echo off ::creating input file for fofcmap example as the input depend on environment variable echo TITLE Fc and Phic calculation from %TOXD%\toxd.pdb > %SCRIPTWIN%\fofcmap1.dat echo MODE SFCALC HKLIN XYZIN >> %SCRIPTWIN%\fofcmap1.dat echo RESOLUTION 10.0 2.7 >> %SCRIPTWIN%\fofcmap1.dat echo GRID 100 60 32 >> %SCRIPTWIN%\fofcmap1.dat echo LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 FREE=FreeR_flag >> %SCRIPTWIN%\fofcmap1.dat echo LABOUT FC=TOXFC PHIC=TOXPHIC >> %SCRIPTWIN%\fofcmap1.dat echo END >> %SCRIPTWIN%\fofcmap1.dat ::creating input file for bulk example as the input depend on environment variable echo %TOXD%\toxd.pdb > bulk3.dat echo %TEMPRES%\toxd_table1.tab >> bulk3.dat echo %TEMPRES%\toxd_tabling.log >> bulk3.dat echo %TEMPRES%\toxd_table1.tabs >> bulk3.dat echo %TEMPRES%\toxd_bulking.inp >> bulk3.dat echo 0.35 ! value of ksol >> bulk3.dat echo 50.0 ! value of Bsol >> bulk3.dat echo 1.4 ! value of the solvent radius used for mask >> bulk3.dat ::creating input file for oasis_sir example as the input depend on environment variable echo read %TEMPRES%\rnase_mod.mtz > %SCRIPTWIN%\oasis_sir2.dat echo calc D col DIFFPTNCD25 = col FPTNCD25 col FNAT - >> %SCRIPTWIN%\oasis_sir2.dat echo calc Q col SIGDIFFPTNCD25 = col SIGFPTNCD25 2 ** col SIGFNAT 2 ** + 0.5 ** >> %SCRIPTWIN%\oasis_sir2.dat echo write %TEMPRES%\rnase_sir.mtz >> %SCRIPTWIN%\oasis_sir2.dat echo y >> %SCRIPTWIN%\oasis_sir2.dat echo exit >> %SCRIPTWIN%\oasis_sir2.dat ::creating input file for rsps example as the input depend on environment variable echo # read spacegroup, file names and cell parameters > %SCRIPTWIN%\rsps2.dat echo # >> %SCRIPTWIN%\rsps2.dat echo spacegroup 19 ! must be before file names >> %SCRIPTWIN%\rsps2.dat echo # reset origin peak to zero >> %SCRIPTWIN%\rsps2.dat echo patfile %TEMPRES%\toxd_aupatt.map type CCP4 reset origin 10.0 0 >> %SCRIPTWIN%\rsps2.dat echo scorfile %TEMPRES%\rsps.map >> %SCRIPTWIN%\rsps2.dat echo pick patterson >> %SCRIPTWIN%\rsps2.dat echo # >> %SCRIPTWIN%\rsps2.dat echo # Harker scan of asymmetric unit >> %SCRIPTWIN%\rsps2.dat echo # Allow one low peak >> %SCRIPTWIN%\rsps2.dat echo # >> %SCRIPTWIN%\rsps2.dat echo vectorset single atoms ; low 0 ; reject 1.0 ; scan au >> %SCRIPTWIN%\rsps2.dat echo pick scoremap 50 >> %SCRIPTWIN%\rsps2.dat echo write positions %TEMPRES%\rsps_harker.pdb >> %SCRIPTWIN%\rsps2.dat echo vlist site 1 10 >> %SCRIPTWIN%\rsps2.dat ::creating input file for sortmtz example as the input depend on environment variable echo H K L M/ISYM BATCH > %SCRIPTWIN%\sortmtz4.dat echo %TEMPRES%\aucn_1.mtz >> %SCRIPTWIN%\sortmtz4.dat echo %TEMPRES%\aucn_2.mtz >> %SCRIPTWIN%\sortmtz4.dat echo %TEMPRES%\aucn_3.mtz >> %SCRIPTWIN%\sortmtz4.dat ::creating input files for beast example as the input depend on environment variables echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast1.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast1.dat echo MODEL mol1 %DATA%\1BIK.pdb IDENT 0.377 >> %SCRIPTWIN%\beast1.dat echo SEARCH mol1 ROTATE FULL 15. >> %SCRIPTWIN%\beast1.dat echo BEST 20 0 >> %SCRIPTWIN%\beast1.dat echo END >> %SCRIPTWIN%\beast1.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast2.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast2.dat echo MODEL mol1 %TOXD%\toxd.pdb IDENT 1.00 >> %SCRIPTWIN%\beast2.dat echo SEARCH mol1 ROTATE AROUND 0.0 0.0 0.0 15.0 >> %SCRIPTWIN%\beast2.dat echo END >> %SCRIPTWIN%\beast2.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast3.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast3.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beast3.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beast3.dat echo SEARCH mol1 ROTATE FULL 15.0 >> %SCRIPTWIN%\beast3.dat echo END >> %SCRIPTWIN%\beast3.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast4.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast4.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beast4.dat echo SEARCH mol1 ROTATE AROUND LIST 3.0 1.0 >> %SCRIPTWIN%\beast4.dat echo RLIST mol1 146.38 23.86 197.31 >> %SCRIPTWIN%\beast4.dat echo RLIST mol1 130.15 17.99 219.53 >> %SCRIPTWIN%\beast4.dat echo RLIST mol1 138.39 20.92 205.97 >> %SCRIPTWIN%\beast4.dat echo END >> %SCRIPTWIN%\beast4.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast5.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast5.dat echo MODEL mol1 %DATA%\1BIK.pdb IDENT 0.377 >> %SCRIPTWIN%\beast5.dat echo 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 >> %SCRIPTWIN%\beast5.dat echo END >> %SCRIPTWIN%\beast5.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast6.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beast6.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beast6.dat echo SEARCH mol1 ROTATE LIST TRANSLATE REGION 0.0 0.5 0.0 0.5 0.0 0.5 0.8 0.2 >> %SCRIPTWIN%\beast6.dat echo RLIST mol1 143.55 22.57 200.87 >> %SCRIPTWIN%\beast6.dat echo RLIST mol1 128.86 18.42 219.80 >> %SCRIPTWIN%\beast6.dat echo RLIST mol1 130.15 17.99 219.53 >> %SCRIPTWIN%\beast6.dat echo END >> %SCRIPTWIN%\beast6.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beast7.dat echo MOLECULE mol1 1.00 >> %SCRIPTWIN%\beast7.dat echo MODEL mol1 %DATA%\1BIK.pdb IDENT 0.377 >> %SCRIPTWIN%\beast7.dat echo 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 >> %SCRIPTWIN%\beast7.dat echo BEST 10 3 >> %SCRIPTWIN%\beast7.dat echo END >> %SCRIPTWIN%\beast7.dat ::creating input file for restrain example as the input depend on environment variable echo TITLE TOXD at 2.3A. > %SCRIPTWIN%\restrain.dat echo XYZIN %DATA%\toxd_in.pdb >> %SCRIPTWIN%\restrain.dat echo HKLIN %TOXD%\toxd.mtz >> %SCRIPTWIN%\restrain.dat echo LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 FREE=FreeR_flag >> %SCRIPTWIN%\restrain.dat echo XYZOUT %TEMPRES%\toxd_out.pdb >> %SCRIPTWIN%\restrain.dat echo HKLOUT %TEMPRES%\toxd_out.mtz >> %SCRIPTWIN%\restrain.dat echo LABOUT FC=FCTOXD3 PHIC=PHICTOXD3 >> %SCRIPTWIN%\restrain.dat echo ! Must supply extra distance restraints for disulphides: >> %SCRIPTWIN%\restrain.dat echo XTRD 7.CB 57.SG 3.034 .033 ! These are from Engh and Huber. >> %SCRIPTWIN%\restrain.dat echo XTRD 7.SG 57.SG 2.03 .008 >> %SCRIPTWIN%\restrain.dat echo XTRD 7.SG 57.CB 3.034 .033 >> %SCRIPTWIN%\restrain.dat echo XTRD 16.CB 40.SG 3.034 .033 >> %SCRIPTWIN%\restrain.dat echo XTRD 16.SG 40.SG 2.03 .008 >> %SCRIPTWIN%\restrain.dat echo XTRD 16.SG 40.CB 3.034 .033 >> %SCRIPTWIN%\restrain.dat echo XTRD 32.CB 53.SG 3.034 .033 >> %SCRIPTWIN%\restrain.dat echo XTRD 32.SG 53.SG 2.03 .008 >> %SCRIPTWIN%\restrain.dat echo XTRD 32.SG 53.CB 3.034 .033 >> %SCRIPTWIN%\restrain.dat echo ! Use PDB file occupancies of 20 atoms starting at 61 O1. >> %SCRIPTWIN%\restrain.dat echo OCCU 61.O1 20 SO4s ! 4 sulphates. >> %SCRIPTWIN%\restrain.dat echo STEER >> %SCRIPTWIN%\restrain.dat echo ! Following items are in NAMELIST format (name=value list). >> %SCRIPTWIN%\restrain.dat echo NCYC=5 ! Do 5 cycles with bulk solvent correction. >> %SCRIPTWIN%\restrain.dat echo REPEL=t ! Activate VDW repulsion restraints just in case. >> %SCRIPTWIN%\restrain.dat echo OCCREF=f ! No occupancy refinement. >> %SCRIPTWIN%\restrain.dat echo SCHEME=2 ! Better than weighting scheme 1 and uses SIGF. >> %SCRIPTWIN%\restrain.dat :: Creating input files for dtrek2scala example as its input depend on environment variable echo TITLE 'dtrek2scala example data set' > %SCRIPTWIN%\dtrek2scala1.dat echo SYMMETRY 96 >> %SCRIPTWIN%\dtrek2scala1.dat echo CRYSTAL 1 >> %SCRIPTWIN%\dtrek2scala1.dat echo PNAME HEWL >> %SCRIPTWIN%\dtrek2scala1.dat echo DNAME Dtrek2scala test >> %SCRIPTWIN%\dtrek2scala1.dat echo TOOFAR 2.0 2.0 0.5 >> %SCRIPTWIN%\dtrek2scala1.dat echo # >> %SCRIPTWIN%\dtrek2scala1.dat echo BATCH 1 >> %SCRIPTWIN%\dtrek2scala1.dat echo FILE %DATA%\dtprofit.ref >> %SCRIPTWIN%\dtrek2scala1.dat echo HFILE %DATA%\dtintegrate.head >> %SCRIPTWIN%\dtrek2scala1.dat echo BTITLE HEWL-test >> %SCRIPTWIN%\dtrek2scala1.dat echo PROCESS >> %SCRIPTWIN%\dtrek2scala1.dat echo H K L M/ISYM BATCH > %SCRIPTWIN%\dtrek2scala2.dat echo %TEMPRES%\HEWL-test.dtrek2scala.mtz >> %SCRIPTWIN%\dtrek2scala2.dat ::creating input file for watncs example as the input depend on environment variable echo pdb %TEMPRES%\rnase_wat.pdb > %SCRIPTWIN%\watncs2.dat echo out %TEMPRES%\rnase_out.pdb >> %SCRIPTWIN%\watncs2.dat echo relate >> %SCRIPTWIN%\watncs2.dat echo 0.970 -0.048 -0.238 >> %SCRIPTWIN%\watncs2.dat echo 0.238 0.384 0.892 >> %SCRIPTWIN%\watncs2.dat echo 0.049 -0.922 0.384 >> %SCRIPTWIN%\watncs2.dat echo -33.27858 21.14615 19.01986 >> %SCRIPTWIN%\watncs2.dat echo error 0.6 >> %SCRIPTWIN%\watncs2.dat echo least 1 >> %SCRIPTWIN%\watncs2.dat ::creating input file for mtzMadMode example as the input depend on environment variable echo read %RNASE%\rnase25.mtz col FNAT SIGFNAT > %SCRIPTWIN%\mtzMad2.dat echo read %TEMPRES%\rnase25_madmod.mtz >> %SCRIPTWIN%\mtzMad2.dat echo write %TEMPRES%\rnase25_all.mtz >> %SCRIPTWIN%\mtzMad2.dat echo exit >> %SCRIPTWIN%\mtzMad2.dat ::creating input files for beast-various example as the input depend on environment variables echo LABIN F=FTOXD3 > %SCRIPTWIN%\beastvar1.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beastvar1.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beastvar1.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beastvar1.dat echo SEARCH mol1 ROTATE AROUND 143.75 21.02 200.76 1.0 0.3 \ >> %SCRIPTWIN%\beastvar1.dat echo TRANSLATE AROUND 0.3789 0.2222 0.4427 0.4 0.1 >> %SCRIPTWIN%\beastvar1.dat echo BEST 20 0 >> %SCRIPTWIN%\beastvar1.dat echo END >> %SCRIPTWIN%\beastvar1.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beastvar2.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beastvar2.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beastvar2.dat echo SEARCH mol1 >> %SCRIPTWIN%\beastvar2.dat echo @%DATA%\toxd.molrep_rf >> %SCRIPTWIN%\beastvar2.dat echo REPORT ALL >> %SCRIPTWIN%\beastvar2.dat echo END >> %SCRIPTWIN%\beastvar2.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beastvar3.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beastvar3.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beastvar3.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beastvar3.dat echo SEARCH mol1 ROTATE FULL 8. >> %SCRIPTWIN%\beastvar3.dat echo BEST 20 >> %SCRIPTWIN%\beastvar3.dat echo END >> %SCRIPTWIN%\beastvar3.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beastvar4.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beastvar4.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beastvar4.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beastvar4.dat echo SEARCH mol1 ROTATE AROUND LIST 3.5 1. >> %SCRIPTWIN%\beastvar4.dat echo RLIST mol1 137.29 21.41 206.63 >> %SCRIPTWIN%\beastvar4.dat echo RLIST mol1 140.14 14.88 206.72 >> %SCRIPTWIN%\beastvar4.dat echo RLIST mol1 130.05 21.41 220.92 >> %SCRIPTWIN%\beastvar4.dat echo RLIST mol1 138.95 27.95 209.05 >> %SCRIPTWIN%\beastvar4.dat echo END >> %SCRIPTWIN%\beastvar4.dat echo LABIN F=FTOXD3 > %SCRIPTWIN%\beastvar5.dat echo MOLECULE mol1 1.0 >> %SCRIPTWIN%\beastvar5.dat echo MODEL mol1 %DATA%\1D0D_B.pdb IDENT 0.364 >> %SCRIPTWIN%\beastvar5.dat echo MODEL mol1 %DATA%\1BIK_2_1D0D_B.pdb IDENT 0.377 >> %SCRIPTWIN%\beastvar5.dat echo SEARCH mol1 ROTATE 143.75 21.02 200.76 \ >> %SCRIPTWIN%\beastvar5.dat echo TRANSLATE REGION 0.0 0.5 0.0 0.5 0.0 0.5 >> %SCRIPTWIN%\beastvar5.dat echo END >> %SCRIPTWIN%\beastvar5.dat ::creating input files for cpirate example as the input depend on environment variables echo mtzin-ref %TEMPRES%\ref.mtz > %SCRIPTWIN%\cpirate1.dat echo colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] >> %SCRIPTWIN%\cpirate1.dat echo colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] >> %SCRIPTWIN%\cpirate1.dat echo mtzin-wrk %TEMPRES%\toxd_phase_mir.mtz >> %SCRIPTWIN%\cpirate1.dat echo colin-wrk-fo /*/*/[FTOXD3,SIGFTOXD3] >> %SCRIPTWIN%\cpirate1.dat echo colin-wrk-hl /*/*/[HLA,HLB,HLC,HLD] >> %SCRIPTWIN%\cpirate1.dat echo colin-wrk-free /*/*/[FreeR_flag] >> %SCRIPTWIN%\cpirate1.dat echo mtzout %TEMPRES%\toxd_phase_mir_pirate1.mtz >> %SCRIPTWIN%\cpirate1.dat echo colout pirate >> %SCRIPTWIN%\cpirate1.dat echo ncycles 3 >> %SCRIPTWIN%\cpirate1.dat echo weight-expllk 0.5 >> %SCRIPTWIN%\cpirate1.dat echo weight-mapllk 0.1 >> %SCRIPTWIN%\cpirate1.dat echo stats-radius 9.0,3.0 >> %SCRIPTWIN%\cpirate1.dat echo skew-content 0.0,0.0 >> %SCRIPTWIN%\cpirate1.dat echo auto-content >> %SCRIPTWIN%\cpirate1.dat echo mtzin %TEMPRES%\toxd_phase_mir_pirate1.mtz > %SCRIPTWIN%\cpirate2.dat echo colin-fc /*/*/[pirate.F_phi.F,pirate.F_phi.phi] >> %SCRIPTWIN%\cpirate2.dat echo mapout %TEMPRES%\toxd_phase_mir_pirate1_fft1.map >> %SCRIPTWIN%\cpirate2.dat echo stats >> %SCRIPTWIN%\cpirate2.dat echo stats-radius 4.0 >> %SCRIPTWIN%\cpirate2.dat