Skip to main content
A Textual and Tonal Tool for Molecular Visualization
Biochemistry and Molecular Biology Education (2008)
  • C. Britt Carlson, Parkland College
  • Timothy J. Cordes
We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating xyz location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked to speech or Braille output, and the ability to scroll along the main chain backbone of a protein structure. This program was initially designed for visually impaired users, and it already has shown its effectiveness in helping a blind researcher study X-ray crystal structure data. Subsequently, TIMMol has been enhanced with a graphical display to act as a bridge to ease communication between sighted and visually impaired users as well as to serve users with spatial visualization difficulties. We performed a pilot study to assess the efficacy of the program in conveying three-dimensional information about proteins with and without graphical output to a general scientific audience. Attitudes regarding using TIMMol were assessed using Rasmol, a common visualization package, for comparison. With the use of text and tones exclusively, a majority of users were able to identify specific secondary structure elements, three-dimensional relationships among atoms, and atoms coordinating a ligand. In addition, a majority of users saw benefits in using TIMMol and would recommend it to those having difficulty with standard tools.
  • Three-dimensional visualization,
  • spatial learning,
  • 3D learning,
  • macromolecular structure
Publication Date
May 23, 2008
Citation Information
C. Britt Carlson and Timothy J. Cordes. "A Textual and Tonal Tool for Molecular Visualization" Biochemistry and Molecular Biology Education Vol. 36 Iss. 3 (2008) p. 203 - 208 ISSN: 1539-3429 (Online)
Available at: