#!/bin/sh # scala-complete.exam # # A run-all script which runs: # pointless, reindex, sortmtz, scala, truncate & freerflag # using some real cubic insulin data (see bug # 3129) with the intention of # making use of a wider list of keywords for these programs. The resulting # reflection file may also be used in a refmac RB refinement example. # # Data used comes from SRS 14.2 measured by John Cowan. # set -e # bug # 3192 - run-all examples produce harvest files - well to counteract # this here set HARVESTHOME to somewhere in $CCP4_SCR HARVESTHOME=$CCP4_SCR export HARVESTHOME # run pointless - though we know the data are in the correct pg pointless \ hklin ${CEXAM}/data/insulin_unmerged.mtz \ hklout ${CCP4_SCR}/sc-exam-in.mtz << eof systematicabsences off eof if [ "$?" -ne "0" ]; then echo "pointless failed" exit 1 fi # run reindex to put the correct spacegroup for insulin - I213 - into # the header reindex \ hklin ${CCP4_SCR}/sc-exam-in.mtz \ hklout ${CCP4_SCR}/sc-exam-i213.mtz << eof symmetry I213 eof if [ "$?" -ne "0" ]; then echo "reindex failed" exit 1 fi # now sort the data sortmtz \ hklin ${CCP4_SCR}/sc-exam-i213.mtz \ hklout ${CCP4_SCR}/sc-exam-sort.mtz << eof H K L M/ISYM BATCH eof if [ "$?" -ne "0" ]; then echo "sortmtz failed" exit 1 fi # and run scala scala \ hklin ${CCP4_SCR}/sc-exam-sort.mtz \ hklout ${CCP4_SCR}/sc-exam-scale.mtz \ scales ${CCP4_SCR}/sc-exam.scales \ rogues ${CCP4_SCR}/sc-exam.rogues \ plot ${CCP4_SCR}/sc-exam.plot \ rogueplot ${CCP4_SCR}/sc-exam.rogueplot \ correlplot ${CCP4_SCR}/sc-exam.correlplot \ normplot ${CCP4_SCR}/sc-exam.normplot << eof run 1 batch 1 to 45 name run 1 project RUNALL crystal INSULIN dataset NATIVE scales rotation spacing 5.000000 secondary 6.000000 bfactor on tails cycles 100 anomalous off eof if [ "$?" -ne "0" ]; then echo "scala failed" exit 1 fi # run scala again for output unmerged - this is to provide test data for a # new chef example scala \ hklin ${CCP4_SCR}/sc-exam-sort.mtz \ hklout ${CCP4_SCR}/sc-exam-scale-unmerged.mtz \ scales ${CCP4_SCR}/sc-exam-unmerged.scales \ rogues ${CCP4_SCR}/sc-exam.rogues \ plot ${CCP4_SCR}/sc-exam.plot \ rogueplot ${CCP4_SCR}/sc-exam.rogueplot \ correlplot ${CCP4_SCR}/sc-exam.correlplot \ normplot ${CCP4_SCR}/sc-exam.normplot << eof run 1 batch 1 to 45 name run 1 project RUNALL crystal INSULIN dataset NATIVE scales rotation spacing 5.000000 secondary 6.000000 bfactor on tails cycles 100 anomalous off output unmerged onlymerge restore ${CCP4_SCR}/sc-exam.scales eof if [ "$?" -ne "0" ]; then echo "scala failed" exit 1 fi # and then truncate truncate \ hklin ${CCP4_SCR}/sc-exam-scale.mtz \ hklout ${CCP4_SCR}/sc-exam-trunc.mtz << eof eof if [ "$?" -ne "0" ]; then echo "truncate failed" exit 1 fi # and finally add the FreeR flag freerflag \ hklin ${CCP4_SCR}/sc-exam-trunc.mtz \ hklout ${CCP4_SCR}/sc-exam-free.mtz << eof eof if [ "$?" -ne "0" ]; then echo "freerflag failed" exit 1 fi