95 lines
1.6 KiB
Bash
Executable File
95 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
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NP=`grep processor /proc/cpuinfo | wc -l`
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if [ $# -ge 1 ]
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then
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FILELST=$1
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else
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FILELST=file.lst
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fi
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if [ $# -ge 2 ]
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then
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FILEGEOM=$2
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else
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FILEGEOM=geom.geom
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fi
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if [ $# -ge 3 ]
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then
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FILECELL=$3
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else
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FILECELL=cell.cell
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fi
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if [ $# -ge 4 ]
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then
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FILESTREAM=$4
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else
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FILESTREAM=stream.stream
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fi
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if [ $# -ge 5 ]
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then
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MILLDIR=$5
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else
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MILLDIR=unknown-mill
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fi
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# list of indexing methods : xgandalf-latt-cell,asdf-latt-cell,dirax-latt-cell,mosflm-latt-cell
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# but usually all is indexed by xgandalf (99.99%)
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# to speed up indexing, one can use : --xgandalf-fast-execution, --highres=1.6 ...
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if [ -e ${FILECELL} ]
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then
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indexamajig -i ${FILELST} \
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-o ${FILESTREAM} \
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--geometry=${FILEGEOM} \
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--pdb=${FILECELL} \
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--indexing=xgandalf-latt-cell \
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--peaks=peakfinder8 \
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--integration=rings-grad \
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--tolerance=10.0,10.0,10.0,2,3,2 \
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--threshold=10 \
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--min-snr=5 \
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--int-radius=2,3,6 \
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-j ${NP} \
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--no-multi \
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--no-retry \
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--check-peaks \
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--max-res=3000 \
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--min-pix-count=2 \
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--local-bg-radius=4 \
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--mille \
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--mille-dir=${MILLDIR}
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else
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indexamajig -i ${FILELST} \
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-o ${FILESTREAM} \
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--geometry=${FILEGEOM} \
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--indexing=xgandalf-latt-cell \
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--peaks=peakfinder8 \
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--integration=rings-grad \
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--tolerance=10.0,10.0,10.0,2,2,2 \
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--threshold=10 \
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--min-snr=5 \
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--int-radius=2,3,6 \
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-j ${NP} \
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--no-multi \
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--no-retry \
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--check-peaks \
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--max-res=3000 \
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--min-pix-count=2 \
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--local-bg-radius=4 \
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--mille \
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--mille-dir=${MILLDIR}
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fi
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chmod -R g+rwx ${MILLDIR}
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