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REFERENCE DATA SET: Difference between revisions
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For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must look like: | Sometimes one wants to use a REFERENCE_DATA_SET which was not itself written out by XDS or XSCALE. | ||
For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must minimally look like: | |||
<pre> | |||
!FORMAT=XDS_ASCII | |||
!END_OF_HEADER | |||
1 0 4 48445. 983.361 | |||
1 0 5 2124.59 283.825 | |||
1 0 6 17955. 493.356 | |||
1 0 7 19328. 510.718 | |||
1 0 8 87172. 3437.40 | |||
... | |||
... | |||
!END_OF_DATA | |||
</pre> | |||
The columns do not have a specified width, and are separated by a blank (Fortran's free format). Additional columns besides h k l I sigI will be ignored. Anomalous data in that file will be treated as required by the setting of FRIEDEL'S_LAW in XDS.INP. | |||
''Please note that the REFERENCE_DATA_SET will only be used if SPACE_GROUP_NUMBER > 0, and proper UNIT_CELL_CONSTANTS are specified in XDS.INP !'' | |||
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> | |||
echo square model amplitudes: | |||
sftools <<EOF | |||
read refine.mtz | |||
select col F-model = present | |||
calc col I-model = col F-model col F-model * | |||
write I-model.mtz col I-model | |||
quit | |||
EOF | |||
echo dump to ASCII format: | |||
mtzdump hklin I-model.mtz > temp.hkl <<EOF | |||
nref 10000000 | |||
end | |||
EOF | |||
echo prepare I-model.hkl: | |||
echo \!FORMAT=XDS_ASCII > 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 | |||
echo \!END_OF_DATA >> I-model.hkl | |||
echo I-model.hkl is now ready to be used as REFERENCE_DATA_SET | |||
rm temp.hkl I-model.mtz | |||
</pre> | |||
For use with XSCALE, the file must look like e.g.: | |||
<pre> | <pre> | ||
!FORMAT=XDS_ASCII | !FORMAT=XDS_ASCII | ||
!NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD= 5 | |||
!ITEM_H=1 | |||
!ITEM_K=2 | |||
!ITEM_L=3 | |||
!ITEM_IOBS=4 | |||
!ITEM_SIGMA(IOBS)=5 | |||
!END_OF_HEADER | !END_OF_HEADER | ||
1 0 4 48445. 983.361 | 1 0 4 48445. 983.361 | ||
| Line 12: | Line 62: | ||
!END_OF_DATA | !END_OF_DATA | ||
</pre> | </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> | |||