xrspace
NAME
xrspace - reciprocal space viewer
DEFINITION
A reciprocal space viewer for examining completeness of
data, differences between data sets, and intensity patterns.
(Note: xrspace works best on color displays.)
USAGE
xrspace [file]
USES
Looking for Symmetry
Checking Systematic absences
Reduce your data in an analogous space group that
doesn't have the absences. i.e. use P222 for P212121.
Looking at heavy atom differences
Are they uniform throughout space or are there just a
few large differences around the beam stop? Use the
delta function after running xmerge.
Comparing 2 merged native data sets
Where are the differences?
Planning Data Collection Strategies
After a run (or part of a run) has been integrated you
can look to see where the data is. Turn off symm and
around which you are collecting data. Use the diagonals
to see if a diagonal looks better. The axis down which
the data has the narrowest range is possibly the
closest one to which you are collecting data. Experi-
ment: integrate frames 1 thru 50 and run xrspace *.urf;
then integrate frames 50 100 and run a second
xrspace*.urf. This shows you the direction in which
data is collected. If you want the h axis and you are
going away from it go the other way!
ENVIRONMENT
xrspace reads the environment variables CRYSTAL and CRYSTAL-
DATA. If CRYSTAL is present, then this is used to set the
crystal type, or else it can be manually entered after the
program starts. CRYSTALDATA is the default directory to look
for the info file of CRYSTAL. When looking for the info file
of the crystal type, it first checks the current directory
and then $CRYSTALDATA/crystal. See the XtalView documenta-
tion (if any) for more details. It only works best on a
color display. It does work on a b&w but needs improvement.
The author has a color display.
DATABASE REQUIREMENTS
xrspace looks for the keywords cell and symm in the
database/info file. If cell is present, it is read and
placed in the Unit Cell field. It can be manually overwrit-
ten if desired. The symmetry operators are read from the
line symm which should be entered in the format used in the
international tables Vol. I. xrspace converts these symmetry
operators to Patterson symmetry by adding a center of sym-
metry.
Example:
cell 48.5 76.3 92.1 90.0 104.0 90.0
symm x,y,z; -x,y+1/2,z;
OPERATION
The application presents a window that is divided into three
main areas: the control panel, a message window, and a can-
vas where the data is displayed as specified by the control
panel settings. The control panel is meant to be read from
top to bottom. Messages are printed in the textpane at the
bottom. Note that the textpane has the ability to save out-
put by means of its pop-up menu. The data is displayed on a
color display coded by a heatscale to represent intensity-
as the data increases in intensity it goes from black to red
to yellow to white. The width of a spot is proportional to F
and its area is proportional to I.
Quit Click to quit. You have one chance to change your mind.
Notebook
Unimplemented
Crystal
Check that the correct crystal is entered here. A
corresponding database file should be in the directory
$CRYSTALDATA - typically ~/xtal_info. If it needs to be
changed, click on this field to move the cursor here
and type in the new crystal and hit <CR>. If at any
time you want to force reading the crystal file (for
instance, you just edited it and fixed something), hit
<CR>.
Unit Cell
The proper unit cell should be displayed here. You can
manually type in any cell and override the one found in
the database file.
Directory
The current directory.
File The current input file. Either from the command line or
manually entered.
Read Clicking this button causes the file to be input.
Type Click on the appropriate file type. .fin (a fin file
(ih,ik,il,f1,s1,f2,s2));.mu (An XENGEN mulist file from
the makemu command); .df (a "double fin
file"(ih,ik,il,f1+,s1+,f1-,s1-,f2+,s2+,f2-,s2-)); .urf
(an urefls XENGEN file from integrate.)
Display Data
This switches between f1 and f2 or |f1-f2| (Delta).
Useful for looking at merged heavy atom datasets or for
anomalous differences.
Planes of
This sets the sectioning direction. You can use the
three principal directions or the major diagonals.
Level
This slider sets the plane level.(I.e., if the plane
direction is h and the level is 0 then the 0kl plane is
displayed.
Slab This sets the number of planes that will be displayed.
Normally they are drawn on top of each other but see
Offset of Vertical Axis.
Spot Size
Scales the size of all the spots up and down. Set this
so that spots do not overlap.
Resolution
This controls a ring which is drawn at the specified
resolution. It does not control the maximum resolution
of the screen; that is set by the limits of the input
data.
Symm Controls whether symmetry is used to generate symmetry
related spots or only the unique data is displayed.
Offset of vertical Axis
This lets you offset planes from each other so that
they are not drawn on top of each other. Try x=2 and
y=3 and make the spot size smaller for an orthographic
display of several planes (slab > 1).
Draw Redraw the screen. After first reading the data this
needs to clicked. Most of the other buttons and sliders
redraw automatically. Pay attention to the message at
the bottom of the window (left footer). If it doesn't
say "Ready for new input" just wait patiently, the
screen is redrawing .
Print
Send postscript output to a printer or file. Type the
name of the printer or the file in the printer field.
General
Clicking on a spot will display its indices and inten-
sities in the message window. These are the unreduced
indices. Don't get too far ahead of the program with
mouse input. Look at the footer to see if you are going
too fast.
NOTES
Works best on a color display. Although, it is usable in
black and white.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1)