This set of web pages will take you through the process of performing a 3D reconstruction from single particle data. These pages will assume that you have a basic understanding of the principles of transmission electron microscopy (cryo or negative stain). Each page will typically contain a minimal outline of the steps you will need to perform, to provide a quick summary for advanced users. Click on one of these outline steps to get detailed instructions for that step. After the description, links to programs associated with this step are provided in parentheses).
Box particles from scanned micrographs or CCD frames (boxer, eman, other programs)
Select the type of particle you have data for:
When beginning a reconstruction you should have some idea of the particle's symmetry. If you know your particle's symmetry, select it from the list below to continue. Sometimes, of course, this simply isn't true. If you don't know your particle's symmetry, you can use symeval to try to determine it. This may or may not give you a conclusive answer. If the answer is inconclusive, the best approach is typically to try a reconstruction with the most likely symmetry, then once a few rounds of refinement are complete, continue refining with no symmetry and see if the model maintains its symmetry.
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