Cordes Timothy J, Carlson C Britt, Forest Katrina T
Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Biochem Mol Biol Educ. 2008 May;36(3):203-8. doi: 10.1002/bmb.20183.
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.
我们开发了三维可视化软件“大分子的音调界面”（Tonal Interface to MacroMolecules，简称TIMMol），用于研究蛋白质结构的原子坐标。其主要功能包括：用音频音调指示x、y、z位置，在一维和三维空间中识别光标位置，可轻松链接到语音或盲文输出的文本输出，以及沿蛋白质结构的主链骨架滚动的功能。该程序最初是为视障用户设计的，并且已经在帮助一位盲人研究人员学习X射线晶体结构数据方面显示出了成效。随后，TIMMol增加了图形显示功能，以作为一种桥梁，方便有视力的用户和视障用户之间的交流，同时也为有空间可视化困难的用户提供服务。我们进行了一项初步研究，以评估该程序在向普通科学受众传达有关蛋白质的三维信息时，有无图形输出的效果。使用常见的可视化软件包Rasmol来评估关于使用TIMMol的态度，以作比较。仅通过文本和音调，大多数用户就能识别特定的二级结构元素、原子之间的三维关系以及与配体配位的原子。此外，大多数用户认为使用TIMMol有好处，并会向那些使用标准工具存在困难的人推荐它。
