Article
A Textual and Tonal Tool for Molecular Visualization
Biochemistry and Molecular Biology Education
(2008)
Abstract
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 x, y, z 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.
Keywords
- Three-dimensional visualization,
- spatial learning,
- 3D learning,
- macromolecular structure
Disciplines
Publication Date
May 23, 2008
DOI
10.1002/bmb.20183
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: http://works.bepress.com/britt-carlson/8/