Question:[:FAQ EMAN USING 22:How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ?] Answer:

• Not exactly. The curve from your data (the power spectrum) is equal to noise + ctf * envelope * structure factor. The curve you're fitting with is just noise + ctf * envelope. The structure factor is missing, and is very important. This problem can be tackeled three ways, described in : the documentation. If you're in the situation where you don't have x-ray data (which you presumably don't), the best results are generally achieved via the following process:

1) you will need several data sets at different defocuses 2) read the first data set into CTFIT 3) set the 'amp' to zero, then use the 4 noise sliders to fit the background by passing through the zeros of the the ctf, and matching the high-resolution end of the curve (where the zeros are no longer visible).

4) Increase the amplitude and adjust the defocus and envelope function as best you can. You should be able to determine the defocus quite accurately. The envelope function is somewhat arbitrary.

5) Read in the second data set, and repeat this process for it. 6) Bring up a second plot window, and set it to display the structure factor. This will show the structure factor for each displayaed data set, calculated from the data. This is not a very accurate calculation, but it's generally good enough.

7) Now, without spoiling the fitting you've just done, adjust all of the parameters of the 2 data sets such that the structure factor curves match as well as you can. Don't worry too much about the divergence at high frequency. Work on getting a match out to the first or second zero, then just try to get the general trend at high frequency to be the same.

8) continue to add the other data sets in the same way. 9) When you've got them all fitted satisfactorally, use the 'phase correct' option as described in the instructions.