CMLSnap: Animated reaction mechanisms

G L Holliday, John B. O. Mitchell, P Murray-Rust

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)
4 Downloads (Pure)


Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions.

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Original languageEnglish
Number of pages6
JournalInternet Journal of Chemistry
Issue number4
Publication statusPublished - 26 Oct 2004


  • Reaction mechanisms
  • Animation
  • Enzyme reaction mechanisms


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