#!/bin/sh
#   First calculate structure factors for model coordinates in P1 cell.
# Dont forget to change the CRYSTL and SCALEi cards at the head 
# of the PDB file to those appropriate for the "P1 " model cell. 
# eg: for a cell 50*50*50 you need this.
#CRYST1   50.00    50.00    50.00   90.00  90.00   90.00
#SCALE1      0.020000  0.000000  0.000000        0.00000
#SCALE2      0.000000  0.020000  0.000000        0.00000
#SCALE3      0.000000  0.000000  0.020000        0.00000

#  toxd_mod_p1.pdb obtained from toxd.pdb by
#  1) changing CRYSTL and SCALEi cards
#  2) removing water molecules.
# this has been done with the supplied version

set -e

#  Read in coordinates to calculate structure factors. 
sfall  HKLOUT $CCP4_SCR/toxd_mod_p1 \
       XYZIN $CEXAM/unix/runnable/toxd_mod_p1.pdb <<-END-sfall
	TITL Phasing on toxd from test data area
	MODE SFCALC XYZIN 
	RESO 100 3 
	SFSG 1
	SYMM 1
	LABO FC=FC_p1 PHIC=PHIC_p1
        NAME PROJECT TOXD CRYSTAL MODEL DATASET CALCULATED
	END 
END-sfall

#
#  Generate E values for Observed F's ( Ian Tickle says so)
#
ecalc hklin $CEXAM/toxd/toxd hklout $CCP4_SCR/toxd_e.mtz <<-EOF
	TITLE TEST OF PROGRAM ECALC WITH REFLECTION DATA
	REFLECTIONS 1500
	RESOLUTION 0
	LABIN FP=FTOXD3  SIGFP=SIGFTOXD3
	EOF
#
#  Generate E values for Calculated F's
#
ecalc hklin $CCP4_SCR/toxd_mod_p1 hklout $CCP4_SCR/toxd_mod_p1_e <<-EOF
	TITLE TEST OF PROGRAM ECALC WITH REFLECTION DATA
	REFLECTIONS 1500
	RESOLUTION 0
	LABIN FP=FC_p1
	EOF
#
# Then run ALMN
#
almn HKLIN $CCP4_SCR/toxd_e HKLIN2 $CCP4_SCR/toxd_mod_p1_e \
   MAPOUT $CCP4_SCR/almn.map <<-END-almn
	CROSS 3 15
	RESO  10 3.4
	TITL  Toxd model rotation function.
	CRYS file 1 orth 1 flim 1 10000000000000 
	LABI FILE 1 F=E
	CRYS file 2 orth 1 flim 1 10000000000000 
	LABI FILE 2 F=E      
	LIMIT 0 90 5 1    !  Beta limit 90 because of symmetry
	!                    If in doubt set Beta limit 180..
	FIND 5 20
	NOPR
	MAP
	END 
	END-almn
#