eman2.protocols.protocol_refineasy module

class eman2.protocols.protocol_refineasy.EmanProtRefine(**kwargs)[source]

Bases: pwem.protocols.protocol_3d.ProtRefine3D

This protocol wraps e2refine_easy.py EMAN2 program.

This is the primary single particle refinement program in EMAN2.1+. It replaces earlier programs such as e2refine.py and e2refine_evenodd.py.

Major features of this program:

  • While a range of command-line options still exist. You should not

normally specify more than a few basic requirements. The rest will be auto-selected for you. * This program will split your data in half and automatically refine the halves independently to produce a gold standard resolution curve for every step in the refinement. * An HTML report file will be generated as this program runs, telling you exactly what it decided to do and why, as well as giving information about runtime, etc while the job is still running. * The gold standard FSC also permits us to automatically filter the structure at each refinement step. The resolution you specify is a target, NOT the filter resolution.

convertImagesStep()[source]
createLinkSteps()[source]
createOutputStep()[source]
refineStep(args)[source]

Run the EMAN program to refine a volume.