2,684
edits
Generate XDS.INP: Difference between revisions
→The script: include POSITION into REFINE(IDXREF) because latest XDS is more robust. Add comments to keywords.
(v 0.75 reversed ORGX and ORGY for marCCD @ ESRF BM14) |
(→The script: include POSITION into REFINE(IDXREF) because latest XDS is more robust. Add comments to keywords.) |
||
| Line 92: | Line 92: | ||
# revision 0.74 . Keitaro 02/08/2017 Add PILATUS3 6M, S/N 60-0127 at CHESS F1 with ROTATION_AXIS=-1 0 0 | # revision 0.74 . Keitaro 02/08/2017 Add PILATUS3 6M, S/N 60-0127 at CHESS F1 with ROTATION_AXIS=-1 0 0 | ||
# revision 0.75 . KD 30/08/2017 reversed ORGX and ORGY for marCCD @ BM14 (Indian beamline @ ESRF) | # revision 0.75 . KD 30/08/2017 reversed ORGX and ORGY for marCCD @ BM14 (Indian beamline @ ESRF) | ||
REVISION="0. | # revision 0.76 . KD 4/09/2017 include POSITION into REFINE(IDXREF) because latest XDS is more robust. Add comments to keywords. | ||
REVISION="0.76 (4-Sep-2017)" | |||
# | # | ||
| Line 655: | Line 656: | ||
echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv ! | echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv ! | ||
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE | echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE ! only read by XYCORR, IDXREF | ||
echo OSCILLATION_RANGE= $OSCILLATION_RANGE | echo OSCILLATION_RANGE= $OSCILLATION_RANGE ! only read by IDXREF | ||
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH ! only read by IDXREF | ||
# now we know everything that is required to generate XDS.INP | # now we know everything that is required to generate XDS.INP | ||
| Line 664: | Line 665: | ||
! written by generate_XDS.INP version $REVISION | ! written by generate_XDS.INP version $REVISION | ||
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | ||
ORGX= $ORGX ORGY= $ORGY ! values from header | ORGX= $ORGX ORGY= $ORGY ! values from frame header; only read by XYCORR, IDXREF | ||
$COMMENT_ORGXY | $COMMENT_ORGXY | ||
DETECTOR_DISTANCE= $DETECTOR_DISTANCE | DETECTOR_DISTANCE= $DETECTOR_DISTANCE ! only read by XYCORR, IDXREF | ||
OSCILLATION_RANGE= $OSCILLATION_RANGE | OSCILLATION_RANGE= $OSCILLATION_RANGE | ||
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | ||
| Line 703: | Line 704: | ||
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE. DISTANCE only for compatibility w/ old XDS. | ! since XDS 01-MAR-2015, POSITION supersedes DISTANCE. DISTANCE only for compatibility w/ old XDS. | ||
! nowadays headers are usually correct so refine DISTANCE/POSITION in INTEGRATE but not IDXREF | ! nowadays headers are usually correct so refine DISTANCE/POSITION in INTEGRATE but not IDXREF | ||
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! | REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS POSITION ! works best with XDS >= BUILT=20170720 | ||
REFINE(INTEGRATE)= DISTANCE POSITION BEAM ORIENTATION ! AXIS CELL | REFINE(INTEGRATE)= DISTANCE POSITION BEAM ORIENTATION ! AXIS CELL | ||
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS DISTANCE POSITION ! Default is: refine everything | ! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS DISTANCE POSITION ! Default is: refine everything | ||
| Line 720: | Line 721: | ||
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 | DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 | ||
DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0 | DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0 | ||
INCIDENT_BEAM_DIRECTION=0 0 1 | INCIDENT_BEAM_DIRECTION=0 0 1 ! only read by IDXREF | ||
ROTATION_AXIS=0 1 0 | ROTATION_AXIS=0 1 0 ! only read by IDXREF | ||
!FRACTION_OF_POLARIZATION=0.98 ! uncomment if synchrotron | !FRACTION_OF_POLARIZATION=0.98 ! uncomment if synchrotron; only used by CORRECT | ||
POLARIZATION_PLANE_NORMAL=1 0 0 | POLARIZATION_PLANE_NORMAL=1 0 0 ! only used by CORRECT | ||
eof | eof | ||
else | else | ||
if [ "$rotation_axis" != "" ]; then | if [ "$rotation_axis" != "" ]; then | ||
echo "ROTATION_AXIS= $rotation_axis" >> XDS.INP | echo "ROTATION_AXIS= $rotation_axis ! only read by IDXREF" >> XDS.INP | ||
elif [ "$REVERSE_PHI" == "no" ]; then | elif [ "$REVERSE_PHI" == "no" ]; then | ||
echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP | echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP | ||
| Line 745: | Line 746: | ||
fi | fi | ||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
INCIDENT_BEAM_DIRECTION=0 0 1 | INCIDENT_BEAM_DIRECTION=0 0 1 ! only read by IDXREF | ||
FRACTION_OF_POLARIZATION=${pol_frac} ! better value is provided by beamline staff! | FRACTION_OF_POLARIZATION=${pol_frac} ! better value is provided by beamline staff! | ||
POLARIZATION_PLANE_NORMAL=0 1 0 | POLARIZATION_PLANE_NORMAL=0 1 0 ! only used by CORRECT | ||
eof | eof | ||
fi | fi | ||