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?