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 picking with this protocol is divided in three steps: 1) Run with ‘Optimize’ option for several (less than 30) micrographs. 2) Execute the wizard to refine the picking parameters. 3) Run with ‘Pick all’ option to pick particles from all micrographs.

The first steps will use internally the option ‘–write-fom-maps’ to write to disk the FOM maps. The expensive part of this calculation is to calculate a probability-based figure-of-merit (related to the cross-correlation coefficient between each rotated reference and all positions in the micrographs. That’s why it is only done in an small subset of the micrographs, where one should use representative micrographs for the entire data set, e.g. a high and a low-defocus one, and/or with thin or thick ice.

Step 2 uses a much cheaper peak-detection algorithm that uses the threshold and minimum distance parameters.

convertInputStep(micsId, refsId, runType)[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.

isRunOptimize()[source]
useInputReferences()[source]