emantomo.protocols.protocol_tomo_subtomogram_refinement module

class emantomo.protocols.protocol_tomo_subtomogram_refinement.EmanProtTomoRefinement(**kwargs)[source]

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()[source]
createOutputStep()[source]
getLastFromOutputPath(pattern)[source]
getLastOutputFolder(files)[source]
getOutputFile(folderpattern, folder, files, pattern)[source]
getOutputPath(*args)[source]
refinementSubtomogram()[source]

Run the Subtomogram refinement.