eman2.protocols.protocol_tomo_subtomogram_refinement module

class eman2.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement(**kwargs)

Bases: pwem.protocols.protocol.EMProtocol, tomo.protocols.protocol_base.ProtTomoBase

This protocol wraps e2spt_refine.py EMAN2 program.

Protocol to performs a conventional iterative subtomogram averaging using the full set of particles. It will take a set of subtomograms (particles) and a subtomogram(reference, potentially comming from the initial model protocol) and 3D reconstruct a subtomogram. It also builds a set of subtomograms that contains the original particles plus the score, coverage and align matrix per subtomogram .

OUTPUT_DIR = 'spt_00'

OUTPUT_PREFIX = 'outputSetOfClassesSubTomograms'

convertInputStep()

createOutputStep()

getLastFromOutputPath(pattern)

getLastOutputFolder(files)

getOutputFile(folderpattern, folder, files, pattern)

getOutputPath(*args)

refinementSubtomogram()

Run the Subtomogram refinement.