xcontur
NAME
xcontur - a page-based contouring program for crystallo-
graphic maps
USAGE
xcontur file.map
METHOD
The map is contoured in sections of x, y, or z. The output
appears in a window that is the same size as an 8-1/2 x 11"
page. The program produces Postscript output which can be
used on any Postscript compatible printer. The output is
fairly WYSIWYG with the exception that nicer fonts are
available on the laser-printer. Stereo is available by
shearing and labels and bonds (lines) can be added or read
from files. No interpolation is used in the contouring. If
smoother sections are desired calculate the map on a finer
grid.
MAIN WINDOW
Crystal
The cell information is used from the crystal file.
Cell The unit cell is used to scale the axes. Non-
orthogonal axes are properly handled. The rows are
always horizontal and the column is at alpha, beta or
gamma depending upon the plane being sectioned.
NX, NY, NZ
This is read from the input map and cannot be changed.
Planes
This sets the sectioning direction in either x, y, or
z. If you change this, then the rows and column direc-
tions are also changed so that they do not conflict.
No attempt is made to detect left-handed configura-
tions. If you stack up sections for a mini-map, you
may need to stack downwards or upwards to get the
proper handedness.
Plane
There are 3 fields here. The first is a numeric field
which can be used to increment/decrement the section
where contouring starts. The second is the value of
this plane in fractions of the unit cell. If you edit
this value and enter it, the nearest plane section will
found. The third is a pull down menu for choosing the
three sections 0.0, 0.5 and 1.0. If the number of sec-
tions is odd, the nearest section will be given for
0.5.
Slab The number of sections to contour. They will all be
overlaid onto each other on the screen although when
they are plotted they can be either overlaid or plotted
on separate sheets. The slab always starts at plane
and increases.
Rows Rows go horizontally across the screen. This sets
whether this direction is x, y, or z. It overrides the
columns when changed if it conflicts, and can be over-
ridden by planes.
Row min
The first value is in terms of grid points in nx, ny or
nz and the second is fractions of the unit cell. You
must enter fractional values for them to take effect.
Columns
This sets the direction of the columns. It has the
lowest priority and so can't actually be used to change
the column direction but does indicate the direction
being used. Both row and plane direction changes will
override the column direction if there is a conflict.
CONTOUR LEVELS
Number
The number of contour levels is set here from a minimum
of 1 to a maximum of 20.
Interval
The interval between successive levels. From a minimum
of 1 to the maximum value of the map.
Start
The level of the first contour level. May be negative.
The slider ranges from the minimum of the map to the
maximum. Upon loading a map both start and the inter-
val are set to the root-mean-square value of the map.
Draw The screen is redrawn when this button is pressed.
Picking in the Canvas
If you pick with the mouse button the fractional coor-
dinates of that point are returned in the message win-
dow. Holding down the SELECT (left) mouse button
causes the outline of the section to drag so that it
can be positioned on the page. When using slabs
greater than 0 the vertical coordinate with the maximum
density value will be printed. This allows finding the
x, y, z coordinate of a peak. The density value
printed is an interpolated value and as such is almost
always lower than the peak value.
VIEW POP-UP
Title
The title is initially set to the map file name. It
is nice to edit it and put something sensible here.
Display Type
You can look at the contours (default) or at the raw
numbers in the map file. However, for the raw numbers
only a small section can be viewed before the numbers
overlap each other and become unreadable.
Row, Column Ticks
The number of grid lines and/or tick marks to make
counting from 0.
Row, Column Origin
The position of the upper left corner of the section.
It is easier to set this by dragging with the mouse in
the canvas window.
Scale Angstroms/cm
You can manually enter a value or pull down a menu of
choices. The scale is accurate for hardcopy but is
correct only if you happen to have the right size moni-
tor. Remember, though, that the canvas window is the
same size as a piece of paper if you haven't resized
it. And so, if the graph fills the window, it will fill
the paper.
Alternate solid and dashed contour
Check this if you wish to do this. Every other level
will be dashed lines for an interesting effect that can
make counting levels easier.
Draw grid of lines
If this is checked, a grid of lines is drawn at the
frequency specified by the row, column ticks.
Auto Center
If this is checked the section is centered on the page
automatically. Must be disabled for stereo to work
properly.
Use Line Width for Depth Cue
While the computer screen does not have enough resolu-
tion for this to be useful, it produces a nice depth
cue on laser printed output and is highly recommended
for multi section slabs. Best to set it just before
printing.
Draw Labels
Enables/disables the drawing of labels. Labels can be
edited using the Labels pop-up or loaded in the File
pop-up. They are drawn on the section only if the x, y,
z coordinate is on that section.
Draw Jack at Label Position
Enables/disables the drawing of a jack at the position
of the label. The size of the jack can be changed with
the slider:
Draw Bonds
Bonds can be drawn superimposed on the sections. They
are drawn only if their x, y, z coordinate is on that
section. The line width of the bond on the printed
output can be varied from thick to thin to make it more
obvious.
Draw side by Side Stereo
The scale is halved and two images for side by side
stereo are drawn by shearing each successive section.
Stereo Separation
Sets the distance the two images are apart from each
other. Hint: Set the contour level very high while
fiddling with the stereo parameters so that drawing is
quick. Once you get them right you can lower the level
for the final picture.
Stereo Depth
This sets the shear angle and modifies the apparent
depth.
Apply
Causes the picture to re-draw.
FILE POP-UP
Filter
This sets a filter for the file list box. It defaults
to *.map and all the files in the current directory
that match the filter will be displayed in the file
list.
List Forces the file list to be updated. Use after changing
the filter or the working directory.
Directory
The current working directory.
Map File
The source of the map. This field can be filled either
from the command line as the first argument, by select-
ing a file name in the file list, or by typing it in.
Labels File
The labels can be loaded from or saved to this file.
It has the format of lines of x y z label, where x, y,
z are the coordinates and label is a text string.
Xpatpred produces a label-file that xcontur can
display.
Bonds File
Bonds can be loaded or saved. The bond file has the vu
format: lines of x1 y1 z1 x2 y2 z2 color. Where x1,
y1, z1 are the starting coordinates of a line and x2,
y2, z2 is the end coordinate. The color is not used by
current version of xcontur. Xfit also displays/creates
vu files and a number of utilities for producing vu
files from PDB files and other sources exist (e.g.,
grinchbones).
Number of Bonds
This is for your information. It is not editable.
File List
To pick a file in the list, click on the file field
that you want to load the input focus into (the little
triangular cursor). Then select a file name using the
SELECT (left) mouse button.
PRINT POP-UP
Print to
You can select a file or a printer. Very large pic-
tures may need to be sent to a file and then printed
with the -s option because they are too large to spool
directly.
Printer
A valid name of a printer connected to your computer.
Leave blank for the default printer.
File Name of the file. The directory in the files pop-up is
added unless the name starts with "./" or "/".
Print sections separately
If this option is checked, each section is printed on a
separate page. This saves you from having to print
them one by one by selecting the entire slab, this
option, and then printing.
LABELS POP-UP
Can be used to edit the labels list. Functions are
insert/replace/delete. Use the File pop-up to load a labels
file.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1), xpatpred(1), grinchbones(1)