CTFFIND3 with DED camera images and Cs corection

Submitted by egiudice on Fri, 2012-09-07 06:24

Forums

ctffind & ctftilt

Hi
I'm trying to estimate the defocs for a large set of image acquired on a titan Krios with CS correction and a falcon 4K DED camera (no scanner), original magnification is 75000, original pixel size is 0.88713 A.
the image are first coarse by a factor two resulting in a pixel size of 1.77426

I used the latest version of Ctffind3 with the following parameter
GridSquare_00079_FoilHole_0074_Data_0004_20120721_181019_c.mrc
GridSquare_00079_FoilHole_0074_Data_0004_20120721_181019_c_ctf.mrc
0,300,.07,75000,13.30695241497094
256,300,4,8000,50000,1000,100

I arbitrarily put the new dAst parameter to 100 because I don't know how to choose the value (PS in the README file of the package there is actually another parameter in the example command line but it is not described)

I put 0 for the Cs due to the internal correction

I put 13.03069 for the pixel size = 1.77426 A *75000

however the result is not very good with only 1 or two zero visible on the amplitude spectrum, while
comparing with imagic, I can see up to five zero

am I doing something wrong ?

(PS I can include images and output if needed)

Thank in advance

E. Giudice

Axel Fri, 2012-09-07 10:00

Everything seems mostly correct. You could perhaps increase the dAst (the amount of astigmatism you believe is in the data) to 1000 to get a more accurate (but slower) result.
Otherwise, I would also recommend using a lower value for the Resmin (you use 300, I use a value such as 50).
My guess is this is all working quite well, but the background ramp subtraction is not working as well as it otherwise could, and thus you see less of the zeros.

Axel Fri, 2012-09-14 10:20

I guess the question is:

Is the result consistent with what you get out of Imagic?

If you get the same result, then there is no problem, right? The fact that you only see one or two zero does not affect the accuracy of the result, only its visualization.