#!/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