REFMAC (CCP4: Supported Program)

User's manual for the program REFMAC, version 5.0.36

Input and output files - Input script

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.

For example:
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

Logical names and description of possible input and output files

HKLIN

Input reflection file. Format MTZ.

HKLOUT

Output reflection file. Format MTZ. Contains coefficients for map calculations.

XYZIN

Input coordinate file. Preferred format PDB. mmCIF can also be used. From mmCIF, REFMAC uses only information necessary for refinement.

XYZOUT

Output coordinate file. Current format is PDB.

TLSIN

Input file containing TLS parameters.

TLSOUT

Output file containing new refined TLS parameters.

SYMOP

File containing symmetry operations. Only set explicitly if non-default symmetry libraries are used.

LIBIN

Input user supplied library of ligand descriptions.

LIBOUT

Output library of descriptions. It will be written if new ligand is encountered.

ATOMSF

File containing atomic form factors. Only set explicitly if non-default atomic structure factor libraries are used.

Command lines

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.