Re: [ccp4bb] Alternatives to ChemDraw 3D

[Martin Stoermer]

This may be somewhat  convoluted but for this exact purpose try ZINC.  
For other drawing things then yes use one of the other packages

http://zinc.docking.org/

Draw the molecule using the widget, save the smiles file and let their  
server make the 3D version for you, properly protonated etc. And you  
get things like logP, and other descriptors as well.

true you get it as .mol2.gz or .sdf.gz but babel is your friend

-Martin