Display Software

This and two continuing pages include descriptions, references, and links to download pages for our laboratory software, all of which is free and open-source. In the list immediately below, each available program is linked to its description on one of our three software pages. In that capsule description, information as to program use and program OS requirements will be conveyed. Also given in that description will be links to: on-line program documentation; the software's download page; and the software's FTP site directory (for archived programs and/or source code). Older versions and experimental versions are available only through links to our FTP site. (Older versions might be desirable either if: a) you are using an old operating system, such as Windows 3.1 or a 68K Macintosh; or b) you find a fatal bug in the current version - if so, please report it. Help is available for using our FTP site, and for trouble shooting downloads in general. Further help in obtaining and using our programs is available: Feedback.

Software available:

Display Programs (this page): Mage - displays, and edits, kinemage graphics; Java Mage - displays kinemages on the Web; Prekin - makes molecular kinemages
All-Atom Contact Programs: Reduce - adds & optimizes hydrogens; Probe - calculates all-atom contacts; Probescripts for O or XtalView; Clashlistcluster; Asn/Gln/His flip scripts; NA contacts - base stack areas; Autobondrot - probe scores on grid of dihedral angle values
Other Software: Contouring - 2D and 3D contours, on orthogonal grids; Dang - dihedral angles from PDB files; Cluster - groups interacting objects; PDBCNS - converts between PDB & CNS formats; Bndlist - finds covalent and hydrogen bonds; Atvol - molecular van der Waals volume

Mage: Mage is a 3D vector display program which shows "kinemage" graphics. Used in both teaching and research, in applications ranging from estuary ecology to X-ray crystallography model quality assessments, Mage displays the 3D relationships between data in an interactive environment which facilitates both open-ended exploration and structured presentation. It includes many tools for on-screen measurement, construction, and editing of the display objects; it can write either kinemage output or various types of 2D image output. It was initially described in Richardson & Richardson (1992) Protein Science, 1, 3-9 and most recently in Richardson & Richardson International Tables for Crystallography. vol. F, chapter 25.2.8.

Mage is available for several popular platforms: Windows, Macintosh, SGI-Irix, and Linux. Pre-compiled executables are available from the Mage download page, as are "MagePaks" - bundles of Mage, Prekin, example/tutorial kinemages and other tutorial text documents. Additionally, many example kinemages (the mage input files) and Mage manuals are available from "The Mage Page". Kinemages are ascii text files with a simple, straighforward format which is user-editable in any text editor. Kinemages are usually generated initially by a feeder program, such as Prekin (see below) which works from molecular coordinates.; Go to the Mage Downloads page for current distribution versions and MagePaks.

Go to the FTP Site for older or experimental versions and source code.

Java Mage: Java Mage is an implementation of Mage to display kinemages in a Java virtual machine, typically over the internet in a Java-capable browser. Thus, you can now use Mage to help explain your protein, nucleic acid or other 3D data directly on your web site without any user downloading needed.
The picture at right shows a static screen capture, but to try out some examples "live", go to the Java Mage portion of this site. There you can also find instructions for using Java Mage kinemages on your own Web site, for which you will need to download the Java classes from the table below.; Go to the MageJava Downloads page for the current distribution java archive file.

Go to the FTP Site for older or experimental versions and also the above.

Prekin: Prekin prepares molecular kinemages (input files for Mage) from PDB-format coordinate files, using either a choice of built-in scripts or a flexible user specification of options. It is available for Macintosh, Windows, Unix and Linux boxes. In Unix or Linux, it can be run from the command line or can be called from inside Mage to, for instance, add rotatable mutant side chains.; The Mage Page has more information on Prekin's use and functionality.

Go to the Prekin Downloads page for current distribution versions and MagePaks.

Go to the FTP Site for older or experimental versions and source code.

Kinemages

Java Mage

Software:

Validation

Rotamers

FTP

2D Gallery

Lab Info

Display

Contacts

Utility