refmac XYZIN foo_cycle_i.brk HKLIN foo.mtz
TLSIN tlsin.txt TLSOUT tlsout.txt
XYZOUT foo_cycle_j.brk HKLOUT foo_cycle_j.mtz
[Keyworded input]
The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.
[Program organisation and communication with it is illustrated in the EXAMPLES section.]