The process of generating a preliminary 3D model begins with raw single particle data. This data is prepared by boxing out particles from scanned micrographs or CCD frames. This process can be performed with a variety of different programs. EMAN has a program called boxer which allows for rapid, easy manual and semiautomatic boxing of images.
For generating a preliminary model, particles from micrographs/frames at a similar defocus should generally be used. No CTF correction is performed at this point.
Particles may then be centered with cenalignint or cenalignacf if they were not centered in boxer. The centered particles are then filtered at the first zero of the Contrast Transfer Function (CTF). An appropriate radius can be determined using ctfit. Then the data can be filtered using proc2d.
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