Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization
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| Title: | Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization |
|---|---|
| Language: | English |
| Authors: | Cordes, Timothy J., Carlson, C. Britt, Forest, Katrina T. |
| Source: | Biochemistry and Molecular Biology Education. May-Jun 2008 36(3):203-208. |
| Availability: | John Wiley & Sons, Inc. Subscription Department, 111 River Street, Hoboken, NJ 07030-5774. Tel: 800-825-7550; Tel: 201-748-6645; Fax: 201-748-6021; e-mail: subinfo@wiley.com; Web site: https://secure.interscience.wiley.com/cgi-bin/jhome/112782101 |
| Peer Reviewed: | Y |
| Physical Description: | |
| Page Count: | 6 |
| Publication Date: | 2008 |
| Document Type: | Journal Articles Reports - Research |
| Education Level: | Higher Education |
| Descriptors: | Computer Uses in Education, Visualization, Spatial Ability, Computer Software, Molecular Biology, Visual Impairments, Braille, Interpersonal Communication, Auditory Stimuli, Attitude Measures, Visual Stimuli, Graduate Students, Researchers |
| DOI: | 10.1002/bmb.20183 |
| ISSN: | 1470-8175 |
| 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. (Contains 1 figure and 1 table.) |
| Abstractor: | As Provided |
| Number of References: | 21 |
| Entry Date: | 2008 |
| Accession Number: | EJ799495 |
| Database: | ERIC |
| 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. (Contains 1 figure and 1 table.) |
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| ISSN: | 1470-8175 |
| DOI: | 10.1002/bmb.20183 |
