Half maps made of noise

Dear cryosparc community,

I hope you can help me with this!

I have a volume coming from 60,000 particles for a 500 kDa complex. The volume ranges between 3 A side chain resolution at the core of the complex, and blob like features in the periphery of the complex. Flexibility is an issue, in fact the only way to get a volume that was not stretched in one direction was to use 3DVA. Overall, the volume is interpretable and the model fits the density reasonably well.

The problem is the half maps. At the first iteration of NUref, they look very similar to my usual density, more noisy but still a solid volume. At the end of it, the half maps are pure noise. I can still recognize the shape of my protein, but made of “dust”. All around it, also noise. This is how the cross correlation graph looks like at the end of the refinement

I noticed the same issue in another unrelated volume, also coming from an even smaller particle stack.

What do you think the cause might be? Is it normal? Of course, this is an issue for deposition and for any validation of the model against the half maps, and I am worried something is off with the data.

Every help is highly appreciated, thank you!

Normal from your description. The half maps are not filtered, and your Nyquist res is at ~1.3Å - so there will be a lot of high frequency noise in the unfiltered maps.

If you want to convince yourself, try importing one of them and use Volume Tools to filter it to the GS-FSC resolution (3.1Å) - what does it look like then?

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Thank you for your quick reply!
Indeed, when importing and filtering, the volume looks again like my protein volume.

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