#!/bin/csh -f # Rnase_sa has 2 molecules in the asymmetric unit. # Search done with molecule A # Fitting may be should be done at higher resolution than other calculations. # Done once with TABFUN rotated. # again without rotation - want one solution wit euler angles 0 0 0 goto lsq # Will need to cat the two molecules together. #goto fitusa #goto fit22 #goto fit2 #goto fitp6522a #goto fitp6522 goto fit # Done at 2.5A - need to recalculate TABFUN #goto trausa1 #goto trap6522 goto tra2 #goto tra # Search for single molecules - only one good solution. #goto rot2 #goto rot #goto tabjd1 #goto tab #####################################################3 # sorting run: Rnase_SA #####################################################3 # mtz file contains cell and symmetry. # /f/scratch/ccp4/amore/amore3 \ hklin $YHKL/rnas25isowangrnasr1.mtz \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ <<'END' #VERBOSE TITLE ** rnase test SORTFUN RESOL 20 3 HKLM 139 139 149 9 LABI FP=FNAT SIGFP=SIGFNAT 'END' tab: #!/bin/csh -f #####################################################3 # tabling run: #####################################################3 # rotate , shift coordinates and produce table: # xyzout is the rotated and shifted coordinates. # #xyzin1 $YPDB/rna_sanat.pdb \ /f/scratch/ccp4/amore/amore3 \ xyzin1 $SCRATCH/rna_sanat1.pdb \ xyzout1 /f/scratch/ccp4/rna_sanat1_amore.pdb \ table1 /f/scratch/ccp4/rna_sanat1.tab \ <<'END' TITLE : Table for MODEL;1ccyrot.pdb VERBOSE #TABFUN SHIFT TABULATE # TABFUN NOROTATE will mean your model is left in its original # orientation - sometimes useful if you are expecting a special result TABFUN # # this will allow TABFUN to work out the appropriate CRYSTL and SCALEi cards. # They will be output with XYZOUT CRYSTAL ORTH 1 CELL 64.900 78.320 38.790 90.00 90.00 90.00 # See documentation for details of this Keyword - may help for large problems # usually not necessary. HKLM 139 139 149 9 MODEL 1 BADD 0 SAMPLE 1 RESO 3 SHANN 2 SCALE 4.0 'END' # ###########################################3 rot: # choose cell for GENE which equals (min box + sphere radius + a bit) # It CANT be bigger than minimal_box*SCALE #####################################################3 #####################################################3 #####################################################3 #!/bin/csh -f # /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ clmn0 /f/scratch/ccp4/rnase.clmn \ table1 /f/scratch/ccp4/rna_sanat1.tab \ hklpck1 /f/scratch/ccp4/rna_sanat1.hkl \ clmn1 /f/scratch/ccp4/rna_sanat1.clmn \ mapout $SCRATCH/amore_rna_sanat1_10-4.map \ <<'END' # HKLM 139 139 149 9 ROTFUN #VERB TITLE : Generate HKLPCK1 from MODEL FRAGMENT 1 # Minimal box: 36.15 33.97 28.79 GENE 1 RESO 15.0 3.5 CELL 70 65 60 90 90 90 CLMN CRYSTAL ORTH 1 FLIM 0.E0 1.E8 SHARP 0.0 RESO 10.0 4 - SPHERE 25 CLMN MODEL 1 FLIM 0.E0 1.E8 RESO 10.0 4 SPHERE 25 ROTA CROSS MODEL 1 BESLIMI 6 120 step 2.5 NSR 0 0 - PKLIM 0.5 NPIC 98 BMAX 180 'END' # #exit # #####################################################3 #!/bin/csh -f # /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ clmn0 /f/scratch/ccp4/rnase.clmn \ table1 /f/scratch/ccp4/rna_sanat1.tab \ hklpck1 /f/scratch/ccp4/rna_sanat1.hkl \ clmn1 /f/scratch/ccp4/rna_sanat1.clmn \ mapout $SCRATCH/amore_rna_sanat1_15-35.map \ <<'END' # ROTFUN #VERB TITLE : Generate HKLPCK1 from MODEL FRAGMENT 1 # Minimal box: 36.15 33.97 28.79 HKLM 139 139 149 9 CLMN CRYSTAL ORTH 1 FLIM 0.E0 1.E8 SHARP 0.0 RESO 15.0 3.5 - SPHERE 20 CLMN MODEL 1 FLIM 0.E0 1.E8 RESO 15.0 3.5 SPHERE 20 ROTA CROSS MODEL 1 BESLIMI 6 120 step 2.5 NSR 0 0 - PKLIM 0.5 NPIC 50 BMAX 180 'END' # # #exit Maximal distance from Center of Mass: 28.90 tra: # Edit out the list of rotfun solutions and inset here. # This is the SLOW step, so go and make a cup of coffee. #####################################################3 # traing run: NMOL = 1 #####################################################3 #!/bin/csh -f # /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ table1 /f/scratch/ccp4/rna_sanat1.tab \ <<'END' TRAFUN CB NMOL 1 RESO 10 4 - PKLIM 0.5 NPIC 10 VERB TITLE : Translation function - Alc 1ccy solutions. P6122 HKLM 139 139 149 9 CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 SOLUTIONRC 1 102.30 80.16 88.22 0.00000 0.00000 0.00000 16.9 0.0 SOLUTIONRC 1 94.00 151.48 88.33 0.00000 0.00000 0.00000 14.1 0.0 'END' exit #exit # Edit out the list of rotfun solutions and inset here. # This is the SLOW step, so go and make a cup of coffee. #exit # tra2: #!/bin/csh -f #####################################################3 # /tra2 #####################################################3 # #!/bin/csh -f /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ table1 /f/scratch/ccp4/rna_sanat1.tab \ <<'END' HKLM 139 139 149 9 TRAFUN CB NMOL 2 RESO 10 4 - PKLIM 0.5 NPIC 10 VERB TITLE : Translation function - Alc 1ccy solutions. P6122 CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 REFSOL AL BE GA X Y Z BF # alc _ 1ccy P6122 SOLUTIONTF1 FIX 1 102.30 80.16 88.22 0.09993 0.41881 0.27173 36.6 47.5 SOLUTIONTF1 1 94.00 151.48 88.33 0.10864 0.36052 0.37966 26.2 50.2 SOLUTIONTF1 FIX 1 94.00 151.48 88.33 0.10864 0.36052 0.37966 26.2 50.2 SOLUTIONTF1 1 102.30 80.16 88.22 0.09993 0.41881 0.27173 36.6 47.5 'END' exit # #!/bin/csh -f /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ table1 /f/scratch/ccp4/rna_sanat2.tab \ <<'END' HKLM 139 139 149 9 TRAFUN CB NMOL 2 RESO 10 4 - PKLIM 0.5 NPIC 10 #VERB TITLE : Translation function - Alc 1ccy solutions. P6122 CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 REFSOL AL BE GA X Y Z BF # alc _ 1ccy P6122 SOLUTIONT FIX 1 94.09 69.96 77.11 0.11176 0.36190 0.38166 25.8 50.5 SOLUTIONT 1 359.57 0.00 0.00 0.40391 0.07943 0.27409 37.0 48.2 SOLUTIONT FIX 1 359.57 0.00 0.00 0.40391 0.07943 0.27409 37.0 48.2 SOLUTIONT 1 94.09 69.96 77.11 0.11176 0.36190 0.38166 25.8 50.5 'END' #exit fit: #!/bin/csh -f /f/scratch/ccp4/amore/amore3 \ hklpck0 /f/scratch/ccp4/rnase.hklamore3 \ table1 /f/scratch/ccp4/rna_sanat1.tab \ <<'END' FITFUN CB NMOL 2 RESO 10 4 ITER 10 CONV 1.E-3 title *** 1ccyrot structure *** P6122 ##verbOSE CRYSTAL ORTH 1 FLIMI 0.E0 1.E8 SHARP 0.0 REFSOL AL BE GA X Y Z BF # pseudo _ 1ccy P6122 HKLM 139 139 149 9 SOLUTIONTF1 1 102.30 80.16 88.22 0.09993 0.41881 0.27173 36.6 47.5 SOLUTIONTF2 1 94.00 151.48 88.33 0.60867 0.35974 0.37967 68.7 34.6 # SOLUTION 1 79.10 83.14 274.83 0.10283 0.07338 0.22939 29.8 49.7 # SOLUTION 1 91.00 25.82 98.34 0.39017 0.63867 0.37811 60.8 38.4 'END' lsq: #!/bin/csh -f # Solution 1 lsqkab \ WORKCD /f/scratch/ccp4/rna_sanat1_amore.pdb \ LSQOP /f/scratch/ccp4/rna_sanat1_sol1.pdb \ << 'END-lsqkab' title Rotating model by almn angles ROTAT EULER 102.64 81.53 87.86 TRAN FRAC 0.09838 0.41934 0.27061 79.0 28.2 output XYZ # ! output file LSQOP with new coords fit WATOM 1 to 10000 end 'END-lsqkab' #!/bin/csh -f # Solution 2 lsqkab \ WORKCD /f/scratch/ccp4/rna_sanat1_amore.pdb \ LSQOP /f/scratch/ccp4/rna_sanat1_sol2.pdb \ << 'END-lsqkab' title Rotating model by almn angles ROTAT EULER 89.27 150.56 84.55 TRAN FRAC 0.60720 0.35807 0.37932 79.0 28.2 output XYZ # ! output file LSQOP with new coords fit WATOM 1 to 10000 end 'END-lsqkab' # You will have to edit these two solution files together.