Generate XDS.INP: Difference between revisions

Generate XDS.INP (view source)

Revision as of 13:12, 27 April 2010

528 bytes added , 27 April 2010

no edit summary

Kay

Bureaucrats

2,651

edits

@@ Line 5: / Line 5: @@
   # purpose: generate XDS.INP
   # revision 0.03 . Kay Diederichs 2/2010
-  # revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calc for ADSC
+  # revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC
-  # tested with own and some JCSG datasets; only MARCCD, ADSC/SMV, PILATUS detectors; for other detectors, values must be manually filled in.
+  # tested with some datasets from ALS, SSRL, SLS and ESRF; only MARCCD, ADSC/SMV, PILATUS detectors; for other detectors, values must be manually filled in.
   #
   # usage: e.g. generate_XDS.INP.rc "frms/mydata_1_???.img"
@@ Line 20: / Line 20: @@
   #
   # known problems:
-  # - for ADSC detectors, the ORGX and ORGY values are inaccurate; the "imgheader" program that I have delivers better values, but I don't know how and why.
+  # - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);
+ #  the "imgheader" program that I have delivers better values, but I don't know how and why.
   #
   # notes for debugging of the script:
@@ Line 111: / Line 112: @@
     DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
-    echo this is an ADSC detector. there are at least two possibilites for obtaining ORGX, ORGY from the header ...
+    echo this is an ADSC detector. Obtaining ORGX, ORGY from the header depends on beamline setup.
     strings `head -1 tmp1` | sed s/\;// > tmp2
@@ Line 120: / Line 121: @@
         NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
         QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
-        ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
+        BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
-        ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
+        BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
   # fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives -
-  # according to Ingo Korndörfer, at ESRF and ... (pls fill in!) the following should be used:
+  # at ESRF and ... (pls fill in!) the following should be used:
-        ORGX=`echo "scale=1; $ORGY/$QX" | bc -l `
+        ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
-        ORGY=`echo "scale=1; $ORGX/$QX" | bc -l `
+        ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
-        echo ATTENTION: at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY (try these in XDS.INP !)
+        echo ATTENTION: at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY
-  # whereas this alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2 and 5.0.3
+ # this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
-        ORGX=`echo "scale=1; $ORGX/$QX" | bc -l `
+       ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
-        ORGY=`echo "scale=1; $NX-$ORGY/$QX" | bc -l `
+       ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
-  # the latter alternative is written into the generated XDS.INP
+       echo ATTENTION: at e.g. ALS 5.0.3 use: ORGX=$ORGX ORGY=$ORGY
+  # this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ...
+        ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
+        ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
+       echo ATTENTION: at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is now written to XDS.INP
+  # the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.
         # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
         DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//`