spider.protocols.protocol_projmatch module

class spider.protocols.protocol_projmatch.DefocusGroupInfo(defocusGroup, template, ih)[source]

Bases: object

Helper class to store some information about defocus groups like the number of particles or the docfile to be generated.

addParticle(img)[source]
close()[source]
class spider.protocols.protocol_projmatch.SpiderProtRefinement(**kwargs)[source]

Bases: pwem.protocols.protocol_3d.ProtRefine3D, spider.protocols.protocol_base.SpiderProtocol

Reference-based refinement using SPIDER AP SHC and AP REF commands.

Iterative refinement improves the accuracy in the determination of orientations. This improvement is accomplished by successive use of more finely-sampled reference projections.

Two different workflows are suggested: with defocus groups or without (gold-standard refinement).

For more information, see: [[http://spider.wadsworth.org/spider_doc/spider/docs/techs/recon/mr.html][SPIDER documentation on projection-matching]]

alignStep()[source]

Create new stacks and selfiles per defocus groups

convertInputStep(particlesId)[source]

Convert all needed inputs before running the refinement script.

createOutputStep()[source]
mergeStep()[source]
projectStep(volumeId)[source]
reconstructStep()[source]
runScriptStep(script)[source]

Just run the script that was generated in convertInputStep.