REFMAC (CCP4: Supported Program)

User's manual for the program refmac_5.*

KEYWORDED INPUT

Anything input on a line after "!" or "#" is ignored and lines can be continued by using a minus (-) sign. The program only checks the first 4 characters of each keyword. The order of the cards is not important except that an END card must be last. Some keywords have various subsidiary keywords. The available keywords in alphabetical order are:

ANGLe, BFACtor/TEMPerature, BINS/RANGE, BLIMit, CELL_parameters, CHIRal_volumes, DAMPing_factor, DISTance, DNAME, END/GO, FREE, HOLD, LABIn, LABOut, MAKE_restraints, MODE, MONItor, NCYCle, NCSR/NONX, NOHARVEST, PHASe, PLANe, PNAME, PRIVATE, RBONd, REFInement, RIGId_body, RSIZE, SCALe, SCPArt, SHANnon_factor, SIGMaA, SOLVent, SPHEricity, SYMM, TLSC, TORSION, TWIN USECWD, VDWR/VAND, WEIG,

Keywords document for 5.5.x:
Labin: labels from mtz
Twin refinement
Simultaneous experimental phasing and refinement
Weighting xray and geometry terms
Using segment id
Harmonic restraints
Various protocols
Principal keywords controlling Xray refinement:
LABI - Input MTZ labels
NCYC - Number of the refinement cycles
REFI - Refinement parameters
SCAL - Scale parameters
SIGM - Parameters of the likelihood (sigmaA)
SOLV - Parameters of the solvent
WEIG - Weighting X-ray vs geometry
All keywords for Xray refinement:
BINS/RANGE - Number of the resolution bins
BLIM - Limits of allowed B value range
CELL - Cell parameters
DAMP - Factors to scale down shifts at every cycle
END/GO - End of keywords; must be last
FREE - Flag of the reflections excluded from the refinement
LABO - Output MTZ labels. Useful for map calculation
MODE - Refinement mode
MONI - Level of monitoring statistics during refinement
PHAS - Parameters for the phased refinement
RIGI - Parameters of the rigid body refinement
SCPA - For scaling of the external partial structure factors
SHAN - Shannon factor to control grid spacings
SYMM - Symmetry
TLSC - Number of TLS cycles
Keywords controlling (geometric) restraints (function very similar to that in PROLSQ):
ANGL - Restraints on bond angles
BFAC/TEMP - Restraints on B values
CHIR - Restraints on chiral volumes
DIST - Restraints on bond distances
HOLD - Restraints against excessive shifts
MAKE - Controls making restraints and checking coordinates against dictionary
NCSR/NONX - Restraints on non-crystallographic symmetry
PLAN - Restraints on planarity
RBON - Rigid bond restraints on the anisotropic B values of bonded atoms
SPHE - Sphericity restraints on the anisotropic B values
TORS - Restraints on the torsion angles
VDWR/VAND - Restraints on VDW repulsions
Optional keywords controlling the data harvesting functionality:
DNAME - Dataset name
NOHARVEST - Harvesting files are not necessary
PNAME - Project name
PRIVATE - Controls modes of the files created for harvesting
RSIZE - Number of characters in one column
USECWD - Controls directory where harvesting files are