Best parameters for negative stain?

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Daniel Asarnow
Best parameters for negative stain?

Hi cisTEM users,

We haven't yet been able to match Relion or cryoSPARC for negative stain data using cisTEM (yet generally surpassing them with cryo images).

What parameters you all have found to be most useful for negative stain images (2D classification and 3D reconstruction) in cisTEM?



We do not have much

We do not have much experience with negative stain data. One parameter to play with might be the amplitude contrast provided in the ctffind panel. Increasing the value to 0.2 or 0.3 might help suppress some of the strong low-resolution signal that may interfere with the processing.

Daniel Asarnow
Thanks, Niko. Axel has us

Thanks, Niko. Axel has us using 0.4 for negative stain, and setting the 2D class refinement limit to 25 A. I've also just found the smoothing factor has a big impact on over-refinement of the stain artifacts, so I'm re-running the same classification (same random start) with different values to see if something specific can be recommended.

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