Tilt angle convention
By default, Dynamo, IMOD and novaCTF all use the same convention for the sign of the tilt angle of an image within a tilt series: At positive tilt angles, the right side of the tilt images is expected to be more underfocused than the left side. To get the right handedness and to ensure a correct CTF correction with those tools, it is recommended to test that the angles in the tilt file of a corresponding tilt series are following this convention. It can be easiest done by estimating the defocus on the left and right side the tilt series and plot it against the angles of the corresponding tilt angle file. The result should look more or less like this:
If this is not the case, the angles in the tilt file have to be adapted accordingly. To be completely certain, a rearrangement of the angles and images in the stack could be made so that it fits the above convention and the first angle in the tilt file is at -60.
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