Representation of aromatized rings

I have a question about how aromatized rings are represented in marvin sketch and draw. Sometimes the are shown with a circle in the middle and other times they are shown with a dashed like around the inside edge of the ring. Additionally, I have seen the representation switch from the dashed like to a circle in the viewing applet after I manipulated the structure in some way.





Why is this difference present?





How can we get it to always show one or the other (we would prefer the circle)?





Any information on this topic would help us.





Thanks,


Al

If the input structure is aromatized, then the aromatized format will be shown, otherwise the Kekule format.





You can aromatize the structure before display using several ways (click on the links):

• Import conversion in the viewer/sketcher using the importConv parameter
• Molecule.aromatize(...)
• MolHandler.aromatize(...)
• MolConverter, for example

  Code:

  molconvert smiles:a input_file

  
  
  
  (also available from the API)
• Standardizer (also available from the API)

Hmm, not exactly what I meant. I'm attaching a couple of images to clarify.

Sorry, I didn't read your letter carefully.


It seems that the structure with dotted lines is 3 dimensional. Only 2D structures are shown with circles.


Check the coordinates. The values at the z axis should all be zero.

Yes, it looks like that fixes it. We had the "rotate in 3D" option selected. When we set that to "rotate" it changes to circles. We just need to select the proper setting in the applet. Thanks for your help.