RasMol and Mage in the Undergraduate Biochemistry Curriculum

Weiner, Steven; Cerpovicz, Paul F.; Dixon, Dabney W.; Harden, Donald B.; Hobbs, Donna S.; Gosnell, Donna L.

doi:10.1021/ed077p401

Cited by 21 publications

(21 citation statements)

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“…When different formatted sections of this PDB file are selected with the mouse, the linked features of the Chimerendered image are dynamically modified. In this way, students learn, for example, that individual amino acid residues are designated by their three-letter abbreviations plus numerical positions in the sequence, whereas "CA" or "ca" usually designates an ␣-carbon atom 4 in expressions like "*.ca" (i.e. all ␣-carbons), "ala.ca" (i.e.…”

Section: Customizing the Web Page Templatesmentioning

confidence: 99%

“…Static images, or external representations as they are sometimes called, are known to promote better understanding of abstract biochemical concepts [19] if appropriately designed and tested [20]. By combining static "snapshots" that illustrate key structural features with the dynamic images produced by the Chime plug-in, we be- 4 "CA" or "ca" can also designate calcium ions when included in the structure. 5 When attempting to copy and paste a Chime-rendered image with the Edit/Copy Chime pop-up menu option, one occasionally encounters a problem with the Windows Clipbrd.exe program, which stores the contents of any copy command.…”

Section: Undergraduate Structure Analysis Projectsmentioning

confidence: 99%

“…However, instructors face the challenge of creating effective structure exploration activities that bypass most of the highly technical, costly, and labor intensive experimental procedures required for determining and analyzing three-dimensional (3D) 1 structures. Many interesting approaches to this educational issue have been reported in the literature [1][2][3][4][5][6][7][8][9][10]. One approach we have taken is to model the process of structure analysis by directly engaging students in problem-solving "experiments" with computer-generated 3D images of solved macromolecular structures.…”

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Simplifying structure analysis projects with customizable chime‐based templates*

Thompson

Sears

2005

Biochem Molecular Bio Educ

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Structure/function relationships are fundamental to understanding the properties of biological molecules, and thus it is imperative that biochemistry students learn how to analyze such relationships. Here we describe Chime-based web page templates and tutorials designed to help students develop their own strategies for exploring macromolecular three-dimensional structures like those on our course website. The templates can easily be customized for any structure of interest, and some templates include a Command Entry Line and a Message Recall Box for more refined macromolecular exploration using RasMol/Chime image modification commands. The tutorials present students with an integrated overview of the image modification capabilities of the Chime plug-in and its underlying RasMol-based command structure as accessed through the Command Entry Line. The tutorial also illustrates how RasMol/Chime command syntax addresses specific formatted structural information in a standard Protein Data Bank file. Judging by the high quality of structure-based presentations given by students who have used these templates and tutorials, it appears that these resources can help students learn to analyze complex macromolecular structures while also providing them with convenient tools for creating scientifically meaningful and visually effective molecular images to share with others. (The templates, tutorials, and our course website can be viewed at the following URLs, respectively: tutor.lscf.ucsb.edu/instdev/sears/ biochemistry/presentations/demos-downloads.htm, tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tutorials/pdbtutorial/frontwindow.html, and tutor.lscf.ucsb.edu/instdev/sears/biochemistry/.)

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Section: Customizing the Web Page Templatesmentioning

confidence: 99%

Section: Undergraduate Structure Analysis Projectsmentioning

confidence: 99%

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confidence: 99%

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Simplifying structure analysis projects with customizable chime‐based templates*

Thompson

Sears

2005

Biochem Molecular Bio Educ

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“…[10][11][12][13][14][15] La visualización científica molecular se ha utilizado como una herramienta valiosa en el aprendizaje de la química en el salón de clases. [16][17][18][19][20] Hay muchos programas disponibles que permiten al alumno manipular y entender modelos de moléculas pequeñas y grandes (macromoléculas). Por varios años el programa más popular para gráficos moleculares ha sido el RasMol, el cual fue desarrollado por Roger Sayle en la Universidad de Edimburgo, Reino Unido, a mediados de los años 90.…”

Section: Introductionunclassified

Integración de visualización científica molecular en el salón de clases

García-Ruiz¹,

Valdez-Velázquez²,

Gómez‐Sandoval³

2008

Quím. Nova

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“…Mage was developed primarily to display proteins and other macromolecules and, not surprisingly, previous articles about Mage in this Journal have dealt with applications in undergraduate biochemistry courses (2,3). Using Mage, we have created interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses: this paper describes some examples of these applications.…”

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Mage: A Tool for Developing Interactive Instructional Graphics

Pavkovic

2005

J. Chem. Educ.

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of Duke University (1). Mage was developed primarily to display proteins and other macromolecules and, not surprisingly, previous articles about Mage in this Journal have dealt with applications in undergraduate biochemistry courses (2,3). Using Mage, we have created interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses: this paper describes some examples of these applications.Mage is straightforward to download from the Web (4) and comes equipped with a rich yet simple vocabulary for constructing associated data files. Mage data files use plain text scripts and are called kinemages. Names of kinemage files are identified by the .kin extension and are easily created or modified using any text editor. Simple generation of kinemage files and subsequent attractive displays make Mage our program of choice for developing interactive instructional graphics. Many diagrams prepared at a chalkboard or on an overhead slide can be organized in Cartesian space in terms of points, lines, spheres, and labels. Such constructions usually can be incorporated into a kinemage, and the resulting interactive three-dimensional image is more clear and impressive than the most carefully hand-drawn original. Furthermore, a recent offering of an associated Mage applet allows direct and quick viewing of kinemage files from any Java-capable Web page (5) and considerably expands its scope of utilization.This article outlines preparation of a simple kinemage data file, offers several examples of Mage applications for instructional classroom use, considers alternate ways of obtaining kinemages (in order to take advantage of the Mage applet), and describes an associated student assignment. Kinemage Data FilesKinemage commands begin with an "at" character (@), and the first command is @kinemage. Two other commonly used commands are @balllist and @vectorlist. The former specifies color, radius and location of spheres (or atoms) while the latter defines color and location of lines (or bonds). Commands and parameters should be entered as lower case characters. List 1 shows lines of code for a short kinemage file. When processed by Mage, this file will cause display of a blue triangle with red spheres at each vertex.Curly brackets are mandatory but labels between them are arbitrary. Entering a square bracket by mistake is the most common programming problem. In the @vectorlist command, letters P (point) and L (line) are mandatory. Several P to L sequences can occur under one @vectorlist command. The file must be saved with the extension .kin, not .txt.Many Mage commands have an associated on-off display button. Buttons control the display of selected portions of a kinemage file and are accessible while the program is executing. If the word "off " is appended to the second line of the kinemage code example shown in List 1, then only the blue triangle will be displayed initially. To view the red spheres, in this instance, users must click the Atoms button in the Mage window. Tutorials, complete docume...

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RasMol and Mage in the Undergraduate Biochemistry Curriculum

Cited by 21 publications

References 3 publications

Simplifying structure analysis projects with customizable chime‐based templates*

Simplifying structure analysis projects with customizable chime‐based templates*

Integración de visualización científica molecular en el salón de clases

Mage: A Tool for Developing Interactive Instructional Graphics

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