REFERENCE DATA SET: Difference between revisions
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Sometimes one wants to use a REFERENCE_DATA_SET which was not itself written out by XDS or XSCALE. | Sometimes one wants to use a REFERENCE_DATA_SET which was not itself written out by XDS or XSCALE, but was created by a different program. Since it is then not a true XDS_ASCII format file, we could call this a pseudo XDS_ASCII file. | ||
For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must minimally look like: | For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must minimally look like: | ||
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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: | echo dump to ASCII format: | ||
| Line 45: | Line 46: | ||
<pre> | <pre> | ||
!FORMAT=XDS_ASCII | !FORMAT=XDS_ASCII | ||
!UNIT_CELL_CONSTANTS= 78 78 78 90 90 90 ! fill in correct values | |||
!SPACE_GROUP_NUMBER= 199 ! fill in correct spacegroup number | |||
!NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD= 5 | !NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD= 5 | ||
!ITEM_H=1 | !ITEM_H=1 | ||
| Line 60: | Line 63: | ||
... | ... | ||
!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> | ||
Latest revision as of 18:56, 16 June 2025
Sometimes one wants to use a REFERENCE_DATA_SET which was not itself written out by XDS or XSCALE, but was created by a different program. Since it is then not a true XDS_ASCII format file, we could call this a pseudo XDS_ASCII file.
For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must minimally look like:
!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
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:
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
For use with XSCALE, the file must look like e.g.:
!FORMAT=XDS_ASCII !UNIT_CELL_CONSTANTS= 78 78 78 90 90 90 ! fill in correct values !SPACE_GROUP_NUMBER= 199 ! fill in correct spacegroup number !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 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
Such a file can be obtained e.g. with
#!/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