xgen script(1) X-GEN General Reference xgen script(1)

Processing a single data run with X-GEN

The following sequence of shell commands will enable a user to process a single set of diffraction data with X-GEN. The annotations following the pound sign in each line of this file contain explanatory material.

In general I recommend leaving the processing results in a directory (folder) that is below the folder in which the raw data sits. Thus if the raw data are in directory /d4/howard/07-26-04/chymo1/, then I recommend creating a directory /d4/howard/07-26-04/chymo1/xgen as a place for processing. The script below assumes this kind of arrangement. The subdirectory need not be named xgen; it could be named process, or fred, or anything else.

The script shown here is set up to perform an automated Bravais lattice calculation during the indexing and refinement process. If you would prefer to confirm the lattice calculation at the point where it is performed, replace the refall command, below, with the command refall -a.

This script is designed to be run from bash or ksh If you run the script from csh or tcsh, replace the command source *.com with the command source *.cmd.

cd /d4/howard/07-26-04/chymo1
mkdir xgen # create a subdirectory for X-GEN processing
cd xgen # change to that directory
xgnow # create environment variables and image index
source *.com # communicate run-time environment to shell
calibrate -j # ensure that we can convert pixels to cm
spots # find bright spots for indexing and refinement
refall # auto-index the data and refine parameters
integrate # compute integrated intensities
reduce # compress integrate output and filter out bad reflections
scalem # scale data, remove outliers, write out files

Try that sequence of events and depart from this recipe only if something hangs up!