BTW, JSpecView has some interesting demos set up:

http://wwwchem.uwimona.edu.jm/spectra/JSpecView/iranim/index.html

For example, this one lets you correlate IR spectral peaks with vibrational modes visualized by Jmol:

http://wwwchem.uwimona.edu.jm/spectra/JSpecView/iranim/oclanilineJ/oclaniline.html

Rajarshi, you seem to be interested in “fragment properties.” But if you have a molecular visualization tool (2D or 3D) which “lets you get under the hood,” you can imagine ways to do it. You point to the great examples in the statistical analysis world. But programs like SPSS or S or R or Matlab… these all have programming languages to let experts script almost anything they want to view. There are some examples of such programmable molecular visualization tools, but not necessarily flexible enough to do this.

Want to know how I’d implement your COOH group example? I’d script something which matches the COOH using SMARTS and sets the color of those atoms based on the numeric data.

In my Ph.D. dissertation, I changed bond orders to reflect actual bond distances, rather than the conventional “three-double bonds to a benzene ring” and “two double bonds to a thiophene.” You immediately saw changes in bonding structure — no need for a strange Excel plot.

No, I can’t do this yet using Avogadro (or anything else). But that’s why I’m posting challenges. This type of feature would clearly be helpful to chemists. Now we need to go try it. Why should we limit ourselves to the traditional chemistry representations?

In general, for atom based properties, I don’t think this would be very difficult. On the other hand making a generalized and intuitive interface to this would be challenging

This problem, is reminiscient of the ‘Grammar of Graphics’ (http://www.spss.com/research/wilkinson/TheGrammarOfGraphics/GOG.html)

http://depth-first.com/articles/2008/02/06/the-chemically-enabled-user-interface-an-introduction-to-leafcutter