Waldorf Salad

July 11, 2007

One thing that really irritates me is badly drawn ChemDraw structures (maybe I should get out more...). ... Simple really... so why do a lot of ChemDraw structures that appear in papers or on slides at conferences look like a six-year old has drawn them with a crayon (and I mean a particularly untalented six-year old at that - one that probably wouldn't even win a Blue Peter drawing competition)? I think it’s just people being lazy...

-Stuart Cantrill, Badly Drawn Bonds

Chemical structures are a language. Like any language, grammar and spelling convey meaning and become "standardized" over time. But as native speakers of any language will tell you, languages also take on important cultural nuances that are difficult to convey to non-native speakers. Chemical structures are no different, as Stuart Cantrill's comments show.

Just about every chemist I've met has opinions on the "right way" to draw chemical structures that go beyond "grammar" and "spelling." These opinions come out most clearly in interdisciplinary environments, where non-chemists create chemical structures. Features such as "unconventional" line proportions, bond angles, or atom label proportions don't affect meaning. But they do violate conventions subconsciously learned over years of training. They look weird and because of this they distract attention and annoy audiences.

Not every badly-drawn structure is the result of laziness. Rather, it's more likely that: (1) the author didn't know there was a problem; (2) the author did know, but underestimated the benefit of correcting the problem; or (3) the author did know but wasn't using a tool that made it possible to correct the problem.

The increasing importance of computers in generating, manipulating, transmitting, and rendering chemical structures means that software developers now face the same choices as individual chemists with respect to quality. Before discounting structure aesthetics as irrelevant, it's worth considering that chemists can and do apply the same judgments to software as they apply to their fellow chemists.