DEF mnmacpro.ncl.ac.uk martin 0.1 SubstituteLigand 11:06 21/Nov/14 SubstituteLigand CString SMILES string defining the structure of the model to be built CC(C)OC1=C(C=CC(=C1)OC)C2=NC(C(N2C(=O)N3CCNC(=O)C3)C4=CC=C(C=C4)Cl)C5=CC=C(C=C5)Cl SMILES String of new ligand multiLine CPdbDataFile False True True Reference PDB will be used to direct spacegroup choice and as start point for molecular replacement - use atom selection to exclude waters and/or ligands CImportUnmergedList 0 CObsDataFile True True Merged reflections e.g. from import, XIA2 or aimless_pipe CFreeRDataFile True True Set of FreeR reflections CMDLMolDataFile True True True True CString 1 CDictDataFile Ligand geometry in REFMAC dict (cif) format True True True True CObsDataFile CFreeRDataFile CDictDataFile CMapCoeffsDataFile 1 2 True CMapCoeffsDataFile 1 1 True CPdbDataFile True CString True UNMERGED,MERGED unmerged,merged UNMERGED Observed data provided as Pipeline can start from merged or unmerged data CString True MOL,DICT,SMILES,SKETCH,NONE MDL Mol file,REFMAC Dict,SMILES String,LIDIA Sketch,NONE SMILES Chemistry of the ligand can be provided in any of the above ways...no ligand means no ligand search CFloatRange Set resolution range (or just high resolution) to cut data for all steps