Explanation of shell scripts used in some of these examples
  • Using a shell script can be a useful way to run autobuster.
  • The scripts here reflect how I refine autobuster.
  • A typical script is 1osgBasicNCS_001_control_noncs
#!/bin/sh -f
# example script showing how autobuster can be run
# setup autoBUSTER
. $BDG_home/setup.sh
# write results to a directory:
(time refine                                    \
   -p 1osg_stripHOH_Brefine.pdb                 \
   -m 1osg.mtz                                  \
   -B "individual"  -noWAT  -r 0.006            \
   -d $RESULTDIR                                \
  ) > $0".log"
if [ $? -ne 0 ]
  exit 1;
# copy out the pdb and mtz files to this directory.
cp $RESULTDIR"/refine.pdb" $0"_refine.pdb"
cp $RESULTDIR"/refine.mtz" $0"_refine.mtz"
  • to run the script download it
  • make it executable use the command
chmod a+x 1osgBasicNCS_001_control_noncs
  • Then run by
./1osgBasicNCS_001_control_noncs &
  • the script runs the refine command it will produce:
    • an output log file with the name 1osgBasicNCS_001_control_noncs.log
    • an autobuster results directory with the name ab_runs/1osgBasicNCS_001_control_noncs_result
    • the file .pdb coordinates and .mtz file will be copied into the current directory with names 1osgBasicNCS_001_control_noncs_result.pdb and 1osgBasicNCS_001_control_noncs_result.mtz
  • The shell variable $0 means the script name so if the script is renamed so will the output files and directory.
  • For efficiency, it is a good idea to make sure that the main autobuster results directory is on a local fast filesystem rather than for example an NFS filesystem. If you are working from a such a directory then before running any scripts use commands like:
mkdir /var/tmp/my_abruns
ln -s /var/tmp/my_abruns abruns
  • these commands create a symbolic link to a local directory and the script will therefore will write to a subdirectory in this.
  • I find this a convenient way to run autobuster:
    • It creates pdb and mtz filenames that are easy to handle with coot.
    • All the commands/options used in an autobuster run are contained with the script.
    • local filesystems are used for the run but the script itself as well as the top log, mtz and pdb files are keep on a more reliable RAID and backed up filesystem.

Page by Oliver Smart original version 21 May 2008. Address problems, corrections and clarifications to buster-develop@globalphasing.com