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2QVO.xds: Difference between revisions
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==XDS data reduction== | ==XDS data reduction== | ||
This is a pared-down XDS.INP (obtained by egrep -v '^ *!' XDS.INP) based upon XDS-MARCDD.INP from the XDS distribution site - it has only those lines that are not commented out | This is a pared-down XDS.INP (obtained by egrep -v '^ *!' XDS.INP) based upon XDS-MARCDD.INP from the XDS distribution site - it has only those lines that are not commented out (to arrive here, one takes the steps outlined in [[Tutorial(First_Steps)]]): | ||
DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD=65000 | DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD=65000 | ||
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 | DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 | ||
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POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 | POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 | ||
SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. | SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. | ||
FRIEDEL'S_LAW=FALSE !Default is TRUE. | FRIEDEL'S_LAW=FALSE !Default is TRUE. | ||
NAME_TEMPLATE_OF_DATA_FRAMES=../../g/040707-8_2_2_1.???? ! TIFF | NAME_TEMPLATE_OF_DATA_FRAMES=../../g/040707-8_2_2_1.???? ! TIFF | ||
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WFAC1=1.5 !This controls the number of rejected MISFITS in CORRECT; a larger value leads to fewer rejections. | WFAC1=1.5 !This controls the number of rejected MISFITS in CORRECT; a larger value leads to fewer rejections. | ||
STRONG_PIXEL=6.0 !used by: COLSPOT | STRONG_PIXEL=6.0 !used by: COLSPOT | ||
Using the above as XDS.INP, we run xds_par for the first time. It will stop after the IDXREF step with the usual error message | |||
!!! ERROR !!! INSUFFICIENT PERCENTAGE (< 70%) OF INDEXED REFLECTIONS | |||
AUTOMATIC DATA PROCESSING STOPPED. AS THE CRITERIA FOR A GOOD | |||
SOLUTION ARE RATHER STRICT, YOU MAY CHOOSE TO CONTINUE DATA | |||
PROCESSING AFTER CHANGING THE "JOB="-CARD IN "XDS.INP" TO | |||
"JOB= DEFPIX INTEGRATE CORRECT". | |||
IF THE BEST SOLUTION IS REALLY NONSENSE YOU SHOULD FIRST HAVE | |||
A LOOK AT THE ASCII-FILE "SPOT.XDS". THIS FILE CONTAINS THE | |||
INITIAL SPOT LIST SORTED IN DECREASING SPOT INTENSITY. SPOTS | |||
NEAR THE END OF THE FILE MAY BE ARTEFACTS AND SHOULD BE ERASED. | |||
ALTERNATIVELY YOU MAY TRY DIFFERENT VALUES FOR "INDEX_ORIGIN" | |||
AS SUGGESTED IN THE ABOVE LISTING. | |||
IF THE CRYSTAL HAS SLIPPED AT THE BEGINNING OF DATA COLLECTION | |||
YOU MAY CHOOSE TO SKIP SOME OF THE FIRST FRAMES BY CHANGING | |||
THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN. | |||
We choose to continue nevertheless and modify XDS.INP to have | |||
JOB= DEFPIX INTEGRATE CORRECT | |||
Again we run xds_par. This runs to completion. The automatic spacegroup determination comes up with | |||
SPACE_GROUP_NUMBER= 75 | |||
UNIT_CELL_CONSTANTS= 53.10 53.10 40.90 90.000 90.000 90.000 | |||
Now we copy these two lines to XDS.INP, replacing the old line SPACE_GROUP_NUMBER=0 . Then we modify the spacegroup number to 77 because we know that the true spacegroup is P4_2. Also, we modify the JOB line once again: | |||
JOB= CORRECT | |||
and run xds_par for the last time. | |||
The resulting output files are XYCORR.LP, INIT.LP, COLSPOT.LP, IDXREF.LP, DEFPIX.LP, INTEGRATE.LP and CORRECT.LP. Data files are XPARM.XDS (from IDXREF), and the XDS_ASCII.HKL file all of which can be downloaded from [[Media:Xds_2qvo.tar.bz2.png|here]]. | The resulting output files are XYCORR.LP, INIT.LP, COLSPOT.LP, IDXREF.LP, DEFPIX.LP, INTEGRATE.LP and CORRECT.LP. Data files are XPARM.XDS (from IDXREF), and the XDS_ASCII.HKL file all of which can be downloaded from [[Media:Xds_2qvo.tar.bz2.png|here]]. | ||
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end | end | ||
This writes | This writes j.hkl, j_fa.hkl and j_fa.ins. However, we overwrite j_fa.ins now: | ||
cat > j_fa.ins <<end | cat > j_fa.ins <<end | ||
TITL j_fa.ins SAD in P42 | TITL j_fa.ins SAD in P42 | ||