#!/bin/sh # refmac-rigid.exam # # A run-all script to run refmac rigid body refinement with the cubic insulin # structure 2bn3 (Nanao & Ravelli) and the results of the run-all script # scala-complete which will scale, merge and massage the measurements of # same. # 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 # check that the input file - ${CCP4_SCR}/sc-exam-free.mtz - exists if test ! -f ${CCP4_SCR}/sc-exam-free.mtz ; then echo "run scala-complete.exam first" exit 1 fi # FIXME - residual mlkf is the default so this should probably be removed # # FIXME - cubic spacegroups cannot have anisotropic b factors for the # bulk solvent model etc: # "lssc anisotropic fixbulk bbulk 200.0" # # run refmac5 refmac5 \ hklin ${CCP4_SCR}/sc-exam-free.mtz \ hklout ${CCP4_SCR}/sc-exam-refmac5.mtz \ xyzin ${CEXAM}/data/insulin_2bn3.pdb \ xyzout ${CCP4_SCR}/rb-exam-refined.pdb << eof labin FP=F SIGFP=SIGF FREE=FreeR_flag refine type rigid rigidbody ncycle 10 rigidbody group 1 from 1 A to 21 A rigidbody group 2 from 1 B to 30 B monitor medium eof