REFMAC (CCP4: Supported Program)
User's manual for the program REFMAC, version 5.0.36
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.
refmac \ hklin file_mtz.mtz \ xyzin file_crd.pdb \ hklout file_refmac.mtz \ xyzout file_refmac.pdb << eor Command lines END eor
Logical names and description of possible input and output files
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.