Tonal interface to MacroMolecules (TIMMol)

A textual and tonal tool for molecular visualization

Authors

  • Timothy J. Cordes,

    Corresponding author
    1. Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
    • Department of Psychiatry, 600 Highland Ave., Room B6/585, Madison, WI 53792
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    • These two authors contributed equally to this work.

    • Fax: 608-263-7263

  • C. Britt Carlson,

    1. Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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    • These two authors contributed equally to this work.

  • Katrina T. Forest

    1. Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
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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.

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