The Markush enumeration tools in ChemAxon V 5.6, which I have been accessing through Marvin Sketch, are very powerful. I haven't yet, however, been able to figure out how to enumerate all of the different stereoisomers of a molecule which contains other Markush definitions. My first thought would have been to take my Markush molecule and assign one of the bonds coming off of a tetrahedral carbon a zigzag line ( which in Marvin Sketch is labeled as bond type "Single Up or Down" ), but the enumerator then simply carries that zigzag line through to all the enumerated possibilities, instead of expanding it. To be sure, if I define a simpler structure with no Markush expansions ( ex. no R-groups, or no frequency variation groups, no positional variation bonds, etc.), then I can use the Tools>Isomers> Stereoisomers menu item to request an isomer expansion, and that works fine, but then I've lost the ability to do the Markush enumeration that I came for in the first place. Is there a way to combine these two capabilities, so that I can perform a Markush enumeration AND generate all of the stereoisomers of the resulting molecules at the same time?
Thanks very much for any help. -Ben