spider.protocols.protocol_align_pairwise module

class spider.protocols.protocol_align_pairwise.SpiderProtAlignPairwise(**args)

Bases: spider.protocols.protocol_align_base.SpiderProtAlign

This protocol wraps SPIDER AP SR command (pairwise alignment).

Reference-free alignment (both translational and rotational) of an image series.

This alignment scheme aligns a pair of images at a time and then averages them. Then, the averages of each of those pairs are aligned and averaged, and then pairs of those pairs, etc. Compared to [[http://spider.wadsworth.org/spider_doc/spider/docs/man/apsr.html][AP SR]], this alignment scheme appears to be less random, which chooses seed images as alignment references.

For more information, see Step 2b at [[http://spider.wadsworth.org/spider_doc/spider/docs/techs/MSA/index.html#pairwise][SPIDER’s MDA online manual]]

alignParticlesStep(innerRadius, outerRadius)

Execute the pairwise.msa script to align the particles.

getAverage()

Implemented in subclasses.