Values for FPART and DFSTD
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A few questions about frealign v8.07:
- what does FPART in card1 refer to?
- what does DFSTD in card7 refer to and what kind of values should it get?
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A few questions about frealign v8.07:
- what does FPART in card1 refer to?
- what does DFSTD in card7 refer to and what kind of values should it get?
First, I would recommend
First, I would recommend using the latest version of frealign from our web page.
Your questions:
FPART refers to defocus refinement per particle. So if you set FDEF = T and FPART = F, defocus is refined per micrograph (FILM in the parameter file). But if you think you have sufficient signal (good images of large viruses), you can try refining the defocus for each particle separately (FPART = T).
DFSTD is only important if you do defocus refinement. If you do not do defocus refinement, it can be set to any value (for example 0.0). If you refine the defocus, set DFSTD = 200.0, for example. DFSTD indicates how certain or uncertain you are about the defocus values you obtained initially (on input).
A word about defocus refinement: The values you get from CTFFIND3 or CTFTILT are pretty good and should get you to at least 4.5 A. If you think you have excellent data, then you can perform one round of defocus refinement. You should not need two or more rounds. If you use more rounds, the defocus values can significantly shift from their original values and might be less accurate than they were before refinement.