Refined table

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The refined table is the result of the alignment iteration. Dynamo produces one refined table per iteration and reference.

It follows the Dynamo convention for tables. In particular, Dynamo should fill some columns in a refined table during alignment:

  • columns 3 (marks if the particle was actually used for the average produced at the iteration)
  • columns 4-9 (the alignment parameters)
  • column 10 10 (the cross correlation coefficient computed for the alignment particle)
  • column 34: In multireference projects, the reference number that the particle has been assigned to.

Accessing the refined table

The ddb command provides easy access to the results of the project. Here some examples of syntax

Display the name of the last computed table (by default, from reference 1) ddb myProjet:t -d

Display the name of the tables computed for all iterations at one given reference: ddb myProjet:t:ite=*:ref=2 -d

Read the refined table of iteration 3 into workspace variable myTable ddb myProjet:t:ite=1 -d

Sanity checks with the refined tables

During a project, it is useful to check how an alignment is going. The refined table gives a couple of handy options to check it visually.


Checking the aligned particles

You can apply the computed alignment parameters into a few particles to check if they make sense. This is specially useful with membrane proteins.

ddbrowse -p myProject will open ddbrowse onto the data and the last available refined table of project myPoject

ddbrowse

Checking the orientations

You can sketch the positions and orientations of particles after an alignment iteration. This is useful when scanning how a set particles selected by Seed oversampling is evolving during the iterarion.

Use dtplot with the oriented_positions option as profile dtplot