Creating a Fo-Fo Map
The calculation of a Fo-Fo map requires three pieces of information -- the two sets of amplitudes and a set of phases. Since Rfactor works with only two files at a time the phases must be placed in the file containing the standard amplitudes (those being subtracted). If the standard was solved using MIR phasing it is quite convenient to store the MIR phases in the HKL file with the measured amplitudes. When this is the case it is quite simple to calculate a Fo-Fo map. One simply has Rfactor calculate a ``Fo-Fc'' map where ``Fo'' is the derivative HKL file and ``Fc'' is the file containing the standard amplitudes and MIR phases.
If you wish to calculate a Fo-Fo map with phases calculated from a model you must perform the additional step of appending the calculated phases to the standard amplitudes. A file containing these mixed coefficients is produced with the SWAP_PHASE coefficient type. Once this chimeric file is created the Fo-Fo map is calculate as described above.
When the PUNCH is issued with the TYPE SWAP_PHASE modifier the resulting coefficients consist of the amplitudes from the file defined on the FO statement while the phases are from the file defined on the FC file.
is set to zero in either case. This must be done because the disordered solvent contributes to both sets of reflections. is only used when comparing measured amplitudes to calculated ones.
Writing a Fo-Fo Map Phased with MIR Phases
$tntbin/rfactor <<$eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 2.3 INCLUDE $tntdata/symmetry/p6122.dat INCLUDE native_model.cor ! Coordinates included INCLUDE $tntdata/formfactor.dat ! to provide molecular ! volume. FO modified_fobs.hkl ! Amplitudes of new protein FC native_fobs.hkl ! Amplitudes and MIR phases SET KSOL 0.0 PUNCH fo-fc.dsn6 DSN6 TYPE FO-FC OVERSAMPLE 4 $eof if ($status >< 0) then exit 1
Writing a Fo-Fo Map Phased with Calculated Phases
$tntbin/rfactor <<$eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 2.3 INCLUDE $tntdata/symmetry/p6122.dat FO native_fobs.hkl ! Amplitudes of standard INCLUDE native_model.cor ! Source of phases INCLUDE $tntdata/formfactor.dat PUNCH fobs_phicalc.hkl HKL TYPE SWAP_PHASE FO modified_fobs.hkl ! Amplitude of new protein FC fobs_phicalc.hkl ! Amplitudes and phases SET KSOL 0.0 PUNCH fo-fo.dsn6 DSN6 TYPE FO-FC OVERSAMPLE 4 $eof if ($status >< 0) then exit 1 # rm fobs_phicalc.hkl #