.eer versus .tif formats

Hi! I am new to CryoEM. Have 3 datasets, one of which was imported in .tif format, the other two were .eer. Should it give worst resolution of the overall model if analysing .tif?

The search on line says it should not matter. An yet…

Welcome. :slight_smile:

All else being equal, the format the data is saved in shouldn’t matter to any appreciable degree. The limit is almost always the grid preparation and the sample preparation or biochemistry of the sample (e.g.: sample stable and whole in cryo-EM but inactive in assays, or active in assays but higher than ideal percentage broken in cryo-EM…)

There are some cases where EER has an advantage over TIFF or MRC, although this is mostly in flexibility of how you motion correct and/or Bayesian polish/Reference Based Motion Correct your data.

The primary advantage of TIFF is file size (storage used) but you are “stuck” with what you acquire if for whatever reason you manage to get to resolutions higher than expected (although there are ways around that). Thus, if you take counting mode data and hit the Nyquist limit, you need to employ PASR to exceed that, while if when acquiring super resolution data you don’t hit the (physical) Nyquist limit, your data is taking up 4x more storage than it really needs to.

However, EER data can be resampled from 4K (physical Nyquist), 8K (super resolution) or 16K (double super resolution is what I’ve taken to calling it) but so far outside of a single “how far can this be pushed?” run, I’m not aware of anyone working with 16K data as hardware demands, both for storage and processing become rather extreme (I saw ~1.5TB RAM used for a single Bayesian polishing process).

Currently what you use will depend on your detector. Gatan K2 or K3 and you’ve got no choice but to use TIFF. With a Falcon 4(i) it used to be just EER or MRC (which almost no one uses any more…)but now that Thermo Fisher Scientific have added TIFF saving to EPU with the latest release, there is a more “storage friendly” option.

That said, even with the ability to save as TIFF, I still collect everything as EER. I’ve had a lot of samples where the flexibility EER provides has given me improvements.

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Thank you for the reply, rbs_sci.

We actually have .eer and then just convert files to .tif.

I am trying to figure out what is exactly the reason that we cannot go beyond resolution 7-8 A. One of the possible issues is the sample itself.

Anyways, thank you.

Yes, could be a range of issues. Can you provide some more information? Total micrographs, total particles, size of particles, quality of 2D classes, particles in good classes, etc.? If it’s not confidential, some images (representative micrograph, 2D classes, initial model) might allow further help.