phenix.protocols.protocol_refinement_base module

class phenix.protocols.protocol_refinement_base.PhenixProtRunRefinementBase(**kwargs)

Bases: pwem.protocols.protocol.EMProtocol

MolProbity is a Phenix application to validate the geometry of an atomic structure derived from a cryo-EM density map.

MOLPROBITYCOOTFILENAME = 'molprobity_coot.py'

MOLPROBITYOUTFILENAME = 'molprobity.out'

MOLPROBITYPKLFILENAME = 'molprobity.pkl'

SUMMARYFILENAME = 'validationSummary.txt'

convertInputStep(tmpMapFileName)

convert 3D maps to MRC ‘.mrc’ format

validateBase(program, label)