Extracting particles

This mini-tutorial will explain how to extract a set of particles from multiple tomograms in a Dynamo catalogue.

Prerequisites

• a Dynamo catalogue containing your tomograms

• models for the particles you wish to extract saved in the catalogue

If you have been picking your particles/supporting geometries in dtmslice, opened from the catalogue manager (dcm) then you’re ready to go!

The procedure

Open your catalogue in dcm and click through the tabs below to see the whole procedure

select tomograms

Select the tomograms you would like to crop from (or use the select all button)

create volume list

The volume list manager can create volume list (.vll) files containing the information needed for cropping particles.

Open the volume list manager from the Crop particles menu at the top of the dcm window.

Create a volume list (.vll) file by

• picking the models from which you want to crop in the GUI

• hitting the create list button.

extract particles

Note

Dynamo data folder A Dynamo data folder contains

• Subvolumes for each particle

• Alignment metadata for each particle (crop.tbl)

• A tomogram-table map file (indices_column20.doc)

In the particle extraction GUI which pops up

• set the particle sidelength to your desired box size

• hit crop particles.

This will generate a Dynamo format data folder in the current directory with the name in the data box.

Attention

We use the data folder in dBoxes… option here to avoid problems with having thousands of files in the same directory. Read more here.

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Once complete, you will have a Dynamo format data folder containing your particles, you’re ready for refinements!