Possible errors in pixel size

In the output rotational average file (my_amp_rot.mrc), is the bright ring (2.4A gold ring?) supposed to be fully visible within the mask if expert options are set to 'NO'?
In my test, at some magnifications, the ring is cut off by the inner circle of the mask. Does that indicate the pixel size I input is wrong? The ring becomes fully visible if I change the resolution limits in the expert options. Actually different resolution limits give me different results.
In addition to the results of estimation, is there a parameter that can indicate the confidence of the estimation?


By design the default settings are supposed to select the 2.4A ring and a small amount on either side. If the ring is being masked for you, then this suggests either your pixel size is not calibrated correctly or that there is a bug in the program. How has your pixel size been calibrated?

When you say you get different results with different resolution limits, how different are they? If the ring is being masked out then the estimation will definitely be affected.

Whilst there is not really a parameter to indicate the confidence of the estimation, the output images can be used to judge. If you exactly overlay the 3 images, and flick between them, you should see that the ring position changes slightly between the amplitude image and the rotational average file (if you have distortion), the corrected image should not change position relative to the rotational average (if the estimation has worked).


My bad. I did use the wrong pixel size.
With the correct value, everything looks normal. I also slightly vary the resolution limit, the results are almost the same, only the distortion angle changes by 0.3 deg.
Thanks for the explanation.