AV3 toolbox

AV3 toolbox for averaging of sub-tomograms. Zoom Image
AV3 toolbox for averaging of sub-tomograms.

The AV3 toolbox is a collection of MATLAB for processing of sub-tomograms extracted from larger tomographic volumes (Förster et al, Meth. Cell.Biol. 2007). Core features of the software include averaging of sub-tomograms and classification of sub-tomograms. Notable applications include:

  • Nuclear pore complex in situ (Beck et al, Nature 2007; Science 2004)
  • Retroviral envelope protein complex and GAG in situ (Förster et al, PNAS 2005; Zanetti et al, PLOS Pathogens 2007, Briggs et al, PNAS 2010)
  • Classification of GroEL vs GroEL/GroES (Förster et al, JSB 2008)


The AV3 toolbox is a set of matlab scripts and as such requires MATLAB to run. It is tested with MATLAB version 7.01.

Obtaining AV3

Constrained Principal Component Analysis - Downloads

Förster F, Pruggnaller S, Seybert A, Frangakis AS,
Classification of Cryo-Electron Sub-Tomograms using Constrained Correlation.
J. Struct. Biol., 161:276-286 (2008).

Simulated tomograms of thermosomes in open and closed conformation

after download, rename to .tar.gz files and extract:

Tomograms of GroEL and GroEL/GroES

Simple script for classification in AV3:
% read motif list
motl = tom_emread('motl_es_top800_1.em');motl=motl.Value;
% define missing wedge in data
wedgelist(3,:)= 60;
% mask for classification
% actual classification
[motl, ccc, coeff] = av3_classify(motl, './particle', mask, wedgelist, .0, 3, 5,1, [1,7], 0);
[av1, av1_un] = av3_average_exact(motl, './particle',wedgelist,0.0,1);
[av2, av2_un] = av3_average_exact(motl, './particle',wedgelist,0.0,2);
[av3, av3_un] = av3_average_exact(motl, './particle',wedgelist,0.0,3);
[av4, av4_un] = av3_average_exact(motl, './particle',wedgelist,0.0,4);
[av5, av5_un] = av3_average_exact(motl, './particle',wedgelist,0.0,5);

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