xgenproc [--help] [--version] [-dns] [-cfhilmpxy<val>] [datadir]
"xgenproc" is a script that allows you to process a single run of
diffraction data through X-GEN, beginning with raw images and culminat-
ing with the production of several ascii files containing merged,
scaled intensity measuremnts. "xgenproc" has been tested primarily on
data obtained from the two beamlines of Southeast Regional Collabora-
tive Access Team, but it should work with data collected on home
sources and from other beamlines too.
The `xgenproc' 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.
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
Then if the data are from the SER-CAT ID line and were collected in
omega, you can process the data by typing "xgenproc -s". The script
will work properly with data from most other sites (including the SER-
CAT ID collected in phi) if you simply type "xgenproc".
Frequently 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 Rmerge values
that you see near the bottom are good), then the processing probably
worked. If you cd to the processing directory (xgen, or xgena, or what-
ever), 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 scaling
results will be near the end.
If it's still unable to find the images, you may need additional
help from the author (email@example.com).
* 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-
% xgenproc -s
- It may not have found enough reasonable centroids to refine
You can circumvent this by specifying a larger minimum number of
centroids. By default the program searches for spots over seven
images or until it finds 400 centroids, whichever comes last.
If 400 isn't enough, specify a larger number, e.g.
% xgenproc -c700
on the BM line or on the ID line with phi data, or
% xgenproc -s -c700
on the ID line with omega data.
- 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 symmetry correctly. If you actually know the spacegroup,
you can specify it at the xgenproc runtime by its International
Tables number. Thus if your crystal is in spacegroup P6(2)22
(International Tables # 180), you can specify it at runtime as:
% xgenproc -i180
You can combine this flag with the others listed aobve if appro-
* It may integrate data satisfactorily at first, but fail farther
* It may integrate satisfactorily, but produce unsatisfactory
R(merge) values in scaling. There are multiple possible causes
for this too:
- The beam-center values are wrong. Look at your .xlg file just
before the last integration; the output from the refinement seg-
ment will contain something that looks like "Start omega: 1.00
chi: 0.00 phi: 0.00 Mainbeam: 1031.0 1041.9" Note that the
Mainbeam position _in pixels_ is specified here. If the Mainbeam
values in this window are seriously off from where we expect
them to be, then we may need to specify them specifically. Here
if we know they really should be [X,Y] = [1021,1048], we can
specify those values at run-time with
% xgenproc -x1021 -y1048
- The spacegroup is wrong. Typically this happens if we have
been too aggressive in assigning a high symmetry when a lower
one is real. Figure out the correct one and specify it:
% xgenproc -i75
- There are icerings in the data that are polluting the results.
This can be readily dealt with in the specific applications
within X-GEN, but not in the one-line processing system.
- The data have been scaled at higher resolution than is really
legitimate. X-GEN by default analyzes the output of the inte-
gration step and estimates the plane-spacing at which the aver-
age value of I/sigma falls to 1.3. It sets the resolution limit
there. That value may be at higher resolution than you really
believe is appropriate. My contention is that you can always
throw out some of your data if there's a little too much
present; you can't get it back if you didn't process at a suffi-
ciently high resolution. If you want to see what the statistics
are like at a different resolution cutoff, you can easily get
those. To do that, change directories to the directory where the
processing was being done, establish the X-GEN environment vari-
ables for your project, and run the X-GEN "stats" application,
specifying the resolution limit that you believe is really
% cd xgena # cd to processing directory
% source *.com # establish environment variables
% stats -on 3.1 # Friedel-mates merged to 3.1A
This tells the application to calculate intensity statistics for
the data out to 3.1 Angstroms, separating Friedel mates for the
+ Does "xgenproc" have run-time options?
% 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 firstname.lastname@example.org.
--help Print this message.
Print a header indicating the version of X-GEN that is running.
-d Compress the images using the "gzip" algorithm after integra-
-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
Specify the number of centroids required for refinement. In
general the `spots' functionality will search for 300 spots; if
it doesn't find that many in the first seven frames, it will
continue looking until it finds 300. Specifying -c<val> will
direct "xgenproc" to look for a different total.
Specify the last image we will process. This enables two differ-
ent capabilities: First, if we are collecting while we're pro-
cessing, we can use this flag to specify the last frame we actu-
ally plan to collect, even if at the time we start running X-
GEN, that frame hasn't been collected yet. Second, if we know
that images 57-180 are garbage, we can specify -h56 to indicate
that we only want to process up through image 56.
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-
Process data images whose filename prefix is <val>. Ordinarily
"xgenproc" 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 "xgenproc" to work with the george1b
data by specifying xgenproc -pgeorge1b
Specify the main-beam X position IN PIXELS as <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.
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.
This facility is available in part to allow "xgenproc" to be run
from a Python or Motif GUI whose concept of "current working
directory" may be muddy.
Process all the images in for the dataset whose prefix is most
plentiful in the current working directory.
xgenproc -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.
Report bugs to Andy Howard at email@example.com or 312-567-5881.
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)
Man(1) output converted with