#! /bin/sh

set -e

if test ! -f $CCP4_SCR/toxd_aupatt.map; then
	echo '! run patterson first' 1>&2
	exit 1
fi

# Generate Patterson vectors from coordinates of Au sites.
# XYZIN - atom coordinates in pdb format
# MAPIN is used to define extent and symmetry of Patterson.
# XYZOUT contains the vectors.

vectors mapin $CCP4_SCR/toxd_aupatt.map xyzout $CCP4_SCR/vectors1.pdb <<EOF
symmetry 19           ! space-group symmetry for atoms: NOT Patterson symmetry
! Au atom sites taken from sites.frc
ATOM   A    0.177  0.104 -0.114
ATOM   B    0.218  0.138 -0.105
END
EOF

# same again but input from PDB file

coordconv XYZIN $CEXAM/data/sites.frc XYZOUT $CCP4_SCR/sites.pdb <<eof
INPUT HA 
OUTPUT PDB ORTH 1
CELL 73.582   38.733   23.189  90.00  90.00  90.00
END
eof

vectors xyzin $CCP4_SCR/sites.pdb mapin $CCP4_SCR/toxd_aupatt.map xyzout $CCP4_SCR/vectors2.pdb <<EOF
symmetry 19           ! space-group symmetry for atoms: NOT Patterson symmetry
END
EOF

# as for first example, but for vectors in volume defined by keyword xyzlim
# rather than defined by mapin

vectors  xyzout $CCP4_SCR/vectors3.pdb <<EOF
symmetry 19           ! space-group symmetry for atoms: NOT Patterson symmetry
CELL   73.582   38.733   23.189  90.00  90.00  90.00
! Au atom sites taken from sites.frc
ATOM   A    0.177  0.104 -0.114
ATOM   B    0.218  0.138 -0.105
xyzlim asu
END
EOF

# example where atoms are input from both xyzin and ATOM keyword lines

vectors xyzin $CCP4_SCR/sites.pdb mapin $CCP4_SCR/toxd_aupatt.map xyzout $CCP4_SCR/vectors4.pdb <<EOF
symmetry 19           ! space-group symmetry for atoms: NOT Patterson symmetry
! Au atom sites taken from sites.frc
ATOM   C    0.177  0.104 -0.114
ATOM   D    0.218  0.138 -0.105
END
EOF

# Now we compare these vectors with the Patterson map.

npo mapin $CCP4_SCR/toxd_aupatt.map xyzin $CCP4_SCR/vectors1.pdb plot $CCP4_SCR/patt.plt <<EOF
TITLE  Vectors for sites A & B
SYMM X,Y,Z
MAP SCALE 4
CONTRS 2000 TO 10000 BY 2000
SECTNS 0 40 4
INPUT BROOK
SOLID
RADII ATOMS ALL -0.5
COLOUR BLUE
PLOT
EOF

# You can view the plot file with xplot84driver
#