Things to Know before running:

This process is highly associated with the previous Manual Picking results where the “seeds” information was stored in the Manual/initParams folder. Of course, you can customize your own “seeds” file by following the principles. For practicing or new users, please finish the 05-Manual Pick before running “Auto Expansion”

Generally, the cross-correlation calculations are performed using the **PEET(Particle) Package**. So, if you have previously used PEET, it would be much easier for you to master the expansion operation. However, this is not necessary since our GUI has integrated all the required modules, and all the PEET processes will be running in the background.

This means, that to use Auto Expansion, the PEET/(Particle) packages must be installed on your machine. The installation instructions can be found here:

Extra-1: PEET/Particle Installation

This section is essentially designed for sequential tasks based on needs as introduced below:

  1. Generate an initial reference from picked particles with/without a template from other places. (Optional. Typically, 50 good seed particles in one tomogram is sufficient)
  2. With a template (from above #1) or from other places (EMDB, etc.), you can get from “seed” particles to an “expanded” particle set for each tomogram. For example, in the HIV gag protein expansion, you can get 3000-5000 expanded particles from the initial 20-30 seed particles per tomogram.
  3. Refine reference from expanded particles. Sometimes, the initial reference generated by #1. is not of good quality. Once you use #2 to get more particles, you can refine your reference/template using the “expanded” particles
  4. With an improved template/reference, run #2 again for better results.

For better management, 3 tabs are used to manage the entire process which includes:

The detailed instructions are listed below.

1. Generate tomograms.star file

2. Pick Parameter