#!/bin/sh # EXAMPLE 1: AUTOMATED MAD SOLUTION WITH DEFAULT PIPELINE (AFRO/CRUNCH2/BP3/SOLOMON/ARP/wARP+REFMAC) set -e # Name of the sub-directory crank will be run in. ROOT=mad_gere # # Step 1: Generate crank XML # gcx HKLIN $CEXAM/tutorial/data/gere_MAD_nat.mtz SEQIN $CEXAM/data/gere.pir HKLOUT $ROOT.mtz << END > $ROOT.log ALLIN outp $ROOT # comment out DNAME INFL and subkeywords for just SAD # remove comments of DNAME HREM for 3 wavelength MAD Xtal DER1 ATOM SE NUMB 2 ! number of heavy atoms/monomer DNAME PEAK COLUmn F+=F_peak(+) SF+=SIGF_peak(+) F-=F_peak(-) SF-=SIGF_peak(-) FORM Se FP=-3.6 FPP=5.4 DNAME INFL COLUmn F+=F_infl(+) SF+=SIGF_infl(+) F-=F_infl(-) SF-=SIGF_infl(-) FORM Se FP=-5.6 FPP=3.4 ! DNAME HREM ! COLUmn F+=F_hrm(+) SF+=SIGF_hrm(+) F-=F_hrm(-) SF-=SIGF_hrm(-) ! FORM Se FP=-2.0 FPP=4.3 ! DNAME LREM ! COLUmn F+=F_lrm(+) SF+=SIGF_lrm(+) F-=F_lrm(-) SF-=SIGF_lrm(-) ! FORM Se FP=-2.3 FPP=1.0 END mkdir $ROOT cd $ROOT # # Step 2: actual crank job! # crank ../$ROOT.xml >> ../$ROOT.log # EXAMPLE 2: AUTOMATED SIRAS SOLUTION WITH DEFAULT PIPELINE (AFRO/CRUNCH2/BP3/SOLOMON/ARP/wARP+REFMAC) ROOT=siras_rnase gcx HKLIN $CEXAM/rnase/rnase25F+F-.mtz SEQIN $CEXAM/rnase/rnase.pir HKLOUT $ROOT.mtz << END > $ROOT.log outp $ROOT # native Xtal NATIVE DName NATIVE COLUmn F=FNAT SF=SIGFNAT # first derivative Xtal DER1 ATOM Pt NUMB 3 ! guess of the number of substructure atoms/monomer DNAME DER1 COLUmn F+=FPTNCD25(+) SF+=SIGFPTNCD25(+) F-=FPTNCD25(-) SF-=SIGFPTNCD25(-) END mkdir $ROOT cd $ROOT crank ../$ROOT.xml >> ../$ROOT.log