Saturday, September 22, 2012


I am now working on a children's show about the science of smell and so I've been doing a good amount of research on historical theories of olfaction. One of the famous monographs on smell is John E. Amoore's Molecular Basis Of Odor in which he uses space filling molecular models (non-computer generated physical models, this was 1970) to try to find correlations between the gross molecular shape of odorant molecules and overarching classes of "primary odors". Amoore is best known for making generalizations like: camphoraceous smells are molecularly "bowl-like" and accepted by a "bowl-like" receptor, musky smells are molecularly "petrie-like" and accepted by a "petrie-like" receptor, floral smells are molecularly "key-like", and so on.

The book is worth skimming even if many of its hypotheses are disproven or based on dated concepts of the senses but one thing I found particularly interesting is the way that some of the odorant molecules are illustrated using a combination of space filling models in silhouette and skeletal notation. Amoore used this as part of what he called the "shadow-matching method." I had never seen this before and was surprised because it is actually a great way to combine the best features of both modes of representation. Spacial dimensions are indicated without looking like a confusing, botryoidal jumble of spheres and all of the readability of skeletal notation is left intact. Obviously this can present some problems, especially for non-planar molecules, which are sometimes forced into a planar conformation for skeletal diagrams but still it's interesting you don't see it more often in textbooks. I know programs like pymol can do similar, more complex versions of this where the 3D Van Der Waals surface envelopes a 3D ball and stick model but what about just a simple representation like the below, are there any programs that do (a clear better aligned version of) that?


Botanical Baron said...

this has actually been my choice reference format for compounds for a few years now; due to the same reasons you stated.

Banal said...

Try playing around with a program called Spartan. You were able to construct molecules similar to your example with "ball and stick" models and space filling shadows. I doubt the company had made any notable changes to their software in recent years so the newer versions should suffice.

Anonymous said...

you can do this on paint shop pro 7, except i cant remember how unless i had a copy in front of me
anyway it's something like that video
or maybe photoshop can do 'feather' too?

Unknown said...

Have you read Jacobson's Organ by Lyall Watson? I highly recommend it.

logoliebe said...

it´s pretty easy to do this in adobe illustrator. how many of those do you need? i could help you out.