(Updated 2011 Jan 11)

Additional batch files

Matched filter:

• oddeven.spi -- merges separate odd and even reconstructions
• make_matched.spi -- generates match filter doc file
• matchedfilter.spi -- applies matched filter to reconstruction

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 MQ 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:

• 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)