relion.protocols.protocol_autopick_ref module

class relion.protocols.protocol_autopick_ref.ProtRelion2Autopick(**args)[source]

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)[source]

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()[source]
getAutopickParams()[source]
getBoxSize()[source]

Return a reasonable box-size in pixels.

getInputDimA()[source]

Return the dimension of input references in A.

getInputReferences()[source]
getMicrographList()[source]

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

useInputReferences()[source]