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REFERENCE DATA SET: Difference between revisions
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add "quit" to sftools commands to avoid error message
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Such a file, which I would call "fake XDS_ASCII" can be obtained with a little effort. As an example, the following assumes existence of a MTZ file refine.mtz containing column F-model: | Such a file, which I would call "fake XDS_ASCII" can be obtained with a little effort. As an example, the following assumes existence of a MTZ file refine.mtz containing column F-model: | ||
<pre> | <pre> | ||
echo square model amplitudes: | |||
sftools <<EOF | sftools <<EOF | ||
read refine.mtz | read refine.mtz | ||
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calc col I-model = col F-model col F-model * | calc col I-model = col F-model col F-model * | ||
write I-model.mtz col I-model | write I-model.mtz col I-model | ||
quit | |||
EOF | EOF | ||
echo dump to ASCII format: | |||
mtzdump hklin I-model.mtz > temp.hkl <<EOF | mtzdump hklin I-model.mtz > temp.hkl <<EOF | ||
nref 10000000 | nref 10000000 | ||
end | end | ||
EOF | EOF | ||
echo prepare I-model.hkl: | |||
echo \!FORMAT=XDS_ASCII > I-model.hkl | echo \!FORMAT=XDS_ASCII > I-model.hkl | ||
echo \!END_OF_HEADER >> I-model.hkl | echo \!END_OF_HEADER >> I-model.hkl | ||
echo pick reflection info from temp.hkl: | |||
awk '/LIST OF REFLECTIONS/,/<B><FONT COLOR=/' temp.hkl | tail -n +4 | head -n -1 | awk '{print $0,1}' >> I-model.hkl | awk '/LIST OF REFLECTIONS/,/<B><FONT COLOR=/' temp.hkl | tail -n +4 | head -n -1 | awk '{print $0,1}' >> I-model.hkl | ||
echo \!END_OF_DATA >> I-model.hkl | echo \!END_OF_DATA >> I-model.hkl | ||
echo I-model.hkl is now ready to be used as REFERENCE_DATA_SET | |||
rm temp.hkl | rm temp.hkl I-model.mtz | ||
</pre> | </pre> | ||
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... | ... | ||
!END_OF_DATA | !END_OF_DATA | ||
</pre> | |||
Such a file can be obtained e.g. with | |||
<pre> | |||
#!/bin/bash | |||
echo square amplitudes: | |||
sftools <<EOF | |||
read $1 | |||
select col FOBS = present | |||
calc col IOBS = col FOBS col FOBS * | |||
calc col SIGIOBS = col FOBS col SIGFOBS * | |||
calc col SIGIOBS = col SIGIOBS 2 * | |||
write $1.mtz col IOBS SIGIOBS | |||
EOF | |||
echo dump to ASCII format: | |||
mtzdump hklin $1.mtz > temp.hkl <<EOF | |||
nref 10000000 | |||
end | |||
EOF | |||
echo prepare XDS_ASCII.HKL: | |||
echo \!FORMAT=XDS_ASCII > $1.hkl | |||
echo \!UNIT_CELL_CONSTANTS=$(grep -A1 dataset$ temp.hkl|tail -1) >> $1.hkl | |||
echo \!SPACE_GROUP_NUMBER=$(awk '/Space group/{gsub(/\)/,"");print $7}' temp.hkl) >> $1.hkl | |||
echo \!ITEM_H=1 >> $1.hkl | |||
echo \!ITEM_K=2 >> $1.hkl | |||
echo \!ITEM_L=3 >> $1.hkl | |||
echo \!ITEM_IOBS=4 >> $1.hkl | |||
echo \!ITEM_SIGMA\(IOBS\)=5 >> $1.hkl | |||
echo \!END_OF_HEADER >> $1.hkl | |||
echo pick reflection info from temp.hkl: | |||
awk '/LIST OF REFLECTIONS/,/<B><FONT COLOR=/' temp.hkl | tail -n +4 | head -n -1 | awk '{print $0,1}' >> $1.hkl | |||
echo \!END_OF_DATA >> $1.hkl | |||
echo $1.hkl is now ready to be used as XDS_ASCII.HKL | |||
rm temp.hkl $1.mtz | |||
</pre> | </pre> | ||