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NAME
X-GEN - xgenstart.py
SYNOPSIS
xgenstart.py [--help] [--version] [-nsuv] [-fhilmpswxy<val>] [datadir]
DESCRIPTION
"xgenstart.py" is a Python script that allows you to analyze a few spe-
cific images, typically test images collected prior to the beginning of
real data collection, in order to obtain an indexing and a refinement
of the crystal and detector parameters and to use that refinement to
calculate a data collection strategy. It assumes that the user has col-
lected a few single images separated fairly widely in scanning angle,
and that the scanning angle values associated with those images are
identifiable from the image headers. Thus if image blah.0000,
blah.0090, blah.0180, and blah.0270 were collected at scanning angle
values of 0, 90, 180, and 270 degrees respectively, then xgenstart.py
will usually be able to determine the unit cell and therefore a data
collection strategy from those four images.
xgenstart.py is based on the formalisms used for the general-purpose
Python script for X-GEN data processing, i.e. xgenproc.py. It omits the
integration, data reduction, and scaling steps, and replaces them with
the strategy determination. It is also set up to expect a few single
images (like the examples mentioned above) rather than a contiguous set
of images, as is more typicaly in full data collection as implemented
with xgenproc.py.
The `xgenstart.py' script is found in the executables directory within
which the rest of the X-GEN executables live. On most machines that
directory will either be /usr/bin itself, or it will be /opt/xgen/exec,
or /home/[INSTALLER]/xgen/exec, where [INSTALLER] is the username of
the person who installed X-GEN on your system. The executables,
libraries, and resource files for X-GEN, along with the script itself,
are available for download from http://xgen.iit.edu. Of course, to run
this, you will also need Python. This script has been tested with
Python 2.3.5, and it probably runs on later versions; it may be compat-
ible with earlier versions too.
If you have collected data into a known directory, you should be able
to use this script in a simple manner. First, set your working direc-
tory to the directory where the data are, e.g.
cd /u1/ID7/03_18_05_uXX/Fred/uglyxtal
Then if the data are from the SER-CAT ID line and were collected in
omega, you can process the data by typing "xgenstart.py -s". The script
will work properly with data from most other sites (including the SER-
CAT ID collected in phi) if you simply type "xgenstart.py". The various
run-time parameters will enable you to tailor your run of xgenstart.py
to the specific circumstances under which you're running it.
Potentially asked questions:
+ How do I know if it has worked?
The processing results will be written to a subdirectory of your cur-
rent directory called xgen. If that directory already exists (because
you or someone else has already processed these data before, or has
processed a different dataset in the same directory), then they'll be
written to the directory xgena. If xgena exists, they'll be written to
xgenb, and so on up through xgenz.
So if the output to your screen looks reasonable (the refinement sta-
tistics that you see near the bottom, just before the strategy calcula-
tion, are good), then the processing probably worked. If you cd to the
processing directory (xgen, or xgena, or whatever), then if you look at
the logfile, you can see how effective the processing was. The logfile
has a name that ends in .xlg.:
% cd xgena
% vi *.xlg
Examine that .xlg file to see the quality of the data. The crystal and
detector parameter refinement steps will be nearly at the bottom.
+ What if that doesn't work?
There are several possible reasons it might not work.
* The software may have failed to find the detector images in the
current directory. If that happens, you may want to specify your
image prefixes explicitly. Thus if your data in
/u1/ID7/03-18_05/UXX/Fred/uglyxtal/ have filenames ugly01.0001,
ugly01.0002, . . . , up through ugly01.0137, then you might want
to try
% xgenstart.py -s -pugly01
If it's still unable to find the images, you may need additional
help from the author (howard@iit.edu).
* It may fail during auto-indexing. There are some special cases
for this problem:</li>
- It may have gotten the stepsize wrong.
Note the rules I've given above. If you collect on the bending-
magnet beamline, or if you collect on the ID line using phi as
your data collection motor, then you don't need to flip the sign
of the stepsize. If you collect on the ID line using omega as
your data collection motor, then you need to specify the sign-
flip:
% xgenstart.py -s
- It may not have found enough reasonable centroids to refine
on.
- The crystal may be twinned or pathological in some other way.
In this case you may need to abandon the non-interactive
approach to using X-GEN and learn how to use the specific appli-
cations within it. Check out the actual documentation for the
individual X-GEN executables at http://xgen.iit.edu.
* It may auto-index correctly, but it may not account for all the
Laue Laue symmetry correctly. If you actually know the space-
group, you can specify it at xgenstart.py runtime by its Inter-
national Tables number. Thus if your crystal is in spacegroup
P6(2)22 (International Tables # 180), you can specify it at run-
time as:
% xgenstart.py -i180
You can combine this flag with the others listed above if appro-
priate.
+ Does "xgenstart.py" have run-time options?
Yes. They're listed under "Options".
+ I want to see the images!
You can readily do so. Change directory to your processing
directory, establish your environment variables, and examine the
images with "pdisplay":
% cd xgen # cd to processing directory
% source *.com # establish environment variables
% pdisplay # examine your images
"pdisplay" has many options that you can explore.
+ I'm stuck in ways that aren't discussed here. What do I do?
Read the full documentation for X-GEN, or call or e-mail Andy:
773-368-5067 (cell), 312-567-5881 (IIT), or howard@iit.edu.
OPTIONS
--help Print this message.
--version
Print a header indicating the version of X-GEN that is running.
-n ordinarily the refinement portion of X-GEN does a simple-minded
recentering of the main beam immediately after auto-indexing.
This option directs the package NOT to do that.
-s Flip the sign of the rotation stepsize from the value that the
program intuits. We try to stay in synch with the stepsize con-
ventions for every goniostat, but if we get it wrong, this
allows recovery.
-u Same as --help, i.e. print this message.
-v Same as --version, i.e. print the X-GEN version number and then
exit.
-h<val>
Specify the last image we will process.
-i<val>
Specify an International Tables spacegroup number. If auto-
indexing succeeds, and the Laue group associated with the speci-
fied spacegroup number is a plausible solution to the Bravais-
lattice calculation, then we will impose this spacegroup number
during processing. To specify a rhombohedral indexing of a rhom-
bohedral unit cell, add 100 to the spacegroup; thus R32 indexed
rhombohedrally is -i255.
-l<val>
Specify the first image we will process. If images 1-13 are
garbage, we can specify -l14.
-m<val>
Search for spot centroids out of <val> different sub-runs of
"spots". If <val> is 4, for example, and there are 120 images in
the FRAMES index, then we will extract spots from images 1, 31,
61, and 91. We'll merge those lists of images together before
auto-indexing and refinement. The default for <val> is 4.
-p<val>
Process data images whose filename prefix is <val>. Ordinarily
"xgenstart" picks the prefix in the data directory for which the
largest number of images is present; this option allows us to
specify exactly which prefix to use. Thus if george1a.0001 -
george1a.0180 and george1b.0137 - george1b.0219 are both present
in a directory, we can tell "xgenstart" to work with the
george1b data by specifying xgenstart -pgeorge1b
-w<val>
In multi-centroid mode (-m<val>), we specify here the number of
contiguous images in each sub-run that will be examined during
indexing. Ordinarily the correct value for this will be 1 unless
the we're doing small-molecule data collection.
-x<val>
Specify the main-beam X position IN PIXELS as <val>.
-y<val>
Specify the main-beam Y position IN PIXELS as <val>. These
options must be specified together. If they are, the script will
run "calibrate -j" with the appropriate beam-center values
before beginning processing.
[datadir]
If a non-flag argument is specified, it is taken to be the name
of the directory in which the search for images is to be per-
formed. By default we specify the current working directory.
xgenstart.py -d -pgeorge1a -h180 -x2028 -y2029
Process the images with
prefix "george1a", assuming that the last usable image will be
number 180; assume that the beam center is at [X,Y] =
[2028,2029]; compress the data after integration.
REPORTING BUGS
Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.
COPYRIGHT
Copyright (C) 2002, Illinois Institute of Technology. See the file
'LICENSE' for information on usage and redistribution of this file, and
for a DISCLAIMER OF ALL WARRANTIES
Version 5.5.5 October 2005 X-GEN(1)
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