(Updated 2013 Jan 21)

Particle verification for single-particle, reference-based reconstruction using multivariate data analysis and classification
As described in J Struct Biol (2008) 161: 41-48.


Outline


Links:

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General notes:

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Recent modifications:

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Quick-start guide

Options limited for the sake of simplicity. For more details, see below.

In toplevel directory (e.g., myproject/):

  1. Unpackage projection-matching batch files
  2. Unpackage verification batch files
  3. Copy params file or spider spi/dat @makeparams
  4. Copy reference volume and/or spider spi/dat @resizevol

In Micrographs/:

  1. mkfilenums.py ../filenums.dat mic*.dat
  2. spider spi/dat @shrink
  3. montagefromdoc.py ../sel_micrograph.dat sm-mic*

In Power_Spectra/:

  1. spider spi/dat @powdefocus
  2. montagefromdoc.py ../sel_micrograph.dat power/pw_avg*
  3. ctfmatch.py power/ctf* &
  4. spider spi/dat @defsort
  5. ctfgroup.py def_sort.dat
  6. spider spi/dat @defavg

In Particles/:

  1. Copy noise file, or spider spi/dat @noise
  2. e2boxer.py
  3. spider spi/dat @eman2spider
  4. spider spi/dat @rewindow
  5. spider spi/dat @numberparticles

In Alignment/:

  1. spider spi/dat @sel_by_group
  2. spider spi/dat @win2stk
  3. spider spi/dat @refproj
  4. ./spider spi/dat @apsh-pubsub &

In Reconstruction/:

  1. spider spi/dat @selectbyviewall
  2. spider spi/dat @filterbyview
  3. spider spi/dat @classify
  4. verifybyview.py
  5. spider spi/dat @combinegoodclasses
  6. (optional) spider spi/dat @recheck
  7. (optional) spider spi/dat @viewaverage
  8. spider spi/dat @histgoodccc
  9. spider spi/dat @goodparticlesbydf
  10. spider spi/dat @dfgoodapsh
  11. (optional) spider spi/dat @select
  12. (optional) spider spi/dat @plotrefviews
  13. (optional) spider spi/dat @display
  14. (optional) spider spi/dat @bestim
  15. ./spider spi/dat bps-pubsub &
  16. (optional) spider spi/dat @slices
  17. spider spi/dat @plotres
  18. spider spi/dat @make_matched
  19. spider spi/dat @matchedfilter
  20. spider spi/dat @consecprepare

In Refinement/:

  1. Edit refine_settings
  2. ./spider pam/dat @pub_refine &
  3. spider spi/dat @plotrefres

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Getting started

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Micrographs -- in Micrographs/ directory

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CTF estimation -- in Power_Spectra/ directory

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Particle-picking -- in Particles/ directory

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Alignment -- in Alignment/ directory

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Verify Particles -- in Reconstruction/ directory

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Compute averages -- also in Reconstruction/ directory

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3D reconstruction -- still in Reconstruction/ directory

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Refinement -- in Refinement/ directory

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Additional batch files

I have some miscellaneous batch files here.