Coordinate Bond Rendering Question

Hi Folks,





How can I draw coordinate bonds in Marvin?





For example, say I have





N.N.O=C1O[Pt]OC(=O)C12CCC2





And want to represent the two Pt-NH3 coordinate bonds with arrows?





Cheers.





Peter

Hello,





To draw a coordinate bond choose the last item from the menu next to the Bond toolbar button


or draw a single bond and change its type by choosing the "Type/Coordinate" menu item from the contextual menu over the bond.





Regards,


Erika.

Hi Erika,





Thanks for the info. Hmm, can see that function exists in the latest version of Marvin, but can't seem to find it in our currently deployed one (4.1.13).





Also,in v5 I can draw the coordinate bond, but when I copy the SMILES string and re-paste it back into Marvin it loses the coordinate bond. Looks like Marvin does not encode the coordinate bond information as an extended SMILES string?





Peter

Dear Peter,





Coordinate bond drawing is a new feature first available in version 5.0.


How did you get the extended SMILES string of the structure? I tried it from File/Save as and Edit/Source ( note that you have set the source type to ChemAxon Extended SMILES ) and had no problem:

Code:

N[Pt]1(N)OC(=O)C2(CCC2)C(=O)O1 |COORDINATE:1.0,1.1|

Regards,


Erika.

Ah - OK. Another reason to upgrade :-)





I initially used the copy as smiles menu item, but as you pointed out it does not incorporate the extended smiles data. When I use the File->SaveAs route then it works as expected.





Thanks for the info.





Peter