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Scale many datasets: Difference between revisions
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→Step 4: process the data by having generate_XDS.INP create XDS.INP for each of them. Then modify that XDS.INP and run xds_par.: add -e to sed commands which is ignored by Linux, and makes Mac understand -i
m (→Step 4: process the data by having generate_XDS.INP create XDS.INP for each of them. Then modify that XDS.INP and run xds_par.: add -e to sed commands which is ignored by Linux, and makes Mac understand -i) |
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generate_XDS.INP "../../cows-pigs-people/${i}_1_00???.cbf.gz" >&generate_XDS.INP.log | generate_XDS.INP "../../cows-pigs-people/${i}_1_00???.cbf.gz" >&generate_XDS.INP.log | ||
# modifications of XDS.INP | # modifications of XDS.INP | ||
# make it read the cbf.gz files a little faster: | # make it read the cbf.gz files a little faster: ATTENTION - fill in the correct path!!! | ||
echo LIB=/usr/local/lib64/xds-zcbf.so >>XDS.INP | echo LIB=/usr/local/lib64/xds-zcbf.so >>XDS.INP | ||
# if commented in, runs only JOB=CORRECT: | # if commented in, runs only JOB=CORRECT: | ||
# sed -i 's/XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE//' XDS.INP | # sed -i -e 's/XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE//' XDS.INP | ||
# use all frames for COLSPOT instead of only the first half: | # use all frames for COLSPOT instead of only the first half: | ||
sed -i 's/SPOT_RANGE=1 50/SPOT_RANGE=1 100/' XDS.INP | sed -i -e 's/SPOT_RANGE=1 50/SPOT_RANGE=1 100/' XDS.INP | ||
# use high-resol cutoff of 1.2A according to some preliminary processing: | # use high-resol cutoff of 1.2A according to some preliminary processing: | ||
sed -i 's/RESOLUTION_RANGE=50 0/RESOLUTION_RANGE=50 1.2/' XDS.INP | sed -i -e 's/RESOLUTION_RANGE=50 0/RESOLUTION_RANGE=50 1.2/' XDS.INP | ||
# use a reference data set to get consistent indexing: | # use a reference data set to get consistent indexing: | ||
sed -i 's$! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL $ REFERENCE_DATA_SET= ../x1_as_reference.hkl $' XDS.INP | sed -i -e 's$! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL $ REFERENCE_DATA_SET= ../x1_as_reference.hkl $' XDS.INP | ||
# (note the use of the $ delimiter instead of / if the pattern has file paths) | # (note the use of the $ delimiter instead of / if the pattern has file paths) | ||
# if using a reference data set, spacegroup and cell constants must be given | # if using a reference data set, spacegroup and cell constants must be given | ||
sed -i 's/SPACE_GROUP_NUMBER=0/SPACE_GROUP_NUMBER= 197/' XDS.INP | sed -i -e 's/SPACE_GROUP_NUMBER=0/SPACE_GROUP_NUMBER= 197/' XDS.INP | ||
sed -i 's/UNIT_CELL_CONSTANTS= 70 80 90 90 90 90/UNIT_CELL_CONSTANTS= 78 78 78 90 90 90/' XDS.INP | sed -i -e 's/UNIT_CELL_CONSTANTS= 70 80 90 90 90 90/UNIT_CELL_CONSTANTS= 78 78 78 90 90 90/' XDS.INP | ||
# run xds and write its terminal output to logfile | # run xds and write its terminal output to logfile | ||
xds_par >&xds.log | xds_par >&xds.log | ||