What's New in MidasPlus?
The MidasPlus 2.1 release is currently shipping. Release 2.1 includes a few new commands, more extensive documentation, small but numerous bug fixes, support for additional platforms, and binaries compiled and tested using the latest releases of the operating system for the various platforms which we support. More information regarding the release can be gleaned from the release notes.
This is our last planned release of MidasPlus. The system was originally designed in 1980, and although it has been continually updated and in 1989 completely rewritten, the basic design can no longer accommodate our future needs. Instead, for the past few years we have been working on the design and implementation of a completely new system known as Chimera. Chimera is designed to take advantage of the three-dimensional graphics capabilities found on new graphics workstations and adapter cards, including hardware texture mapping and volume visualization. In addition, Chimera has been designed with extensibility as a key goal. It will be possible for users with relatively modest programming skills to be able to create new extensions to Chimera without the need to modify any Chimera source code. Chimera will incorporate both a new graphical user interface (GUI) and substantial new modeling, display, and data interchange functionality. Additional information describing Chimera is available.
The following items are for those sites still running MidasPlus version 2.0. The items below are integrated into the 2.1 release.
David Konerding, a graduate student in the biophysics program at UCSF, has written a delegate program to display molecular dynamics trajectories within MidasPlus. Via a simple point-and-click interface, trajectories can be played forwards or backwards or in single steps; arbitrary MidasPlus commands to manipulate or analyze the structure may be executed at any step. Input is either a series of consecutively numbered PDB files or an AMBER-formatted trajectory or restart file. David Konerding's MidasMovie page includes a detailed description, instructions, and the delegate itself, which is written in Python.
Dr. Hans De Winter, of the REGA-Institute of Medical Research in Leuven, Belgium, has generously made available a delegate (named gd) that he wrote for the display of energy contour information generated by Peter Goodford's GRID program. The gd delegate can also be used to prepare input for the GRID program. Gd's capabilities are described in detail in the gd manual page. Versions of the delegate for IRIX 5.3 and IRIX 6.2 are available for FTP, as well as the source code for the delegate. The FTP files are compressed tar archives, which means that once you retrieve them, you can install them on your SGI with:
zcat ftpfile | tar xvf -
This will result in the executable and man page being put in the appropriate locations in the /usr/local/midas hierarchy. The source code archive will instead create a subdirectory of your current directory named "gd".
Please direct any questions or comments to Eric Pettersen.
The tutorials described below are accessible using any World-Wide Web browser such as Netscape or Mosaic.
The tutorial developed by Arthur Glasfeld at Reed College is designed to provide a gradual introduction to the functionality available in MidasPlus as well as to introduce students to structural biochemistry concepts. The on-line tutorial consists of ten exercises, each containing sample images, data files, and the appropriate MidasPlus commands used to solve the proposed modeling problem.
The tutorial developed by Elaine Meng is a more condensed introduction to MidasPlus commands, including the rendering programs ribbonjr, conic, and neon.
We welcome your comments and suggestions on these tutorials. We can be reached via e-mail at email@example.com.
MidasPlus under Linux
We have recently completed a port of MidasPlus to Intel 386/486/Pentium platforms running under the ``Linux'' version of UNIX, both on desktop and laptop machines. Two versions exist, one using commercially available versions of both OpenGL and Motif libraries from Metro Link, and the other using Metro Link's Motif and an OpenGL replacement package from Mesa. The Metro Link version of OpenGL has the advantage that support has been promised for hardware-based graphics rendering using, for example, a Matrox Millenium card. All the basic MidasPlus functionality is complete, but a couple of auxiliary programs currently don't work (i.e. neon and dms). The Linux version of MidasPlus linked with the Mesa library is included on the release 2.1 CD-ROM.
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