phichi: Find unit cell using Dirax from phi and phi/chi images
The "phichi" program can calculate an accurate unit cell from pairs of
corresponding phi and phi/chi scans with the help of the "dirax"
program [J.Appl.Cryst (1992) 25:92-96]. The phi/chi procedure is
described in J.Appl.Cryst (2000) 33:893-898 and patented by Nonius.
Usage
The program is invoked by the command line:
phichi [options] [make|<imagefilenames>]
Different image file types are
recognized from their names.
Images must be given as pairs of (phi,phi/chi) scans around
the same central position. If the "make" option is given instead, a
standard phi/chi data collection will be performed and the resulting
files analyzed.
The program will write "c" vectors corresponding to peaks located in
each pair of scans to a file "cell.drx". It will then run the "dirax"
program (to obtain dirax, read contact the authors via schreurs@chem.uu.nl, and read
the page in the KappaCCD user discussions to find out how to install
it) to find the cell, and use the dirax "ccd cell" command to write
the resulting cell to a file "cell.rmat", which can be used by the
programs in the collect suite.
A "set2"-like procedure is used to merge C vectors for Friedel paired reflections
if available, increasing the accuracy of the results.
Options
Options that influence the analysis are:
- intcrit=#
-
Specify the criterion to decide
whether two intensities of reflections are identical (default value
0.5 (given in the collect configuration file), lower values are more strict)
- radcrit=#
-
Specify the criterion to decide whether two reflection positions
possibly correspond (default value is 0.16 mm, specified in the
collect configuration file).
- gui and nogui
-
Instructs the program to show its progress in a graphical user
interface or to be completely controlled from the command line.
"nogui" is the default.
- refine and norefine
-
Instructs the program not refine or not to refine the detector position
after the cell is first determined. The default is determined by
the cellrefinedetector
configuration parameter.
The following options are available in combination with the "make" argument
(and silently ignored if "make" is not specified):
- dx=#
-
Crystal to detector distance (in mm) to use for the measurement.
- exposuretime=#
-
The exposure time (in seconds) per image (2 frames).
- chi=#
-
The chi angle for the phi/chi scans (in degrees). There is no good reason
to change this from the default value of 10 degrees.
- phi=#
-
The central phi position (in degrees).
- frameangle=#
-
The phi rotation angle (in degrees).
- theta=#
-
The theta position (in degrees). Normally 0, but for very small cells
you might want a theta offset.
- kv=# and ma=#
-
The generator setting to go to before starting the measurement. If no
generator setting is given, the generator is automatically powered up
to standard settings if necessary.
- powerdown
-
Requests an explicit power down of the generator after the measurement.
- npairs=#
-
Specifies the number of phi and phi/chi scan pairs that is to be
collected. Default is 4, which should normally be sufficient; if the
number is raised it is strongly suggested to keep it even.
Prerequisites
This program needs distortion correction (see programs makedistor and makedetalign) for proper functioning.
