#!/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