density (U1C) - MidasPlus delegate for displaying formatted X-PLOR electron density data

DENSITY(U1C)SF

NAME

density - MidasPlus delegate for displaying formatted X-PLOR electron density data

MIDAS COMMAND SYNTAX

Command: delegate start dens density mapfile1 [ mapfile2 ... ]

DESCRIPTION

Density is a MidasPlus delegate for displaying electron density contour maps generated from X-PLOR .map files. The .map files must be of the formatted type. When requested, density will create a MIDAS object representing the electron density at one or more contour levels, and open it for display as a user-specified model number. Density assumes that the structure associated with the electron density is open as model 0, and therefore rotates and translates the density object it creates to align it with model 0. The user can specify the size of the grid to be created and where it is centered.

     Density is a program designed to run in conjunction with
     MIDAS using the MidasPlus delegate mechanism.  The standard
     way that density is invoked is for the user to start a MIDAS
     session, and issue the MIDAS command
          delegate start dens density mapfile1 [ mapfile2 ... ]
     which runs density with the specified formatted X-PLOR .map
     files and tells MIDAS to pass commands beginning with dens
     through to density for further processing.  The commands
     that density can handle are described below.

COMMANDS

     When density is acting as a delegate for MIDAS (as in the
     example above), the user can give it commands by typing
          dens density_command
     in the MIDAS command window.  The list of commands is given
     below.

size grid_units: Specifies the size of the grid that is to be contoured. The default size is 20 units. The size of an individual grid unit is determined by X-PLOR at the time the .map file is created. It is generally a few percent of the unit cell size.

center atom: Defines the center of the contoured region. The easiest way to specify the central atom is by using the MIDAS pick mechanism described under ``Atom Picking'' in Part II of the MidasPlus manual.

          contour_color [ contour_level contour_color ... ]
          display mapfile_prefix model_number contour_level
               The display command generates the electron density
               contours at the specified contour levels in the
               specified colors and opens them as model
               model_number.  Up to four contour level/color
               pairs can be specified.  Mapfile_prefix is one of
               the X-PLOR map file names specified on the
               delegate start command line, with the .map
               extension removed.  Contour maps can be closed
               using the ~open model_number command, and can be
               turned off and on with the [~]objdisplay
               model_number command.

Note that density only examines the first character of any command keyword, so for instance the command display could be shortened to disp or just d if desired.

EXAMPLES

The following commands would be used to open contour maps at levels +2.0, colored blue and red, around the iron atom in residue HEM from the X-PLOR file dens.map as model 1 in MIDAS.

delegate start dens density: dens.map Read the data from the X-PLOR map file dens.map.

dens center: #0:HEM@FE Center the contours about the iron atom in the HEM residue.

dens display dens 1 -2.0 blue 2.0 red: Display contours at levels +2.0, colored blue and red, in model 1. Since the grid size was not explicitly specified, it defaults to 20 units.

CAVEATS

The contour maps should always be rotated and translated in synchrony with model 0 (the structure). Should they ever be mistakenly manipulated out of alignment, they can be realigned by using the MIDAS matrixcopy command.

Different areas of the protein can be contoured at the same time by specifying a new center and opening additional contour maps into other model numbers.

AUTHOR

Christian Schafmeister, UCSF