ccp4.protocols.protocol_refmac module¶

class ccp4.protocols.protocol_refmac.CCP4ProtRunRefmac(**kwargs)[source]¶

Bases: pwem.protocols.protocol.EMProtocol

Automatic refinement program in Fourier space of macromolecule structures regarding electron density maps. Generates files for volumes and FSCs to submit structures to EMDB

OutPdbFileName = 'refmac-refined.pdb'¶

PDBSET = 'pdbset'¶

REFMAC = 'refmac5'¶

convertInputStep()[source]¶: convert 3Dmaps to MRC ‘.mrc’ format

createDataDictStep()[source]¶: Precompute parameters to be used by refmac

createMapMtzRefmacStep()[source]¶

createMaskLogFileName = 'mask.log'¶

createRefineScriptFileStep()[source]¶

createRefmacOutputStep()[source]¶

executeMapMtzRefmacStep()[source]¶

executeRefineRefmacStep()[source]¶

refineLogFileName = 'refine.log'¶

refmacMap2MtzScriptFileName = 'map2mtz_refmac.sh'¶

refmacRefineScriptFileName = 'refine_refmac.sh'¶

classmethod validateInstallation()[source]¶: Check if the installation of this protocol is correct. By default, we will check if the protocols’ package provide a validateInstallation function and use it. Returning an empty list means that the installation is correct and there are not errors. If some errors are found, a list with the error messages will be returned.