phenix.protocols.protocol_emringer module

class phenix.protocols.protocol_emringer.PhenixProtRunEMRinger(**kwargs)

Bases: pwem.protocols.protocol.EMProtocol

EMRinger is a Phenix application to validate the agreement between the initial map and the derived low-resolution atomic structure. This program samples the density around Chi1 angles of protein sidechains. Electronic density and appropriate rotameric angles must coincide for each residue if the atomic structure backbone has been perfectly fitted to the map.

EMRINGERFILE = 'emringer.map'

EMRINGERMAXZSCOREFILENAME = 'zscores.pkl'

EMRINGEROPTIMALTHRESHOLDFILENAME = 'thresholds.pkl'

EMRINGERROTAMERRATIOSFILENAME = 'rotamer_ratios.pkl'

EMRINGERSCORESFILENAME = 'emringer_scores.pkl'

EMRINGERTRANSFERFILENAME = 'emringer_transfer.txt'

convertInputStep()

convert 3D maps to MRC ‘.mrc’ format

createOutputStep()

is_tool(name)

Check whether name is on PATH.

runEMRingerStep()