User 010ddfdc89
20-05-2008 08:44:32
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
ChemAxon e500b51457
20-05-2008 11:41:16
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.
User 010ddfdc89
21-05-2008 08:50:34
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
ChemAxon e500b51457
22-05-2008 11:26:14
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.
User 010ddfdc89
23-05-2008 03:12:34
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