#!/bin/csh -f goto here #####################################################3 # sorting run: #####################################################3 # mtz file contains cell and symmetry. # amore \ hklin $CTEST/toxd/toxd.mtz \ hklpck0 $SCRATCH/toxd.hkl \ <<'END' VERBOSE TITLE ** packing h k l F for crystal** SORTFUN RESOL 100. 3. LABI FP=FTOXD3 SIGFP=SIGFTOXD3 'END' #!bin/csh -f #####################################################3 # tabling run: #####################################################3 # rotate , shift coordinates and produce table: # xyzout is the rotated and shifted coordinates. # amore \ xyzin1 $CTEST/toxd/toxd.pdb \ xyzout1 $SCRATCH/toxd.pdb \ TABLE1 $SCRATCH/search.tab \ <<'END' TITLE : Produce table for MODEL FRAGMENT VERBOSE TABFUN CRYSTAL ORTH 1 CELL 73.58 38.73 23.19 90 90 90 MODEL 1 BREPLACE 0 BADD 0 SAMPLE 1 TMIN 3 SHANN 2 SCALE 4.0 'END' # # Q. for Jorge: I am still not very clear about the relationship of # "dmin" and "shann" and box "scale" here. #####################################################3 # roting run: #####################################################3 #!/bin/csh -f # amore \ TABLE1 $SCRATCH/search.tab \ HKLPCK1 $SCRATCH/search.hkl \ hklpck0 $SCRATCH/toxd.hkl \ clmn1 $SCRATCH/search.clmn \ clmn0 $SCRATCH/toxd.clmn \ MAPOUT $SCRATCH/amore.map \ <<'END' # ROTFUN VERB TITLE : Generate HKLPCK1 from MODEL FRAGMENT 1 GENE 1 RESO 20.0 4.0 CELL 80 75 65 90 90 90 NMOL 1 CLMN CRYSTAL ORTH 1 FLIM 0.E0 1.E8 SHARP 0.0 RESO 20.0 4.0 - SPHERE 0.0 20 CLMN MODEL 1 FLIM 0.E0 1.E8 RESO 20.0 4.0 SPHERE 0.0 20 ROTA CROSS MODEL 1 BESLIMI 6 120 STEP 2.5 NSR 0 0 - PKLIM 0.5 NPIC 50 BMAX 90 'END' # # Q. for Jorge: I am still not very clear about the relationship of # "bessel limits" and "dang" here. # Q2. No idea about NSR values. # Q3. RPTS? DELTA??? - seems very small.. exit #####################################################3 # traing run: NMOL = 1 #####################################################3 #!/bin/csh -f # amore \ TABLE1 $SCRATCH/search.tab \ hklpck0 $SCRATCH/toxd.hkl \ MAPOUT $SCRATCH/amore.map \ <<'END' TRAFUN CB NMOL 1 RESO 8 4 - PKLIM 0.5 NPIC 100 VERB TITLE : Translation function CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 SOLUTION 1 30.46 79.40 248.27 0.00000 0.00000 0.00000 28.5 0.0 # As the mapout is requested, we need to do each solution in a seperate # run - else the map is over written & only refers to the final sol #SOLUTION 1 24.90 75.58 178.38 0.00000 0.00000 0.00000 17.2 0.0 #SOLUTION 1 70.01 44.53 325.55 0.00000 0.00000 0.00000 14.5 0.0 'END' # Qs. TMIN SHANN?? # Comment: Symmetry changed to P65 - they werent sure of Spacegroup at # first. # Comment SOLUTION stuff cut out of LOG file. Not sure that it is worth # writing fort.9 and having all the oic stuff. Just as easy with # an editor. exit #####################################################3 # traing run: NMOL = 2 #####################################################3 #!/bin/csh -f amore \ TABLE1 $SCRATCH/search.tab \ hklpck0 $SCRATCH/toxd.hkl \ TRAFUN $SCRATCH/trafun.9 \ <<'END' TRAFUN CB NMOL 2 RESO 8 4 - RPTS 0.5 NPIC 10 SYMM P212121 VERB TITLE : Translation function - 2 mols together. CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 SOLUTION FIX 1 27.76 100.74 350.08 0.14596 0.56602 0.00000 17.4 52.5 SOLUTION 1 27.94 115.80 353.60 0.14747 0.59881 0.00000 19.3 52.0 SOLUTION 1 45.98 98.41 293.85 0.00000 0.00000 0.00000 7.4 0.0 'END' #####################################################3 # traing run: NMOL = 3 #####################################################3 #!/bin/csh -f amore \ TABLE1 $SCRATCH/search.tab \ hklpck0 $SCRATCH/toxd.hkl \ <<'END' TRAFUN CB NMOL 3 RESO 8 4 - PKLIM 0.5 NPIC 10 SYMM P212121 VERB TITLE : Translation function - 3 mols together. CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 SOLUTION FIX 1 25.21 105.57 339.45 0.11330 0.56704 0.00000 38.0 46.7 SOLUTION FIX 1 27.76 100.74 350.08 0.14660 0.57107 0.65289 38.0 46.7 SOLUTION 1 27.94 115.80 353.60 0.14943 0.60250 0.00000 10.3 54.5 SOLUTION FIX 1 25.21 105.57 339.45 0.11330 0.56704 0.00000 38.0 46.7 SOLUTION FIX 1 27.94 115.80 353.60 0.14943 0.60250 0.00000 10.3 54.5 SOLUTION 1 27.76 100.74 350.08 0.14660 0.57107 0.00000 38.0 46.7 SOLUTION FIX 1 27.94 115.80 353.60 0.14943 0.60250 0.00000 10.3 54.5 SOLUTION FIX 1 27.76 100.74 350.08 0.14660 0.57107 0.65289 38.0 46.7 SOLUTION 1 25.21 105.57 339.45 0.11330 0.56704 0.00000 38.0 46.7 'END' # #!/bin/csh -f #####################################################3 # fiting run: #####################################################3 # here: amore \ TABLE1 $SCRATCH/search.tab \ hklpck0 $SCRATCH/toxd.hkl \ <<'END' FITFUN CB NMOL 1 RESO 20 4.5 ITER 10 CONV 1.E-3 title VERBOSE CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 REFSOL AL BE GA X Y Z BF SOLUTION 1 30.46 79.40 248.27 0.10148 0.18489 0.42647 78.4 28.9 SOLUTION 1 24.90 75.58 178.38 0.24202 0.46692 0.34705 23.7 53.4 SOLUTION 1 70.01 44.53 325.55 0.35779 0.13919 0.46713 21.0 54.7 'END' exit # #/bin/csh -f ########### ########### ########### ########### # MR2IC - ing Shifting back to original space group. ########### ########### ########### ########### # The keyword SHIFt can be given with other keywords (TABFun, ROTFun, etc) # or by it self. If on its own give the TABLING output For Center of Mass # and Euler angles with SHIFT 'Model_No.' COM . . . EULE . . . # Alternativly when with the TABFUN keyword the Center of Mass & # Euler angles are already calculated - So don't need to be read in. # After FITFun or TRAFun the new Solutions are used. # # Needed input HKLPCK0 - For the cell. # amore HKLPCK0 $SCRATCH/toxd.hkl \ SHIFT 1 EULER 179.62 69.89 33.13 COM -8.64 9.84 2.90 SOLU 1 81.51 46.59 10.10 0.11227 0.30425 0.25867 42.2 55.7 8. SOLU 1 91.01 79.14 168.07 0.43855 0.00328 0.25466 47.5 56.4 23. SOLU 1 99.47 133.13 191.13 0.38797 0.30447 0.24184 42.1 55.8 8. 'END' # # Example of running at the same time as TABFUN # amore xyzin1 $CTEST/toxd/toxd.pdb \ xyzout1 $SCRATCH/toxd.pdb \ TABLE1 $SCRATCH/search.tab \ TABLOUT $SCRATCH/tablout.9 << 'END' TABFUN VERBOSE MODEL 1 BREPLACE 0 BADD 0 SAMPLE 1 TMIN 3 SHANN 2 SCALE 4.0 SHIFT 1 SOLU 1 81.51 46.59 10.10 0.11227 0.30425 0.25867 42.2 55.7 8. SOLU 1 91.01 79.14 168.07 0.43855 0.00328 0.25466 47.5 56.4 23. SOLU 1 99.47 133.13 191.13 0.38797 0.30447 0.24184 42.1 55.8 8. 'END'