gd manual

NAME

gd - a MidasPlus delegate which serves as an interface between MidasPlus and Peter Goodford's GRID program [1].

MIDAS COMMAND SYNTAX

Command: delegate start g gd [-rfile_name]

If the -r flag is used, then all communication between gd and MidasPlus is recorded in file file_name.

DESCRIPTION

Gd is a MidasPlus delegate to allow the visualization of three-dimensional energy maps output by Peter Goodford's GRID program [1]. Gd contours these maps at user-defined energy levels, which are then displayed by MidasPlus along with the molecules under study. Gd can also produce GRID input files with correct BOT(XYZ)...TOP(XYZ) coordinates for the molecules (or parts of molecules) of interest.

When gd is acting as a delegate for MidasPlus, the user can supply commands by typing

g gd_command [parameters]

at the MidasPlus command prompt. Many commands need additional parameters, and all parameter values remain set until the user wishes to change them by supplying other values.

COMMANDS

Basically, the commands of gd can be classified in two categories: commands used in conjunction with the contouring and display of three-dimensional energy maps output by GRID, and commands used to generate GRID input files after the user has defined which atoms need to be included in the GRID box. The list of commands is given below:-

'GRID-CONTOURING' COMMANDS:

These commands all have to do with the contouring and visualization of three-dimensional energy maps output by GRID:- color [color_spec] Color_spec can be simply a single Midas color, including user-defined colors (see the colordef command in the MidasPlus manual), or two colors and a mixture fraction (separated by commas with no blanks). The mixture fraction is a number between 0 and 1, and indicates the relative amounts of the two colors to use. Zero indicates 'use exclusively the first color', while 1 indicates 'use only the second color'. The default value for color_spec is 'gray'. The color command can be used for coloring the GRID box boundaries (see the show_box command), min and max labels, and energy contours (see the contour command). level [contour_level] Contour_level is the level at which contouring takes place. If the level is outside the range of values found in the GRID file, no contouring takes place. The user can prompt for these maximum and minimum values with the max and min commands (see below). The default value for contour_level is -5. max [label [model_number]] The max command returns the maximum energy value found in the GRID file. When a label parameter is provided, this label will be displayed as model model_number at the position of maximum energy. When no model_number is provided, the lowest available model number will be used. No default value is provided for label, so plotting will not occur by default. min [label [model_number]] The min command returns the minimum energy value found in the GRID file. When a label parameter is provided, this label will be displayed as model model_number at the position of minimum energy. When no model_number is provided, the lowest available model number will be used. No default value is provided for label, so plotting will not occur by default. show_box [model_number] This command displays the boundaries of the GRID box as defined in the GRID file. If no model_number is defined, the lowest available model number will be used. gridkont [file_name] File_name is the name of the unformatted three-dimensional energy file produced by GRID. The default value for file_name is 'gridkont.dat'. status The status command prompts the program for the current values of color_spec, contour_level, and file_name. contour [model_number] [at level] [color color_spec] Starts the contouring procedure and displays the computed contours as model model_number at contour level level using color color_spec. If model_number is absent, the lowest available model number will be used. If the specified model_number already exists, no contours will be drawn. Level and color_spec can also be specified using the level and color commands (see above). 'GRIDIN-CREATION' COMMANDS: These commands deal with the creation of a GRID input file:- define_grid [extent [show [model_number]]] Define_grid calculates the size of a box encompassing all atoms displayed in the viewing window. If the additional parameter extent is given, then the box size is increased along all sides by 2*extent Å. The default value for extent is 0. If the optional keywords show [model_number] are given, then the grid boundaries will be displayed as model model_number. If model_number is not supplied in conjunction with the keyword show, the lowest available model number will be used to display the box boundaries. makegrid [file_name] This command writes a template input file for GRID, called file_name. If no explicit file_name is provided by the user it defaults to 'grid.in'. Makegrid can only be executed after having defined a grid with define_grid. The following commands set specific GRID variables to user-defined values, and are used by makegrid to generate the GRID input file:- npla [number_of_planes_per_Angstrom] Sets the GRID variable NPLA. Defaults to 1. probe [probe_type] Sets the type of the probe. Defaults to the water probe 'oh2'. See the GRID manual for other possibilities. KNOWN BUGS The color of an object (i.e. energy contour, min/max label, and GRID box boundaries) has to be defined before the actual object is drawn. Once displayed, there is no way to change its color except by deleting the object (~open model_number), redefining its color with color color_spec, and regenerating the object using the appropiate command. Dashed lines cannot be produced. AUTHOR Hans De Winter, Laboratory of Medicinal Chemistry, REGA-Institute of Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium. REFERENCE [1] Goodford, P.J. 'A computational procedure for determining energetically favorable binding sites on biologically important molecules'. (1985). J. Med. Chem. 28, 849-857. The GRID program can be obtained from Molecular Discovery Ltd, West Way House, Elms Parade, Oxford OX2 9LL, England, or by contacting Peter Goodford himself at peter@biop.ox.ac.uk.