Thanks Reinier,

I dont think I was specific enough and I dont think my scripting abilities are of a high enough standard to interpret your examples correctly.

If I have a molecule, which posses a double bond (amongst many others) between two atoms labelled atom1 and atom2 and I want to just switch that particular bond to a single bond, without globally affecting any other bonds in the structure how would I do that?

As i'm learning more about PERL and MS scripting I think I might need to define the specific bond before trying to convert it: it seems easier to make a specific bond between two atoms than it does to change the type or delete a bond between specific atoms.

Thanks

Jon