Question: Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ?
Answer: This can be done in EMAN, though it doesn't use rotational power spectra. Real-space approaches are more accurate, though proper centering is critical. Past attempts at the rotational power spectrum approach (on several test cases) showed it to be unreliable and imprecise.
First, center the particles: cenalignint particles.hed maxshift=<pixels>
- (warning, this can use a lot of memory. You should have 3x as much ram as the size of the file you operate on. If not, use the frac= option)
- or - proc2d particles.hed centered.hed <center | acfcenter>
One of those three should do a decent job centering your particles (they do not need to be in the same orientation).
Then take the centered data and run : startcsym centered.hed <# top view particles to keep> sym=<trial symmetry>
While this is also designed to look for side views, it will find top views (with the corresponding symmetry) very nicely.
So, pick a trial symmetry, and run startcsym. Then look at the first 2 image in classes.hed and the first image in sym.hed. The first image in classes.hed is an unsymmetrized particle with the strongest specified symmetry. The first image in sym.hed is a symmetrized version. If the two look the same and have a visible symmetry, you've probably got the right answer. Repeat for all possible symmetries. The answer will usually stand out very clearly, and can be presented in publication by showing the 2 images side-by-side for each trial symmetry. Note that there are some known situations (detached virus portal complexes, for example) where a single data set may contain particles with multiple symmetries.