Tuesday, July 21, 2009

Building a complicated molecule: 2D to 3D

In a previous post I showed how to build a complicated molecule with Avogadro. Here I show how to build it in 2D first and then convert it to 3D.

I use PubChem Editor to build a 2D structure and insert it into Avogadro using the insert SMILES option. JChemPaint is another free option for drawing the 2D structure.

Avogadro does not process the chirality info (the @ signs) in the SMILES string correctly, so some more editing is needed. Hopefully this is fixed in future versions of Avogadro (I use 0.9.5).

There is some discussion over at Rich Apodaca's blog about whether building in 2D or 3D is easier. Try for yourself and make up your own mind.

Update: the program Marvin Sketch can also be used for 2D to 3D conversion, and the chirality info is interpreted correctly.


Anonymous said...


Please keep the screencasts coming. They're a great learning tool for me and have so far solved a few problems I've encountered with Avogadro and GAMES. Thanks for the blog.


Jan Jensen said...


glad to hear it's useful. Suggestions for new screencasts welcome.


NUchem said...


A couple of ideas for future casts...

1) HOMO/LUMO of optimized GAMESS structures viewed in MacMolPlt
2) Showing an opt/freq calc in MacMolPlt
3) How to stop a GAMESS calc and then restart from the last optimization step.

I think a screencast of how to actually install GAMESS on a computer would be helpful for newbies. I for example had problems trying to figure out what went where as far as scatch files, .inp files, etc for my Macbook Pro. I still need to figure out GAMESSQ so it'll work properly. Sometimes the very beginning of a comp program can help a lot. I know a few of my colleagues get very fustrated when reading how to install GAMESS on a computer. It's not very straightforward how to install for a personal computer. Granted GAMESS best for larger systems, but when Spartan is in excess of $1000, GAMESS (which is free) for personal use is a much better alternative. Again thanks for the blog and more suggestions to come :)


Jan Jensen said...

All good suggestions. I think I might start with the installation ...

Jim said...

Jan -

Have to drop by more often - job well done my freind. Keep up the good work.

Jan Jensen said...

Jim - Thank you! Always nice to hear.