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 boxing of images. Eventually this program will include options for automated particle selection, but for now, if you wish to try automated particle selection, you'll have to try another program, such as Pam Thuman-Commike's PTOOL.
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.
Once the particles have been selected and saved in a single file, they should be centered within the box. This process can be performed with cenalignint.
The centering process will generate 2 files: ali.img and bad.img. Any particles which could not be consistently centered are placed in bad.img. The good particles in ali.hed may then optionally be filtered to help reduce high frequency noise. Ctfit can be used to determine a good filter radius to use (just after the 1st zero of the CTF), then proc2d can be used to filter the data.
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