#!/bin/sh
#
# Rotation search (full) for toxd using 1BIK.pdb
# This is a quick test to see if the program's working properly.
# It happens to find the right orientation by luck, but the sampling
# of orientations is much too coarse.  A sampling interval of 3.6 is
# my normal default at the moment.  Eventually, the program will supply
# a sensible default based on size, resolution and model quality.
# SEARCH mol1 ROTATE FULL 
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof 
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/data/1BIK.pdb IDENT 0.377
SEARCH mol1 ROTATE FULL 15.
BEST 20 0
END
eof

#******************************************************************************

#
# Rotation search (limited) of toxd using the solution toxd.pdb file (!)
# Search restricted to around the origin because using a model pre-aligned
#   to the solution
# SEARCH mol1 ROTATE AROUND 0.0 0.0 0.0 3.0
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof 
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/toxd/toxd.pdb IDENT 1.00
SEARCH mol1 ROTATE AROUND 0.0 0.0 0.0 15.0
END
eof

#******************************************************************************

#
# Rotation search of toxd data using an ensemble of 2 models
# The two models are 1BIK.pdb and the B chain of 1D0D.pdb
# The models must be aligned to each other:
#   here 1BIK has been aligned to the B chain of 1D0D.pdb
# SEARCH mol1 ROTATE FULL 3.6
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/data/1D0D_B.pdb IDENT 0.364
MODEL mol1 $CEXAM/data/1BIK_2_1D0D_B.pdb IDENT 0.377
SEARCH mol1 ROTATE FULL 15.0
END
eof

#******************************************************************************

#
# Rotation search (refinement of previous rotation search solutions)
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/data/1D0D_B.pdb IDENT 0.364
SEARCH mol1 ROTATE AROUND LIST 3.0 1.0 
RLIST mol1 146.38  23.86 197.31 
RLIST mol1 130.15  17.99 219.53
RLIST mol1 138.39  20.92 205.97
END
eof

#******************************************************************************

#
# Translation search (full) around one rotation search solution  
# Normally should use a sampling of dmin/4 or finer.
#            TRANSLATE REGION 0.0 0.5 0.0 0.5 0.0 0.5 0.5
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/data/1BIK.pdb IDENT 0.377
SEARCH mol1 ROTATE 171.26 17.99 226.09 \
            TRANSLATE REGION 0.0 0.5 0.0 0.5 0.0 0.5 1.5
END
eof

#******************************************************************************

#
# Translation search (full) around three rotation search solutions
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof
LABIN F=FTOXD3
MOLECULE mol1 1.0
MODEL mol1 $CEXAM/data/1D0D_B.pdb IDENT 0.364
SEARCH mol1 ROTATE LIST \
            TRANSLATE REGION 0.0 0.5 0.0 0.5 0.0 0.5 0.8 0.2
RLIST mol1 143.55  22.57 200.87
RLIST mol1 128.86  18.42 219.80
RLIST mol1 130.15  17.99 219.53
END
eof

#******************************************************************************

#
# Final refinement search (6D) around a specific rotation and translation
#
beast HKLIN $CEXAM/toxd/toxd.mtz << eof
LABIN F=FTOXD3
MOLECULE mol1 1.00
MODEL mol1 $CEXAM/data/1BIK.pdb IDENT 0.377
SEARCH mol1 ROTATE AROUND 171.26 17.99 226.09 1.0 0.3 \
            TRANSLATE AROUND 0.4931 0.0842 0.0425 0.4 0.1 
BEST 10 3
END
eof