MAPSLICER (CCP4: Supported Program)

NAME

mapslicer - interactive viewer for contoured sections through CCP4 map files.

SYNOPSIS

mapslicer [ mapfilename ]

DESCRIPTION

MapSlicer 2.1

MapSlicer reads in CCP4 format map files and can display contoured sections though the map along any of the principal axes. MapSlicer uses code from the CCP4 graphical user interface ccp4i in addition to a set of custom Tcl commands (see ccp4mapwish).

MapSlicer offers the following functions:

Read in CCP4 map file, pick any section or stack of sections (``slab'') on any axis and display contour levels
Shortcuts to Harker sections
Can alter contour levels, section limits and grid
Can alter screen scaling
Can zoom into areas of the display
Can display info on map header and currently displayed section
Displays cursor position in fractional coordinates, and the density at that point
Print section to a postscript file with user-defined scaling (eg mm per angstrom)

The mapslicer script runs through ccp4mapwish, which is a customised version of the TCL/Tk interpreter wish.

USAGE

Most of MapSlicer's functionality can be accessed quickly through the controls on the left-hand side of the window. Other options are available through menus at the top of the main window.

File menu:

Open new map file: Select a new map to view. Any existing map currently being viewed will be overwritten in the viewer's memory.
Save section: Save the current section to a postscript file.
Print: Print the current section to a postscript file.
Exit: Close the viewer.

Section menu:

Section limits: Allows you to change properties of the grid, the extent of the section displayed, and the orientation of the view.
Contour levels: Allows you to change the contour levels displayed. This is based on the old NPO keywords.

Info menu:

About map ...: Displays a window with information about the current map.
About section ...: Displays a window with information about the current section, including the contour levels.
About MapSlicer ...: Starts a hypertext viewer to display this file.

MapSlicer Modes

MapSlicer operates in four distinct modes, which are selected via the Mode menu on the left-hand side of the screen. Depending on the mode, different controls will be become visible:

Section mode: MapSlicer displays a single section at a time. The current section can be changed by editing the section number in the entry box, or by clicking on the arrows to move up or down by one section.
The current axis can be changed by selecting the new axis from the menu.
In this mode the option to display a "greyscale" view is also available. If this option is selected then the greyscale is superimposed beneath the contours - see the section on greyscale views for more information.
Slab mode: Similar to Section mode, except that the display shows a stack of sections superimposed one on top of the other. The slab is defined by a starting section, a depth (number of sections between the start and end) and a step size (specifying how many sections in the slab will actually be drawn).
Any of these attributes can be edited directly to change the current slab display. Alternatively the arrows can be used to move the start position up or down by one section.
The current axis can be changed by selecting the new axis from the menu.
Harker mode: This requires that the Harker spacegroup be specified. A menu will then list the possible Harker sections for that spacegroup, and selecting a particular menu entry will jump directly to the appropriate axis and section.
If the selected Harker section is not in the current map then a warning will be displayed. If no Harker sections are available then the menu will display "None".
Mask mode: This is the default mode if a CCP4 mask file is loaded. The display shows a black ("zeroes") and white ("ones") view.
(This is essentially a contourless greyscale view of the map.)

Other controls

The remaining controls are not dependent on the mode

Scale: Specifies how large each Ångstrom is shown on the display, in either mm or screen pixels. The scale is a real number for either units, and can be edited directly in the display.
AutoScale: Resets the view to show the whole section at a scale of 2mm per Ångstrom.
Undo Zoom: Restores the view to that prior to the last zoom operation that was performed.

Zoom Facility

The Zoom facility allows the user to select a smaller area of the current display and rescales to show that area only.

The Zoom is enabled by click-and-holding the left mouse button (to set one corner of the zoom area), dragging the mouse pulls out a box which defines the zoom area, releasing the mouse button then performs the zoom operation.

The scale will be reset automatically so that the screen area occupied by the new view is roughly the same as before the zoom. This is calculated based on area, and seems to work best for roughly square zoom areas.

A zoom operation can be reversed using the Undo Zoom button.

Greyscale Views

The greyscale view sets tones of grey for each cell in the visible map section, based on the value of the map at the grid point at the centre of the cell, scaled linearly relative to the minimum and maximum values within the current view. Darker areas have lower density values than lighter areas.

This means that features in the greyscale view may appear to be "flattened out" for sections which are dominated by only a few disproportionately high peaks (such as sections in a patterson map which include the origin peak). This can be counteracted to some degree by using the zoom function to "crop out" the high peaks from the section being viewed.

Comments and feedback on the greyscale view are welcome.

AUTHOR

Peter Briggs