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Xdsconv: Difference between revisions
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[http:// | [http://xds.mpimf-heidelberg.mpg.de/html_doc/xdsconv_parameters.html XDSCONV] is the conversion program of the [[XDS]] suite. | ||
Possible output formats are SHELX, CNS, CCP4 (for F | Possible output formats are SHELX, CNS, CCP4 (for F,SigF,DF,SigDF,isym), CCP4_F (for F,SigF,F(+),SigF(+),F(-),SigF(-)), CCP4_I (for IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-)) and CCP4_I+F (for IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-),FP,SIGFP,F(+),SIGF(+),F(-),SIGF(-)) - the "+" and "-" varieties are only output if FRIEDEL'S_LAW=FALSE. | ||
---- | ---- | ||
XDSCONV does outlier rejection in some modes. | XDSCONV does outlier rejection in some modes. | ||
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In the case of a MTZ file that should be used for molecular replacement and refinement, the CAD step could be used to transfer the R_free flag from a different dataset to this new dataset. Alternatively, change of labels and transfer of columns can be done in the ccp4i GUI. | In the case of a MTZ file that should be used for molecular replacement and refinement, the CAD step could be used to transfer the R_free flag from a different dataset to this new dataset. Alternatively, change of labels and transfer of columns can be done in the ccp4i GUI. | ||
== explanation of typical output == | |||
<pre> | |||
========== CONTROL CARDS ========== | |||
INPUT_FILE=XDS_ASCII.HKL | |||
OUTPUT_FILE=temp.hkl CCP4 | |||
SPACE_GROUP_NUMBER= 199 | |||
UNIT_CELL_CONSTANTS= 78.09 78.09 78.09 90.000 90.000 90.000 | |||
FRIEDEL'S_LAW=FALSE | |||
MERGE=TRUE | |||
NUMBER OF REFLECTION RECORDS ON INPUT FILE 217611 ! observations ("spots") | |||
NUMBER OF IGNORED REFLECTIONS (I< -3.0*SIGMA) 0 ! merged (unique) reflections, Friedels counted separately | |||
NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE 23155 ! merged (unique) reflections, Friedels counted separately | |||
NUMBER OF UNIQUE REFLECTIONS ASSIGNED TO TEST SET 0 | |||
NUMBER OF UNIQUE TEST REFLECTIONS INHERITED 0 | |||
NUMBER OF UNIQUE TEST REFLECTIONS NEWLY GENERATED 0 | |||
NUMBER OF REFLECTION RECORDS ON OUTPUT FILE 12264 ! merged (unique) reflections; a Friedel pair is counted as one reflection for the MTZ file | |||
NUMBER OF RECORDS ASSIGNED TO WORKING SET 12264 ! but since each unique reflection is stored with its anomalous signal no information is lost | |||
NUMBER OF RECORDS ASSIGNED TO TEST SET 0 | |||
</pre> | |||
'''Obviously, the meaning of the word "reflection" differs between the output lines; some explanation is given after the exclamation mark. | |||
''' | |||
== how to obtain a MTZ file with DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) == | == how to obtain a MTZ file with DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) == | ||
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rm temp1.mtz | rm temp1.mtz | ||
# correct for FreeRflag (if new file has more reflections than reference file) | |||
freerflag hklin ${BASE%.HKL}.mtz hklout temp1.mtz << eof | tee ${BASE%.HKL}_freerflag.log | |||
COMPLETE FREE=${FREERFLAG} | |||
end | |||
eof | |||
# correct for real data in case Rfree data set contains too many hkls | # correct for real data in case Rfree data set contains too many hkls | ||