(Updated 2012 May 17)

Miscellaneous procedure files

Additional procedure files

Matched filter:

• bps-matched.spi -- Computes group reconstructions and applies matched filter to each
• oddeven.spi -- Merges separate odd and even reconstructions

For data recovery:

• goodparticlesbymic.spi -- Generates selected-particle lists for each micrograph
• goodsndc.spi -- Generates doc files for only selected particles
• realign.spi -- Regenerates dala01_*** stacks
• byhand2goodclasses.spi -- Creates select/prj***/goodclasses files from byhand*** files

CTF-related:

• regroup.spi -- Re-generates files using new defocus groupings
• uses output of goodparticlesbymic.spi
• simctf.spi -- Simulates transfer function given a set of defocus groups

Figures:

• montagebyview.spi -- Generates SPIDER and/or TIFF files of montages of particles
• requires mnsfromdoc.spi
• labelmics.spi -- Draws circle around particles in (shrunken) micrographs

For cross-validation ("free FSC"):

• Described in Shaikh T.R., Hegerl R., Frank J. (2003) J Struct Biol. 142: 301-10.
• refproj-freefsc.spi -- Masks soft shell out of Fourier transform of reference
• freefsc.gnu -- Gnuplot script to compare FSC curves before and after cross-validation

For 'AP MQ' compatibility:

• apsh2mq.spi -- Converts 'AP SH/REF' files to 'AP MQ' format for a series of micrographs
• dfapsh2mq.spi -- Converts 'AP SH/REF' files to 'AP M'Q format for a series of defocus-groups
• dfapmq2sh.spi -- Converts 'AP MQ' files to 'AP SH/REF 'format for a series of defocus-groups
• getstats.spi -- Gets minimum, maximum from a series of images

Miscellaneous:

• unstack-frommic.spi -- Unstacks images
• mergeselectbydf.spi -- Merges two selection files
• intersect-by-view.spi -- Generates subsets for each reference-view -- useful for supervised-classification
• intersect-by-group.spi -- Generates subsets of defocus-group selection files -- useful for supervised-classification
• reselect-byview.spi -- Separates defocus-group lists (sel_particles_***) by view -- useful for supervised-classification output
• badparticlesbydf.spi -- Generates doc files for excluded images in the format of goodparticles
• global2df.spi -- Separates global-particle list into defocus groups -- useful for classification of unstacked images (e.g., XMIPP)