A REFMAC input script has the same form as the most of the CCP4 programs; i.e.:
refmac logical_file1 <actual_file1> logical_file2 <actual_file2> \ ... << eor Command lines END eor
Where logical_filei are logical names of files to be used and actual_filei are actual file names.
Restrained refinement with file_crd.pdb as input coordinate file and file_mtz.mtz as input reflection file and results written to output files file_refmac.mtz (reflection file to be used for map caclulation) and file_refmac.pdb (coordinate file):
refmac \ hklin file_mtz.mtz \ xyzin file_crd.pdb \ hklout file_refmac.mtz \ xyzout file_refmac.pdb << eor Command lines END eor
Command lines could directly contain keywords as described in the Keyworded input section.
Command lines could also contain a file of command lines. In this case a @ sign should preceed the file name. For example:
refmac hklin file_mtz.mtz \ xyzin file_crd.pdb \ hklout file_refmac.mtz \ xyzout file_refmac.pdb << eor LABIn .... @my_favourite_defaults_for_low_resolution .... END eor
Then "my_favourite_defaults_for_low_resolution" could contain following the keywords:
# # Do not use hydrogens even if they are in the input file # MAKE_restraints HYDRogens No # # Set all B values to 30 before starting refinement # BFACtors SET_to 30 # #Do 10 cycle of TLS refinement before individual atomic # REFInement TLSCycle 10 # # Do overall B value refinement # BREFinement OVERall # # Use tight restraints # WEIGt MATRix 0.1 # # Fix Babinet's B value to 200 # SCALe LSSCale FIXBulk BBULk 200 # # Damp down shifts by 0.3 at every cycle # DAMPing_factors 0.3 0.3
See Examples section for scripts for various purposes.