ctffind3 versions
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Hi Niko,
am currently testing version 3.2 and 3.3 of ctffind3.
Interestingly, when I use the same images to determine defoci/ang parameters with both version, I do get different output values in both, defoci and ang.
Also, the output image from version 3.2 shows crisp Thon rings ... compared to the output form the newer version. Is there any post-processing done with the output image ? Can you let me know, what has changed going from version 3.2 to 3.3 and whether the parameters obtained from the previous verions are still valid ?
Best,
-T.
V 3.2
REFINING CTF PARAMETERS...
DFMID1 DFMID2 ANGAST CC
31602.04 33185.19 78.56 0.22147 Final Values
V 3.3
DFMID1 DFMID2 ANGAST CC
33275.07 31649.47 -7.38 0.20085 Final Values
The difference between
The difference between versions 3.2 and 3.3 is the low-resolution limit set internally in the program. In version 3.2, the lowest allowed resolution was 20 Å. If a user set the low-resolution limit to a lower value, it was internally reset to 20 Å. The low-resolution limit prevents the high intensity near the origin of the power spectrum to be included in the CTF fit. However, some users found that the 20 Å limit was to high and the CTF fit failed. In the new version 3.3 the limit is now 50 Å. Users should always check in the diagnostic output of the fit if they have set their low-resolution limit appropriately to exclude the high intensity at the origin. If some of this strong intensity is included, it may lead to inaccurate results. The inclusion of the high intensity will also scale the power spectrum differently and lead to an impression of weaker Thon rings, as you describe in your example.
In your example, the two results are very similar. The main difference is the order of the two defocus values, DFMID1 and DFMID2. However, the angle, ANGAST is also different, by about 90°. Therefore, the ellipse described by the three values remains almost the same and the fit should be almost the same. Smaller differences of 100 Å or less are within the accuracy of the measurement and, therefore, insignificant.