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REFERENCE DATA SET: Difference between revisions

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Created page with "For a file to be accepted as a REFERENCE_DATA_SET by XDS, it must look like: !FORMAT=XDS_ASCII !END_OF_HEADER 1 0 4 48445. 983.361 1 0 5 2124.59 283.825 ..."
 
m use the word "pseudo" in the description so the article can more easily be found
 
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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, 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:
<pre>
!FORMAT=XDS_ASCII
!FORMAT=XDS_ASCII
!END_OF_HEADER
!END_OF_HEADER
Line 11: Line 13:
...
...
!END_OF_DATA
!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.


Such a file, which I would call "fake XDS_ASCII" can be easily obtained. 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>
!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
</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>
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