Following is given an example command file for calculating the required information for this module. The file names used in this example are those given in the TNT_EXAMPLES: area for the Phosphoramidon inhibitor of thermolysin. Since the program Averager_I is VMS specific the example is a VMS command file.
Usually one performs only rigid body refinement with the rotation function module. Therefore this example uses only the low resolution data and does not calculate curvatures.
A complication of this module is that the space group of the calculations changes from place to place. One must be very careful to use the crystal's space group, P1, and the Patterson space group at the proper times. To make the space group clear the example does not use a TNT control file.
$ ! $ ! SF's for the inhibitor-enzyme complex in P1. $ ! $ RUN TNT_UTIL:FOURIER CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 5 INCLUDE TNT_DATA:FORMFACTOR.DAT INCLUDE INIT.COR PUNCH TESTFC.HKL HKL $ ! $ ! Average the Patterson coefficients from our model over $ ! the Patterson symmetry. This program will not handle $ ! the center of symmetry operator in the Patterson $ ! symmetry. It must be left out. This ommission does $ ! not affect the result of the calculation. $ ! $ ASSIGN /USER TESTFC.HKL FOR010 $ ASSIGN /USER TESTFC_I_SYM.HKL FOR011 $ RUN TNT_FFT:AVERAGER_I 94.1,94.1,131.4,90.,90.,120., x, y, z; x-y, x, z; -y, x-y, z; -x, -y, z; y-x, -x, z; y, y-x, z; x-y, -y, -z; -y, -x, -z; -x, y-x, -z; y-x, y, -z; y, x, -z; x, x-y, -z. 5.0, 20.0 $ ! $ RUN REFROOT:[TNT.RFACTOR]RFACTOR CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 5.0 INCLUDE TNT_SYMMETRY:P6MM.DAT FO TNT_EXAMPLES:TLN_PHRM.HKL FC TESTFC_I_SYM.HKL SET KSOL 0.8 INCLUDE INIT.COR INCLUDE TNT_DATA:FORMFACTOR.DAT FUNCTION FUNCTION.DAT MODULE ROTATION PUNCH COEFS.PAK PACKED TYPE ROTATION_GRD $ ! $ DELETE TESTFC_I_SYM.HKL; $ ! $ ! Expand the fourier coefficients in COEFS.PAK from $ ! P6MM to space group P1. One can either use the center $ ! of symmetry or not. It does not matter. $ ! $ ASSIGN/USER COEFS.PAK FOR010 $ ASSIGN/USER COEFS_P1.PAK FOR011 $ RUN TNT_FFT:EXPANDER 94.1,94.1,131.4,90.,90.,120., x, y, z; x-y, x, z; -y, x-y, z; -x, -y, z; y-x, -x, z; y, y-x, z; x-y, -y, -z; -y, -x, -z; -x, y-x, -z; y-x, y, -z; y, x, -z; x, x-y, -z. 20.0,5.0, X,Y,Z. $ ! $ DELETE COEFS.PAK; $ ! $ ! Here we have to multiply COEFS_P1.PAK point for $ ! point with TESTFC.HKL. $ ! $ RUN TNT_UTIL:FOURIER FILE FC TESTFC.HKL FORMAT HKL FILE ROTFUN COEFS_P1.PAK FORMAT PACKED PUNCH ROTATION.PAK PACKED MULTIPLY FC ROTFUN $ ! $ DELETE COEFS_P1.PAK;, TESTFC.HKL; $ ! $ ! Calculate the gradient of the rotation function with $ ! respect to our model. The model and therefore the $ ! calculations are in P1. $ ! $ RUN REFROOT:[TNT.RFACTOR]RFACTOR CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 5.0 INCLUDE TNT_DATA:FORMFACTOR.DAT INCLUDE INIT.COR FILE COEFS ROTATION.PAK FORMAT PACKED AGARWAL GRADIENT.DAT MODULE ROTATION SOURCE COEFS $ ! $ DELETE ROTATION.PAK; $ ! $ COPY FUNCTION.DAT,GRADIENT.DAT ROTATION.DAT $ DELETE FUNCTION.DAT;, GRADIENT.DAT; $ ! $ ! ***** End of modules and into control program **** $ ! $ RUN REFROOT:[TNT.SHIFT]SHIFT INCLUDE ROTATION.DAT INCLUDE OLDDIR.DAT INCLUDE INIT.COR COMBINE XYZ * CONSTANT B CONSTANT OCC $ ! $ ! More clean up. $ ! $ DELETE OLDDIR.DAT;, ROTATION.DAT; $ !
This is the command file for the short loops of the same cycle.
$ ! $ ! SF's for the inhibitor-enzyme complex in P1. $ ! $ RUN TNT_UTIL:FOURIER CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 5 INCLUDE TNT_DATA:FORMFACTOR.DAT INCLUDE SHIFTED.COR PUNCH TESTFC.HKL HKL $ ! $ ! Average the Patterson coefficients from our model over $ ! the Patterson symmetry. This program will not handle $ ! the center of symmetry operator in the Patterson $ ! symmetry. It must be left out. This ommission does $ ! not affect the result of the calculation. $ ! $ ASSIGN /USER TESTFC.HKL FOR010 $ ASSIGN /USER TESTFC_I_SYM.HKL FOR011 $ RUN TNT_FFT:AVERAGER_I 94.1,94.1,131.4,90.,90.,120., x, y, z; x-y, x, z; -y, x-y, z; -x, -y, z; y-x, -x, z; y, y-x, z; x-y, -y, -z; -y, -x, -z; -x, y-x, -z; y-x, y, -z; y, x, -z; x, x-y, -z. 5.0, 20.0 $ ! $ DELETE TESTFC.HKL; $ ! $ RUN REFROOT:[TNT.RFACTOR]RFACTOR CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 5.0 INCLUDE TNT_SYMMETRY:P6MM.DAT FO TNT_EXAMPLES:TLN_PHRM.HKL FC TESTFC_I_SYM.HKL INCLUDE SCALES.DAT FUNCTION ROTATION.DAT MODULE ROTATION $ ! $ DELETE TESTFC_I_SYM.HKL; $ ! $ ! Get rid of the old SHIFTED.COR. $ ! $ DELETE SHIFTED.COR; $ ! $ ! Now move the atoms as directed. $ ! $ ASSIGN/USER SHIFT.OUT SYS$OUTPUT $ RUN REFROOT:[TNT.SHIFT]SHIFT INCLUDE STPFIL.DAT INCLUDE ROTATION.DAT INCLUDE INIT.COR INCLUDE NEWDIR.DAT $ ! $ TYPE SHIFT.OUT $ ! $ DELETE ROTATION.DAT; $ PURGE STPFIL.DAT