XDSGUI User tools

This page is for sharing useful scripts to use in XDSGUI User tools

Update beam center

Read beam center from IDXREF.LP, then adjust location to frame coordinates in case of 2-theta offset

Formatted code:

X=$(perl -e '
# Read IDXREF.LP to get refined beam center, save in $x, $y
open(F,"<IDXREF.LP") or die;
while(<F>){
  if(/BEAM +(\S*\d) +(\S*\d)/){ $x=$1; $y=$2; } # get X,Y beam
}
# Read XDS.INP to get parameters needed to adjust for horizontal 2-theta offset (vertical offsets not supported)
open(F,"<XDS.INP") or die;
while(<F>){
  if(/^[^!]*DETECTOR_DISTANCE= *(\S*\d)/) { $d=$1; } # d = detector distance
  if(/^[^!]*DIRECTION_OF_DETECTOR_X-AXIS= *(\S*\d) +\S*\d +(\S*\d)/) { $x1=$1; $x3=$2; } # x1,x3 = horizontal rotation part of X-axis
  if(/^[^!]*QX= *(\S*\d)/) { $qx=$1;} # qx = detector resolution
}
printf "ORGX=%.2f ORGY=%.2f\n",$x-$x3/$x1*$d/$qx, $y;'
) && sed -e 's/^ *\(ORGX=\)/'"$X"' !\1/;' XDS.INP > x && mv -f x XDS.INP

One-liner for use in XDSGUI

X=$(perl -e 'open(F,"<IDXREF.LP");while(<F>){if(/BEAM +(\S*\d) +(\S*\d)/){$x=$1;$y=$2;}}open(F,"<XDS.INP");while(<F>){if(/^[^!]*DETECTOR_DISTANCE= *(\S*\d)/){$d=$1;}if(/^[^!]*DIRECTION_OF_DETECTOR_X-AXIS= *(\S*\d) +\S*\d +(\S*\d)/){$x1=$1;$x3=$2;}if(/^[^!]*QX= *(\S*\d)/){$qx=$1;}}printf "ORGX=%.2f ORGY=%.2f\n",$x-$x3/$x1*$d/$qx,$y;')&& sed -e 's/^ *\(ORGX=\)/'"$X"' !\1/;' XDS.INP>x && mv -f x XDS.INP

Run Phenix xtriage

Run phenix xtriage, and display the result in a text viewer. Change gview if necessary

phenix.xtriage output_file_name.mtz  scaling.input.xray_data.obs_labels=IMEAN,SIGIMEAN >xtriage.log && gview xtriage.log