Using different data collection strategies
Depending on the employed software and its features, different strategies can be employed for tilted data collection. Ideally, one would obtain the atlas (and optionally the square and hole images) at 0°, but the high-magnification images would be obtained at a fixed tilt angle. This can be achieved in SerialEM, whereby the tilt angle for the high-magnification image is set independently of the tilt angle for all other low magnification images, thus enabling the user to perform all operations at an angle of 0°, but obtain the high-magnification image at a fixed tilt. This requires that the eucentric height be identified for each high-magnification target. Note however, at the time of this writing, not all software packages support streamlined switching between untilted (low magnification) images and tilted (high-magnification) images. In addition to the technique described above, one can also collect an entire dataset at tilt. For this one would collect the atlas with the stage alpha set to some tilt angle, and perform all data collection at a fixed tilt angle. Both of the above procedures, as well as the one described in the "procedure" section, have been successfully employed.
It should be kept in mind that some programs like to have CTF information prior to picking (e.g. Relion), in which case, it would make sense to first run a global CTF estimation, then pick particles, and then use the resulting particle coordinates to re-do local CTF estimation on a per-particle basis in GCTF.