Hello CryoSPARC users! We have just released several new and updated guide pages! A brief summary of the additions and changes follows. We hope that the guide serves as a useful resource for all members of the cryo-EM community regardless of their experience level, and we look forward to hearing your feedback on these pages and any others!
Refinement and Reconstruction
The following refinement and reconstruction pages have been re-written from the ground up:
As with other job page updates, the new pages are in a standardized format and include new figures and explanations of commonly changed parameters. We hope these job pages serve as a useful reference when you’re setting up new refinements!
3D Refinement
The 3D Refinement cover page has been significantly expanded. It now includes detailed discussion of:
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How images are aligned to volumes, included an updated and expanded discussion of the Branch and Bound algorithm
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How volumes are produced from images and poses, including a detailed discussion of the Fourier slice theorem
We expect that this page will be most useful for new users who are learning about refinements for the first time, but it is also helpful as a refresher or teaching aid for advanced users.
Foundations: The FSC and Gold-Standard Refinement
We have added a new Cryo-EM Foundations page discussing the Fourier Shell Correlation and Gold-Standard Refinement. This page provides detailed discussion of:
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Overfitting in cryo-EM
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Why lowpass filtering references helps reduce overfitting
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The derivation and meaning of the Fourier Shell Correlation
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The importance of gold-standard half-set separation in cryo-EM
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The meaning and limitations of the GSFSC resolution
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The impact of mask shape and size on the FSC
It also includes a brief background on the Fourier transform and Fourier space generally. We expect that this page will be most useful for newer users first grappling with the FSC, but advanced users may find it useful in developing an intuitive, qualitative understanding of a topic that is typically approached from an analytical angle.
Symmetry in CryoSPARC
Finally, another Foundations page was added enumerating the symmetry types and conventions in CryoSPARC.