Ask Ubuntu is a question and answer site for Ubuntu users and developers. Join them; it only takes a minute:

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

I'd like to be able to create a table displaying different substituents and bonds inside the different members of drug groups like the morphinan opioids and as part of that it would be great if I could create a atom-numbered diagram of morphinan to refer to in said table. I'd just like to know if it is possible to do this in MarvinSketch and, if so, how. I am using MarvinSketch 5.12.3 if it is relevant.

EDIT: I would like MarvinSketch to automatically number each atom. That is, I would like each atom to be assigned the number it is given when naming in IUPAC.

share|improve this question
up vote 2 down vote accepted

You can use the manual mapping function (mouseover + m and the number you wish to add to the atom) to reorder the default atom numbering. There is more information about using the manual mapping function in Marvin here.

share|improve this answer
Um, sorry I wasn't as specific as I had originally thought, please refer to my latest edit (after "EDIT:"). – Brenton Horne Apr 20 '13 at 21:57
There is an IUPAC module in biopython. A Python scripting question would be a topic for Stackoverflow. – karel Apr 20 '13 at 23:55

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.