EMAN Tutorial

How to do a Reconstruction

Particle with icosahedral symmetry

WARNING: While EMAN does have support for icosahedral symmetry, it has not yet been tested or optimized completely. It may work well, it may work poorly, it may not work at all (depending on the particle). In the release version this support should be more complete, with options for using techniques specific to icosahedral particles. Feel free to experiment with the current version, but please don't judge the program based on the current state of icosahedral reconstructions!

The first step in performing an icosahedral reconstruction is generating a preliminary model. This is accomplished by searching for particles with 5 fold, 3 fold and 2 fold symmetry. These 3 views are then used to construct an initial model which is then refined. No CTF correction is done in this part of the procedure. The model generated here is usually very bad. This is expected and is not a problem. Don't expect this model to look anything like your final reconstruction.

  1. Determine defocus of particles from each micrograph. (ctfit)

  2. Combine particles from micrographs with similar defocus and filter at the first zero. (proc2d)

  3. Center the particles within their boxes. (cenalignint)

  4. Use starticos to generate a preliminary model. (starticos)

  5. You can optionally remove the intermediate files.

  6. Now you should decide if you want to do CTF correction or not:

Yes, I want to make a CTF corrected structure.

No, I'll try the uncorrected structure first.


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