by v5.12.2">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray atomID="a1 a2 a3 a4" elementType="C C Pd X" sgroupRef="sg1 sg1 0 0" x2="-0.824999988079071 -0.8249999880790709 -2.9700000286102295 -0.824999988079071" y2="2.5850000381469727 1.0450000381469726 1.815000057220459 1.8150000381469726"/>
<bondArray>
<bond atomRefs2="a1 a2" order="2"/>
<bond atomRefs2="a4 a3" convention="cxn:coord"/>
</bondArray>
<molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a1 a2" center="a4"/>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

I find it impossible to select both C atoms and the multiatom attachment point and move them all.  Moreover, if I move the individual C atoms, the multiatom attachment point does not move along with them.  This behavior is undesirable.  Whenever I move atoms involved in a multiatom attachment point, the multiatom attachment point should move along with them to remain in their geometric center.  And it should be possible to select the atoms and the multiatom attachment point and move them all simultaneously.

ChemAxon 23cc8b5e66

09-04-2013 14:15:43

Dear Bob,


This is how Marvin is designed: the multicenter attachment point and the multicenter atoms (here the ethylene atoms) can be selected and moved separately. If you select them together, then you will move them together.
In your example the problem is that the multicenter attachment hides the moving sqare tool because the ethylene atoms and the multicenter are too close.
If you try this with e.g. a cyclopentadiene (larger structure) you will see the behavior you have described.


There is a workaround for the ethylene as well, described below the Moving_multicenter.png:
You can change the active tool of a selection by pressing the Space key on the keyboard: Selection->Moving Square->2D Rotation Symbol->3D Rotation Symbol->Selection...


I hope this helps.


Best regards:
Viktor

ChemAxon 23cc8b5e66

09-04-2013 14:26:22

In a larger multicenter structure the Moving Square can be reached as usual.

User 870ab5b546

09-04-2013 14:27:55

Thanks, I did not know that space bar trick...