Output values

Submitted by Unknown on Wed, 2009-12-09 19:17

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ctffind & ctftilt

My question regards the output I get from ctffind3:

In your paper titled "Accurate determination of local defocus and specimen tilt in electron microscopy," the two defocus values computed by ctffind for image b3730 (given in Table 1) are said to be 597.5 nm and 525.1 nm. Using ctffind3.exe I entered the exact parameters described in page 339 of that paper, and I can't seem to make sense of the output I get.

For CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]

I entered

2.0, 200.0, 0.07, 60000.0, 7.5

and for Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep

I entered

128, 20.0, 0.3, 100.0, 1000.0, 50.0

to get this output:

REFINING CTF PARAMETERS...

DFMID1 DFMID2 ANGAST CC

700.00 750.00 43.93 0.01308 Final Values.

Do DFMID1 and DFMID2 correspond to DF1 and DF2, respectively? Is there is something that I am doing wrong and/or that I am missing?

niko Wed, 2009-12-09 19:19

The refined values you obtained are incorrect (they are in A, not in nm). You should get the correct (or close to correct) values when you increase the search range. Use 1000, 5000, 500 for dFMin[A], dFMax[A], FStep, and 20.0,3.0, for ResMin[A], ResMax[A] (0.3 A is probably well beyond the Nyquist limit of your images).