XDSGUI User tools

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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;
  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;
  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