I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in the bond length compared to some reference structure. In this way, the intensity in a color range red-white-blue would be given by the difference between the relaxed and unrelaxed bond lengths, similarly to the figure attached.

I have tried to make this figure using jmol, but I didn't have success so far. Could anyone suggest a program that is able to do such figure? Or could someone point out any suggestion of how to do this color maps on chemical bonds?

Color map on graphene structure according to the changes in the bond length. Extracted from the book Nanodevices and Nanomaterials for Ecological Security.

I will be grateful for any help you can provide.

All the best

  • $\begingroup$ Welcome to Chemistry.SE! Take the tour to get familiar with this site. Mathematical expressions and equations can be formatted using LATEX syntax. If you receive useful answers, consider accepting one. $\endgroup$ – bon Jan 17 '17 at 16:05
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    $\begingroup$ This is quite a special request and you probably have better luck contacting the authors of the paper (could you include the reference please) how they obtained this image. None of the programs I work with (molden, chemcraft) seem to be able to do so. $\endgroup$ – Martin - マーチン Jan 19 '17 at 6:02
  • $\begingroup$ I guess it should be possible to search for certain distances between two atoms and color those bonds differently with PyMol, but it would involve some scripting. $\endgroup$ – DSVA Jan 19 '17 at 15:57
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    $\begingroup$ Thank you for the comments and suggestions. The problem has been solved using Jmol program. After some discussion in the Jmol mailing list, prof. Robert Hanson suggested a very simple script that can assign colors to the bonds according to the respective length. PS.: The figure attached to my comment was taken from the book "Nanodevices and Nanomaterials for Ecological Security, Ed. Springer", chapter 5, author Arkady V. Krasheninnikov. $\endgroup$ – Max Pinheiro Jan 21 '17 at 23:00
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    $\begingroup$ @Max Pinheiro you should make your comment an answer to your question so it shows up as answered. $\endgroup$ – Tyberius Mar 25 '17 at 3:14

StrainViz is the program that might be useful [1].


  1. Colwell, C. E.; Price, T. W.; Stauch, T.; Jasti, R. Strain Visualization for Strained Macrocycles. Chem. Sci. 2020, 11 (15), 3923–3930. DOI: 10.1039/D0SC00629G.
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