Image generation of markush fragments

 

Hi

I'm displaying a number of SMILES strings that have R-groups, an example is this:-

*C(*)c1ccccc1

when I generate images from them the '*'s are replaced by 'A's, which I just don't like.

Is there a way that I can force the 'A's back to '*'s, or maybe have them as R1, R2 etc ?

Many thanks

Ceara

Marvin interprets '*' signs as any-atoms, this is why they are displayed as 'A'.

ChemAxon extended SMILES can store R-atoms:

• C(
• )c1ccccc1 |$_R1;;_R2;;;;;;$|
  
  

  If you use this format then your R-atoms will be displayed as R1, R2, ...