Les amis d'O

Gerard J. Kleywegt
Department of Molecular Biology
Biomedical Centre, Uppsala University
Uppsala - Sweden

In this article we shall take a closer look at three of the lesser-known utility programs from Uppsala that work in conjunction with O [1].


SOD [2] stands for "Sequences to O Datablocks", i.e. it is a program that converts sequences into information that can be used in or by O. The program can read individual and aligned sequences in a number of formats. It can be used to do the following:


One of the useful features in O is its use of datablocks (of type real, integer, character or text) to represent information pertaining to a molecule as a whole, to each of its residues, or to each of its atoms [3] . Although O contains a number of commands to manipulate datablocks, a separate utility program (ODBMAN, for "O DataBlock MANipulation" [4] ) is also available. Its options (besides trivial I/O-related ones) fall into the following categories:


Many of the Uppsala programs (e.g. , ODBMAN, MOLEMAN2, LSQMAN, DATAMAN, MAPMAN) produce (ASCII) plot files in a meta-format. O2D [6] is a simple program to convert such plot files into other formats. Usually, this program will be used to convert plot files into PostScript files, but the program can also produce tab-delimited ASCII files, which can be read by most popular spreadsheet and graphing programs on the market, and hence used to produce more professional-looking graphs. The SGI version of this program in addition allows the user to plot data interactively in graphics windows. O2D can produce line and scatter plots, histograms and simple pie charts of 1D data, and contour plots of 2D data. In interactive mode, there are also simple facilities for integrating curves or contour plots, and to manipulate the display. The (ASCII) meta-format for both 1D and 2D plots is simple, using six-character keywords (see the manual for details). There is also a C-shell script available which will do a batch conversion of many plot files to PostScript.


SOD, ODBMAN, and O2D are part of the X-UTIL package, which is available free of charge to academic users from Commercial users may contact GJK for more information ( ). For more information about O , contact Alwyn Jones ( ). The O WWW site is at , and the Uppsala Software Factory can be found at .


USF Latest update at 12 February, 1998.