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Generate XDS.INP: Difference between revisions
xds_graph.sh will now run xdsstat, if available, and display Rmeas and Rd per image.
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Olibclarke (talk | contribs) (xds_graph.sh will now run xdsstat, if available, and display Rmeas and Rd per image.) |
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# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues | # revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues | ||
# revision 0.26 Oliver Clarke 10/12 - Added generation of shell scripts for conversion to MTZ and visualisation of statistics. Other minor alterations to XDS.INP. | # revision 0.26 Oliver Clarke 10/12 - Added generation of shell scripts for conversion to MTZ and visualisation of statistics. Other minor alterations to XDS.INP. | ||
REVISION="0. | # revision 0.27 Oliver Clarke 10/12 - xds_graph.sh will now run xdsstat, if available, and plot Rmeas and Rd per image. | ||
REVISION="0.27 (19-Oct-2012)" | |||
# | # | ||
# usage: e.g. xds_generate_all "frms/mydata_1_???.img" | # usage: e.g. xds_generate_all "frms/mydata_1_???.img" | ||
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X_RAY_WAVELENGTH=XXX | X_RAY_WAVELENGTH=XXX | ||
X_RAY_ENERGY=XXX | X_RAY_ENERGY=XXX | ||
STARTING_ANGLE=XXX | |||
QX=XXX | QX=XXX | ||
QY=XXX | QY=XXX | ||
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PHIEND=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}') | PHIEND=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | ||
STARTING_ANGLE=`echo "scale=3; ($PHISTART/1000)" | bc -l` | |||
let SKIP=1024+256+128+256+128+4 | let SKIP=1024+256+128+256+128+4 | ||
QX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}') | QX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
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# find NX, QX, ORGX and ORGY: | # find NX, QX, ORGX and ORGY: | ||
X_RAY_ENERGY=`echo "12398.5/$X_RAY_WAVELENGTH" | bc -l | awk '{printf "%5.1f", $1}'` | X_RAY_ENERGY=`echo "12398.5/$X_RAY_WAVELENGTH" | bc -l | awk '{printf "%5.1f", $1}'` | ||
STARTING_ANGLE=`grep PHI tmp2 | sed s/PHI=//` | |||
NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | ||
QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | ||
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tail -f -n1 INTEGRATE_STATS.LP & | tail -f -n1 INTEGRATE_STATS.LP & | ||
exec > INTEGRATE_STATS.LP 2>&1 | exec > INTEGRATE_STATS.LP 2>&1 | ||
if command -v xdsstat >/dev/null; then | |||
echo \"\" | xdsstat > XDSSTAT.LP | |||
echo \"\" | xdsstat 100 6 > XDSSTAT.LP_low | |||
echo \" | |||
\\\$TABLE:Rmeas vs image (to 6A): | |||
\\\$SCATTER:Rmeas vs image for low resolution reflections:A:1,2: \\$\\$ | |||
IMAGE RMEAS | |||
\\$\\$ \\$\\$ | |||
\" | |||
grep ' L\$' XDSSTAT.LP_low | awk '{print \$1,\$9}' | |||
echo \" \\$\\$ \" | |||
echo \" | |||
\\\$TABLE:Rmeas vs image (all): | |||
\\\$SCATTER:Rmeas vs image (all reflections):A:1,2: \\$\\$ | |||
IMAGE RMEAS | |||
\\$\\$ \\$\\$ | |||
\" | |||
grep ' L$' XDSSTAT.LP | awk '{print \$1,\$9}' | |||
echo \" \\$\\$ \" | |||
echo \" | |||
\\\$TABLE:Rd vs image (to 6A): | |||
\\\$SCATTER:Rd (from XDSSTAT) for low resolution reflections:A:1,2: \\$\\$ | |||
IMAGE RD | |||
\\$\\$ \\$\\$ | |||
\" | |||
grep 'DIFFERENCE' XDSSTAT.LP_low | awk '{print \$1,\$7}' | |||
echo \" \\$\\$ \" | |||
echo \" | |||
\\\$TABLE:Rd vs image (all): | |||
\\\$SCATTER:Rd (from XDSSTAT) for all reflections:A:1,2: \\$\\$ | |||
IMAGE RD | |||
\\$\\$ \\$\\$ | |||
\" | |||
grep 'DIFFERENCE' XDSSTAT.LP | awk '{print \$1,\$7}' | |||
echo \" \\$\\$ \" | |||
fi | |||
echo \" | echo \" | ||
\\\$TABLE: XDS Integration Statistics : | \\\$TABLE: XDS Integration Statistics : | ||
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Two shell scripts have been generated that may be of use. | Two shell scripts have been generated that may be of use. | ||
The first, xds_graph.sh, will plot various statistics after an XDS run. | The first, xds_graph.sh, will plot various statistics after an XDS run. | ||
After both INTEGRATE and CORRECT have finished, run it by typing \"./xds_graph.sh\" | After both INTEGRATE and CORRECT have finished, run it by typing \"./xds_graph.sh\" | ||
without the quotation marks. This script uses loggraph to plot data, so you will | without the quotation marks. This script uses loggraph to plot data, so you will | ||
need CCP4 to see the graphical output. All the raw data is piped out to a log file, | need CCP4 to see the graphical output. All the raw data is piped out to a log file, | ||
INTEGRATE_STATS.LP. | INTEGRATE_STATS.LP. | ||
If XDSSTAT is present in your path, xds_graph will also plot some of the statistics it | |||
calculates - specifically the Rmeas and Rd per image, for all reflections and only | |||
low resolution reflections. | |||
The second script, xds_to_ccp4.sh, will take XDS_ASCII.HKL and generate both a CCP4 | The second script, xds_to_ccp4.sh, will take XDS_ASCII.HKL and generate both a CCP4 | ||