#!/bin/csh -fe
#
#  to make PROTIN dictionary distance list using MAKEDICT
#  Need these entries to be added protin dictionary
#  (In York on $CLIBD/protin.dic)
#  They must be inserted in the correct place.
#  Copy the dictionary to your area and edit it as appropriate.
#  assign DICTPROTN to mydict.dat when you run PROTIN.
# You will need:
#
#   1) A set of coordinates for an "IDEAL" substrate in PDB format
#  They can be anywhere in space as long as they are correctly bonded.
# (Covalent bonds to other atoms should be defined as SPECIAL distance in
# PROTIN)
#
#  Example:                                code(=1) resno       resname 
#                                                 1   46          IPH  
#    X(A)       Y(A)      Z(A)           atomtype  atomno code(=-1)     atomname
#   0.69500   1.20400   0.00000              1         1   -1               C1   
#   0.69500   1.20400   0.00000              1         1   -1               C1   
#  -1.39000   0.00000   0.00000              1         3   -1               C3   
#  -0.69500  -1.20400   0.00000              1         4   -1               C4   
#   0.69500  -1.20400   0.00000              1         5   -1               C5   
#   1.39000   0.00000   0.00000              1         6   -1               C6   
#   1.38500  -2.39900  -0.01500              3         7   -1               O5   
#  -1.72000   2.97900  -0.02300              0         8   -1               I2   
#............................................................................
#  Note: resno is the number in the PROTIN dictionary. Replace some substrate
#  you dont want, and pirate its number.
#  resnam and atomname MUST match the one you use for your coordinates.
#
#  atomtype is only used when defined VDWR for this atom.
#  See VDWR  keyword in PROTIN.
#  Defaults are: C 1, N 2, O 3, S 4, FE 5, H 6, P 7, I 8, C' 9
#
#   2)  A list of contacts...
#  Example:
# Format is 
#resnam    resno   no_of_contacts 
#IPH          46   18
#<atno1 atno2 ikwt ibwt> ...... Format n (2i3,2i4)..
#  2  1 1 3  3  1 2 4  5  1 2 4  6  1 1 3  8  1 2 4  3  2 1 3  4  2 2 4  6  2 2 4
#  8  2 1 3  4  3 1 3  5  3 2 4  8  3 2 4  5  4 1 3  6  4 2 4  7  4 2 4  6  5 1 3
#  7  5 1 3  7  6 2 4
#
# NB: MAKEDICT generates these automatically from the information
# in 1).
#
#3) List of planes.
#   You will have to work these out yourself.
#   Example of format if there are more than one plane per group.
#   There must be a number at the end of the line.
#
#PSS 54  7  7   1   2   3   4   5   6  14                                      30
#PSS 54  7  7   7   8   9  10  11  12  13                                      30
#
#  Example:
#resnam resno no_atoms_plane no_atoms_plane  atno1 atno2 .... atnoi
#IPH 46  8  8   1   2   3   4   5   6   7   8                                    
#
# NB: MAKEDICT will generate this if you supply the appropriate
# information using the PLANE keyword.
#
#4) List of chiral volumes
#   You will have to work these out yourself.
# resnam resno code(=1) atno1 atno2 atno3 atno4  ( names only for convenience)
#
#  Example:
#COA  33  1   11    2   12   17       C1' N9  C2' O4'  
#COA  33  1   12   11   13   14       C2' C1' O2' C3'
#COA  33  1   14   12   15   16       C3' C2' O3' C4'
#COA  33  1   16   14   17   18       C4' C2' O4' C5'                                    #
# NB: MAKEDICT will generate this if you supply the appropriate
# information using the CHIRAL keyword.
#
# 5) I do not bother  to set up non bonded contacts..
#
#
# Example command file using MAKEDICT to set up the
# dictionary entries.
#
# This is a simple example using the SUL residue cut
# out of toxd.pdb
#
makedict XYZIN $CEXAM/data/toxd_sul.pdb \
         DICT $CCP4_SCR/toxd_sul.dict \
<<eof-makedict
INPUT PDB      ! Input coordinates from pdb file
OUTPUT PROTIN  ! Output protin dictionary format
RESIDUE JNK    ! Name of residue in dictionary file; default is
               ! name in pdb file
CENTRE S       ! Centred on atom S; default is first atom
eof-makedict
#
