ccp4mapwish is a customised version of the wish program, consisting of the Tcl command language, the Tk toolkit, the CCP4 MapSlicer Command Library, and a main program that reads commands from standard input or from a file. It creates a main window and then processes Tcl commands.
The MapSlicer Command Library can also exist as a loadable library libccp4map.so, which can be imported into wish at run-time using the Tcl load command.
The program and library are currently supported on a number of platforms (Irix, OSF1, SunOS, Linux, Windows). Please contact CCP4 if you are interested in using either on other platforms.
The MapSlicer command library used in ccpmapwish offers a number of commands in addition to those found in standard Tcl/Tk:
readmap, deletemap, mapinfo, section
Tcl command to load a map into memory from the specified file
Arguments:
mapid "handle" string identifying the map in memory mapfile file to read from
Returns:
0 = completed ok -1 = map already loaded -2 = error reading from map file -3 = couldn't allocate memory
Tcl command to interrogate the map held in memory.
mapid is the handle identifying the map stored in memory; if no mapid is given then all the currently stored mapids are returned as a list.
A maximum of one keyword is allowed:
[none] = returns 1 if the map is currently held in memory
spacegroup = returns spacegroup number
maximum = returns maximum density in map
minimum = returns minimum density
mean = returns mean density
rms = returns rms density
cell = returns cell info as a list of 6 numbers
limits = return start...stop on x..y..z as a list of 6 numbers
map = writes out map...careful!
title = returns the title from the map header
grid = returns the number of grid points along x,y,z cell
edges as list of 3 numbers
type = returns "map", "mask" or "other" depending on the
mode of the original map file
mode = mode of the map file
Returns:
-1 = no map loaded Otherwise returns requested info, see keywords.
Tcl command to release the memory holding the map and remove it from the array of stored maps.
mapid is the handle identifying the map which is to be deleted.
Returns:
-1 = no map currently stored 0 = successful
This implements the Tcl command section for manipulating CCP4 section structures in memory.
<name> is the handle id for a section structure in memory. option and the args determine the exact behaviour of the command. The following options are available:
init, configure, contours, coords, render, delete, exists, info
In addition the init and configure options can accept a number of extra arguments.
section <name> init <mapid> <axis> <section> ?<section2> ?<slab_step>?? ?option value ...?
Initialise a new section structure called <name>, with section number <section> on axis <axis> from map <mapid>
If <section2> is also specified then the section is actually a slab of sections from <section> to <section2>. An optional third number specifies the slab_step size between the two limits.
See below for details of additional optional arguments.
section <name> configure ?option? ?value? ?option value ...?
Change the settings in the existing section structure <name> If option is specified with no value then the current setting is returned.
See below for details of additional optional arguments.
section <name> contours <type> range <min> <max> <interval> ?option ...?
section <name> contours <type> list value ?value ...? ?option ...?
section <name> contours
Set or update the contour levels for section <name>
<type> is one of abs, sigma or frac range: contour levels will be set starting from <min> in steps of <interval> up to <max> list: contour levels as an explicit list of values Option can be one or more of: -negcontours: generate equivalent negative contour levels -meanoffset : generate contour levels starting from the mean density in the map (default is from zero) Without any arguments, return the contours as a list of absolute values.
section <name> coords <canvas> x y ?-precision value?
Return the fractional coordinates in section <name> corresponding to the canvas coordinates x,y as rendered on <canvas>
The optional -precision argument specifies the number of decimal places to return.
section <name> render <canvas> ?arg arg ...?
Draw contours on <canvas> with the settings in <name>
-scale <scale> : sets the scaling to <scal><units>/Angstrom if no units are specified then defaults to pixels -greyscale : draw a greyscale backdrop (default is not to draw greyscale) -nocontours : don't display contour lines (default is to draw contours)
Delete the section structure <name> from memory
Check whether the section <name> currently exists
Returns 1 if section is registered, 0 otherwise
Inquiry about general properties of the section <name>
option can be one of:
exists : return 1 if <name> exists, 0 otherwise
extent : return limits of the section within the map
nb these may be different from those used in
the display (see config -limits)
mapid : return the id of the parent map
Arguments
The init and configure options can take a number of additional optional arguments:
-axis <axis> : set axis from which to take section
-bbox <boolean> : set whether bounding box is drawn
-grid <boolean> : set whether grid lines are drawn
-gridlabels <boolean> : set whether grid labels are drawn
-gridspacing <u> <v> : set the spacing of gridlines on each axis
-limits <x1> <x2> <y1> <y2> : set limits of the section in the display
If <x1>...<y2> are all > 1 then the limits
are taken to be in grid units; otherwise they
are taken as fractional units.
-precision <ndp> : set the number of d.p. for gridlabels
-section <sec> ?<sec2> ?<step>?? : change section number or slab
definition
-labels <boolean> : set whether axis labels are drawn
-axislabels <xlabel> <ylabel> <zlabel> : set the labels displayed for the x y and z axis
-view <orientation> : set the viewing orientation to "lhs" or "rhs" (default is "rhs")
As of CCP4 5.0, ccp4mapwish has been updated to use the C library functions for handling map files which simplifies the requirements of the program substantially.
Building ccp4mapwish requires the following files and libraries:
These should automatically be detected by configure upon installation of the suite.
Example script to display a section:
# First set up a canvas to display sections set canv1 [canvas .c] pack $canv1 # Read in a map with name m1 readmap m1 toxd.map # Initialise a section called s1 from the map section s1 init z 5 # Initialise contour levels to display section s1 contours sigma range 1.0 5.0 0.5 -negcontours # Display the section in the canvas section s1 render $canv1 -scale 2mm
Peter Briggs, CCP4.