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daverage is the basic command line option for averaging particles in a data folder using alignment parameters expresed inside a table.


The basic syntax of the command is:

 output = daverage('myData','t','myTable.tbl');

where output is an structure recording several items (including of course the density map). If you want to use a linux-like notation, you can produce a left-hand-side output wuth the flag ws (short for workspace), i.e.

daverage myData -t myTable.tbl -ws output


Data folder

The location of the particles can be passed through:


A regular Dynamo table, than can be passed as file or numeric matrix.



The output structure has several fields.

  • .average_raw:
    without compensation for overweighting of fourier pixels
  • .average:
    with compensation for the fourier overweighting
  • .fweight:
    map of overrrepresentation of fourier components in the output property .average_raw
  • .fmask:
    binary mask denoting available fourier coefficients
  • .variance:
    variance map
  • .fsc:
    fsc values
  • .fsc_labels:
    useful information to annotate fsc plots
  • .tags:
    list of tags that did actually contribute to the
                       averaging procedure.
  • This is useful to control which is the final
                       result of confronting which data is available,
                       which tags are marked in the table, and also
                       which particles where excluded.
  • .nanContributions
    map with the number of particles that contributed
                       a NaN value for each pixel.

Averaging procedure

Rotation and shift


NaN compensation

Missing wedge compensation