2.31 ********************
* PRECESS WRITE-UP *
********************
PRECESS can be used to construct and display "pseudo" precession
photographs created from input reflection data files. On SGI
hardware either precess or precess_X can be used. On other hardware
only precess_X can be used. Note also that if precess is run on
an SGI workstation, it should be invoked from a WINTERM window and
NOT from an XTERM window. Precess_X can be invoked from either
window. The user can interactively select the zone to display, and
scroll up or down through neighboring zones, selecting information
for any reflection by moving the cursor to it. Several input file
formats are recognized, including any of the "scaled" files used
within PHASES, XENGEN style "MULISTS" or "UREFLS" files, SCALEPACK
style files or a simple free format input file.
Data within the displayed zone are grouped into bins (256 for the
IRIS GL version, and 101 for X-window version) based on intensity,
and displayed with a corresponding gray scale scheme. Alternatively,
a full color display can be used. If requested, a pseudo background
based on the mean sigma's as a function of resolution can be added
to the display, creating a realistic image complete with beam stop
shadow. If a "scaled" file is input, the user is prompted for the
file type and to select either the native intensities or intensity
differences (isomorphous or anomalous, depending on the input file
type) for display.
The program will first prompt for an input "parameter file"
The program then prompts for a file name, which should be the
name of a data file with a .mu, .urf, .scl, .sca or a .dat extension,
for a resolution cutoff, for the desired zone, whether a pseudo
background is to be included, and whether a color or continuous gray
scale photograph display is desired.
After reading in the data file, a reasonable color scheme is
determined and the desired zone is displayed along with a menu. The
data is selected, when possible, in a manner which preserves anomalous
scattering information and, when possible, the actual measurements
for symmetry related reflections are used. Finally however, rather
than leaving "holes" in the picture, symmetry operations (including
freidel's relationship) are used to fill in missing data. Thus
the resulting display will conform to the true diffraction symmetry
if all required data were present on the input file, but if some
reflections were missing but their symmetry mates were present, the
intensities for the mates are used.
Moving the cursor to a menu item and pressing a mouse button will
then carry out the selected option. In most cases any of the mouse
buttons will suffice, but for some items the buttons have different
functions.
The "UP" and "DOWN" menu items change the color map
intensity thresholds, and thus the image intensity scale. For each
of these options the left mouse button makes a slight change, the
middle button a moderate change and the right button a substantial
change.
Pressing any mouse button while in the "EXIT" field terminates the
program.
Pressing the left or right mouse button while in the "ZONE" field will
toggle the next zone index direction (indicated by the arrow).
Pressing the middle mouse button while in this field will read in and
display the next (or previous) zone as desired, using the current
color intensity scheme.
Moving the cursor in the data display area results in the resolution
and intensity at the current cursor position to be displayed. If one
is near a bragg reflection however, the indices, integrated intensity
and its standard deviation are displayed along with the resolution.
Pressing any mouse button while in the "NEW DIRECTION" field will
allow the user to select another zonal direction (e.g. hk0 when
h0l was originally choosen), and/or select a new resolution cutoff.
Pressing any mouse button while in the "SAVE IMAGE" menu area will
save the entire screen contents as an "image" file, with the name
"prec_N.rgb", where N is a one or two digit number. Numbers start
from zero and are automatically incremented each time an image is
saved. Up to 100 images can be made in any job. NOTE!! This option
is not yet functional on the X-window version of precess.
For the purpose of photographing the display, it is often desirable
to remove the menu and color map since there is usually too much
contrast variation between them and the frame data for both to be
reliably recorded with the same exposure. The menu display can be
toggled on/off by pressing any mouse button while the cursor is
anywhere to the right of the menu items. Note however, that when the
menu is off all other functions are disabled, thus it must be
toggled back on to restore interactive functionality, and to enable
exiting from the program.
***** FILES *****
The type of input reflection file is deduced from the ending
part of the filename. Recognized endings are:
.MU, .mu, .SCL, .scl, .SCA, .sca, .URF, .urf, .DAT or .dat
XENGEN output will typically be either .MU format ( having F's,
NOT I's), or .URF format, although the .URF files can currently
be used only if they were created on a UNIX computer.
Any of the "scaled" file formats accepted by PHASIT can also be
used here, and will be assumed if a ".SCL" or ".sca" ending is
used. If this option is input, the user also will be asked as to
what type of data is in the file, and whether to display the native
intensities or intensity differences (isomorphous or anomalous,
as appropriate for the file type).
If the filename ends with ".SCA" or ".sca", then a SCALEPACK
file is assumed. After a variable number of header records
(see the FILE FORMATS section), reflection records follow and
contain
H, K, L, I+, sig(I+), I-, sig(I-)
in format (3I4, 4F8.1)
Note the use of intensities rather than F's. The last two items
in each record may be omitted. If present, they would be used
only if I+ was not measured.
A general, free format file can be used and is assumed if the
file ends in ".DAT" or ".dat", in which case each record must
contain
IH, IK, IL, F, SIG(F)
readable in free format, i.e. at least one blank or a comma
separates the entries.