It is best to use the queues on either the Alphas or Oahu...of course, the Alphas are much faster.  Several people have had difficulty setting up their .cshrc files to run programs in the queues.  If you are one of these people, please see Chris or Matt for help.

Set up a file called myjob.csh containing a customized version of the following:

   cd $HOME/mydirectory/shelx/
   set d1 = "`date +'%d%m%y%H%M%S'`"
   set d2 = "`echo 'myfile.'$d1'.out'`"
   echo "output file is $d2"
   shelxl myfile > $d2

where ???? is the appropriate queue name.  For the Alphas, this would be xa128, xa384, or xa1024.  If you have time to waste, run it on Oahu with xq2, xq24, or xq_unlim.
 

This will generate a bunch of files in your working directory:

    myfile.lst ( a verbose output of what has happened during refinement)
    myfile.res ( can be renamed myfile.ins and re-run through Shelx without any alteration if so desired)
    myfile.fcf (structure factor file used in calculating electron density maps)
    myfile.pdb (standard format .pdb file)
    myfile.date&time.out

NOTE:  Unlike CNS, Shelx will OVERWRITE all of these files (except the .out file) in subsequent refinement runs.  As a safety measure, RENAME all of the files after each round of refinement.

The .out file is useful for monitoring your progress, and will look something like:

This show you the values for wR2 before each cycle, the amount of data and parameters used, the GooF (Goodness of Fit) with and without the restraints, and the atoms that had the largest shifts in their position and thermal parameters.  Towards the end, you are given the final values of R_free and R, both for data above 4(F_o) and for all data.