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

       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 (

       *      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

       *      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
              R(merge) calculations.

       + 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


       --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
              allows recovery.

              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 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

Version 5.5.5                    October 2005                         X-GEN(1)

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