relion.protocols.protocol_bayesian_polishing module

class relion.protocols.protocol_bayesian_polishing.ProtRelionBayesianPolishing(**args)

Bases: pwem.protocols.protocol_particles.ProtParticles, relion.protocols.protocol_base.ProtRelionBase

Wrapper protocol for the Relion’s Bayesian Polishing.

As of release 3.0, Relion also implements a new Bayesian approach to beam induced motion correction. This approach aims to optimise a regularised likelihood, which allows us to associate with each hypothetical set of particle trajectories a prior likelihood that favors spatially coherent and temporally smooth motion without imposing any hard constraints. The smoothness prior term requires three parameters that describe the statistics of the observed motion. To estimate the prior that yields the best motion tracks for this particular dataset, we can first run the program in ‘training mode’. Once the estimates have been obtained, one can then run the program again to fit tracks for the motion of all particles in the data set and to produce adequately weighted averages of the aligned movie frames.

OP_POLISH = 1

OP_TRAIN = 0

convertInputStep(movId, partId, postId)

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(id=1)

trainOrPolishStep(operation)