Hello,
I am a structural biologist studying single-particle protein structures using CryoSPARC.
I have a question regarding particle picking methods such as template picking or TOPAZ training.
I am wondering if these approaches might introduce phase bias.
Of course, for well-resolved and homogeneous particles, this may not be a major concern.
However, I am currently working with very low-resolution particle data, focusing only on explaining particle orientations rather than achieving high-resolution reconstructions.
In this context, if I selectively pick particles located at positions where I hypothesize they should be, and then generate a 3D map based on those,
would it be problematic to claim that only a subset of particles adopt such a conformation, among the many possible structures?
Hi @JHKIM, welcome to the forum!
You’re right that, as with phase bias in x-ray crystallography, template bias is a concern in cryoEM. However, during template picking both the templates and the micrographs are lowpass filtered (to 20 Å by default). Thus, if your final reconstruction has a better resolution than this, you can be more confident that you’ve uncovered a real result.
As for the second part of your question, I think if all maps are believable, you can safely claim that some particles adopt each of the conformations you find. However, I would personally not make any claims about relative population of each state/conformation. We discuss this more in a recent workshop recording if you’re inteterested in hearing more.
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