Changes

1,436 bytes added ,  18:43, 19 October 2012
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="0.26 (18-Oct-2012)"                                                                                 
+
# 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
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