relion.protocols.protocol_autopick_ref module

class relion.protocols.protocol_autopick_ref.ProtRelion2Autopick(**args)

Bases: relion.protocols.protocol_autopick.ProtRelionAutopickBase

This protocol runs Relion autopicking (version > 3.0).

This Relion protocol uses the ‘relion_autopick’ program to pick particles from micrographs, either using references (2D averages or 3D volumes)

The wrapper implementation does not read/write any FOM maps compared to Relion

convertInputStep(micsId, refsId)

Create the input file in STAR format as expected by Relion. If the input particles comes from Relion, just link the file. Params:

particlesId: use this parameters just to force redo of convert if

the input particles are changed.

createOutputStep()

getAutopickParams()

getBoxSize()

Return a reasonable box-size in pixels.

getInputDimA()

Return the dimension of input references in A.

getInputReferences()

getMicrographList()

Return the list of micrographs (either a subset or the full set) that will be used for optimizing the parameters or the picking.

useInputReferences()