DEF martin 0.0.1 refmac 09:42 23/Dec/12 Model refinement with refmac. CPdbDataFile True True False True 1,0 File containing model coordinates (PDB/mmCIF). CObsDataFile True False True File containing structure factor amplitudes/intensities and uncertainties (F/SigF or I/SigI). CFreeRDataFile True True True F_SIGF Free R set corresponding to the reflection data. See the "Generate a Free R set" task in the "Data reduction" section. CPhsDataFile True True False F_SIGF CTLSDataFile True True True True File specifying TLS groups. If not provided, auto TLS refinement can still be performed (see the "Options" tab). CRefmacRestraintsDataFile True True CDictDataFile application/refmac-dictionary Ligand geometry file Restraint dictionary (mmCIF file) representing ideal ligand geometry. Ligand geometry cif Ligand description True True True True CPdbDataFile 1 True CMapCoeffsDataFile 21 True CMapCoeffsDataFile 11 True CMapCoeffsDataFile 21 True CMapCoeffsDataFile 11 True CPhsDataFile True CCootHistoryDataFile True CTLSDataFile True CDictDataFile True CPostscriptDataFile True CRefinementPerformance CString CInt 10 0 Number of REFMAC5 refinement cycles to perform. CBoolean False Automatically identify and use TLS groups during refinement. Adds 21 parameters per group, representing anisotropic displacement (concerted screw motion of rigid bodies). CInt 5 0 Number of cycles used to refine TLS parameters - these are refined separately, prior to the main refinement cycles. CInt 5 0 Number of cycles used to refine TLS parameters - these are refined separately, prior to the main refinement cycles. CString True AUTO,MANUAL automatic,manual AUTO If automatic weighting is selected, Refmac will adjust the weight each refinement cycle in order to try and ensure reasonable geometry on average. CFloat 0.0 Constant weight controlling the relative contribution of data (reflections) and restraint (geometry) terms. CBoolean False Specify whether it is known that the crystal is twinned (if in doubt, leave unticked). CString True I,F intensities (I),SF amplitudes (F) Either use intensities directly, or alternatively use SF amplitudes. I CBoolean True Specify whether or not riding hydrogen atoms are to be used during refinement. CString True ALL,YES generate riding hydrogens,only if present in file Specify whether riding hydrogens are to be generated and used, or whether hydrogens are only to be used if already present in the input coordinate file. ALL CString True NO,YES,ALL NO CBoolean False Restrain NCS-related molecules to ensure that they are structurally consistent with each other. CString True L,G local,global L Specify whether local or global NCS restraints should be used. Default: local. CString True A automatically A At present, only automatic NCS restraints can be specified from within the interface. For manual specification, see the help page. CBoolean False CBoolean False Use jelly-body restraints to stabilise refinement, ensuring that the model doesn't change too much from one cycle to the next (more cycles required). CFloat 0.01 Lower values allow the model to change less each cycle. Default: 0.01. CFloat 4.2 Maximum interatomic distance for jelly-body restraints. Controls flexibility. Default: 4.2. CBoolean False CString True isotropic,anisotropic,overall,mixed isotropic/anisotropic ISOT,ANIS,OVER,MIXED ISOT Specifies B-factor parameterisation. Default: isotropic. CBoolean True CBoolean False Perform anisotropic regularised map sharpening when calculating electron density maps. CBoolean False By default, the sharpening parameter is automatically set to the overall model B-factor after refinement. CFloat Specify custom sharpening parameter, which is the B-factor to "remove" from the map. CBoolean True Reset all atomic B-factors to a fixed value prior to refinement (advised when performing TLS refinement). CFloat 30 CBoolean False Reset all atomic B-factors to a fixed value prior to refinement. CFloat CFloat CBoolean False CFloat CFloat CString True NOTHING,OUTPUTMAPS,SADREFINEMENT Ignore anomalous scattering,Anomalous map calculation only,For SAD refinement NOTHING CWavelength 10.0 Override wavelength True CBoolean True CString True REFMACDEFAULT,BABINET,SIMPLE,WILSON Refmac default,Bulk (Babinet),Solvent explicit,Wilson scaling REFMACDEFAULT CString # Replace this with optional additional keyword input