Spider stacks
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I have been trying to do RCT of my receptor with Michael Radermacher and at this point I want to try FREALIGN v7. I have made a couple of attempts, however, there appears to be a problem with the file format of my images, as FREALIGN gives an error when reading the file. I used EMAN to create stacks for refinement with EMAN and then used em2em to convert them into SPIDER stacks. The original images are stored as single SPIDER files, as that is the format Michael is most comfortable with.
Therefore I have a few questions. Does FREALIGN need the particles to be in a stack? How do I make a stack with selected particles in SPIDER? Do I preserve the angle information for each particle from SPIDER, or do I let FREALIGN assign the initial angles?
Frealign needs a stack of
Frealign needs a stack of images. However, this is a stack that is really just a 3D file. So you have to convert your Spider stack into a 3D file using the Spider command SK (or SK R).
There are a bunch of scripts that might be useful when you try to convert your Spider angles to Frealign angles (see our download page). In particular, gather_spi.com might to more or less what you need.
Finally, the current version of Frealign is 8 (see our download page).