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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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END | END | ||
EOF | EOF | ||
The following script does the same for the input file (first parameter to the script), but also adds a SUFFIX (second parameter) to the columns to better identify the data, and optionally copies the Rfree-flag from a reference mtz-file (third parameter). If the Rfree-flag is NOT named "FreeR_flag" (the default from ccp4i), you can provide its name as fourth parameter. All steps are logged into log-files, temporary files are deleted. The input file should end with .HKL (rather than e.g. .hkl). | |||
The script also sets the resolution to that of the observed data using sftools. Otherwise the resolution of the reference data set might be shown if that is higher. You can call this script 'xds2mtz.sh'. If it is executed without arguments, you get a short usage instruction. | |||
<nowiki>#!/bin/bash | |||
function usage { | |||
echo "Usage: xds2mtz file.HKL SUFFIX [Rfree.mtz [RfreeFlag]]" | |||
echo "" | |||
echo " file.HKL: Output from XDS or XSCALE" | |||
echo " SUFFIX: Columns suffix, e.g. FP_SUFFIX" | |||
echo " Rfree.mtz: Reference mtz-file for Rfree transfer" | |||
echo " RfreeFlag: Label for Rfree set, defaults to \"FreeR_flag\"" | |||
echo "" | |||
} | |||
if [ -z $1 ]; then | |||
echo "*** Error: Missing input XDS file name" | |||
usage | |||
exit -1; | |||
fi | |||
if [ ! -f $1 ]; then | |||
echo "*** Error: File $1 does not exist" | |||
usage | |||
exit -1; | |||
fi | |||
BASE=$(basename $1) | |||
SUFFIX=$2 | |||
RFREE=$3 | |||
FLAG=$4 | |||
echo "Base = $BASE, Suffix = $SUFFIX" | |||
echo "INPUT_FILE= $1" > XDSCONV.INP | |||
echo "OUTPUT_FILE= temp1.hkl CCP4" >> XDSCONV.INP | |||
xdsconv && f2mtz HKLOUT temp1.mtz <F2MTZ.INP | tee ${BASE%.HKL}_dano.log | |||
echo "INPUT_FILE= $1" > XDSCONV.INP | |||
echo "OUTPUT_FILE= temp2.hkl CCP4_F" >> XDSCONV.INP | |||
xdsconv && f2mtz HKLOUT temp2.mtz <F2MTZ.INP |tee ${BASE%.HKL}_pm.log | |||
if [ -z $3 ]; then | |||
echo "Proceeding without Rfree reference file" | |||
cad HKLIN1 temp1.mtz HKLIN2 temp2.mtz HKLOUT ${BASE%.HKL}.mtz << eof | tee ${BASE%.HKL}_cad.log | |||
LABIN FILE 1 E1=FP E2=SIGFP E3=DANO E4=SIGDANO | |||
LABIN FILE 2 E1=F(+) E2=SIGF(+) E3=F(-) E4=SIGF(-) | |||
LABOUT FILE 1 E1=FP_$SUFFIX E2=SIGFP_$SUFFIX E3=DANO_$SUFFIX E4=SIGDANO_$SUFFIX | |||
LABOUT FILE 2 E1=F(+)_$SUFFIX E2=SIGF(+)_$SUFFIX E3=F(-)_$SUFFIX E4=SIGF(-)_$SUFFIX | |||
eof | |||
else | |||
echo "Copying Rfree from file $3" | |||
if [ -z $4 ]; then | |||
FREERFLAG="FreeR_flag" # ccp4 standard name | |||
else | |||
FREERFLAG=$4 | |||
fi | |||
echo "Extracting flagged indices from ${FREERFLAG}" | |||
cad HKLIN1 temp1.mtz \ | |||
HKLIN2 temp2.mtz \ | |||
HKLIN3 $3 \ | |||
HKLOUT ${BASE%.HKL}.mtz << eof | tee ${BASE%.HKL}_cad.log | |||
LABIN FILE 1 E1=FP E2=SIGFP E3=DANO E4=SIGDANO | |||
LABIN FILE 2 E1=F(+) E2=SIGF(+) E3=F(-) E4=SIGF(-) | |||
LABIN FILE 3 E1=${FREERFLAG} | |||
LABOUT FILE 1 E1=FP_$SUFFIX E2=SIGFP_$SUFFIX E3=DANO_$SUFFIX E4=SIGDANO_$SUFFIX | |||
LABOUT FILE 2 E1=F(+)_$SUFFIX E2=SIGF(+)_$SUFFIX E3=F(-)_$SUFFIX E4=SIGF(-)_$SUFFIX | |||
LABOUT FILE 3 E1=${FREERFLAG} | |||
eof | |||
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 | |||
# thanks to Andrey Lebedev | |||
sftools << eof | tee ${BASE%.HKL}_sftools.log | |||
READ ${BASE%.HKL}.mtz | |||
SELECT ONLY COLUMN FP_$SUFFIX PRESENT | |||
WRITE temp1.mtz | |||
END | |||
eof | |||
mv temp1.mtz ${BASE%.HKL}.mtz | |||
fi | |||
rm -f XDSCONV.INP temp1.hkl temp1.mtz temp2.hkl temp2.mtz F2MTZ.INP XDSCONV.LP</nowiki> | |||
== Hint for long-time XDSCONV users == | == Hint for long-time XDSCONV users == | ||