Question about corrected half-maps

[Vitor Hugo Balasco Serrão]

Hi there,

My apologies for the naive question, but I've been playing with spisonet in some datasets, and what would be the most appropriate way to proceed after it? 

I mean, we have the corrected half-maps, would the only option refine it in Relion or can we use other approaches (loading into cryosparc, trying deep-enhancer, etc)?

I'd like to hear your thoughts and suggestions what is the best way to proceed after using spisonet.

Thank you!

Vitor Hugo Balasco Serrão, Ph.D.

Research Specialist

Biomolecular Cryo-Electron Microscopy Facility

Department of Chemistry and Biochemistry

University California - Santa Cruz

1156 High St - Santa Cruz, CA - 95060

Phone: +1 831/4007378

vbal...@ucsc.edu

[YUNTAO LIU]

Hi Vitor Hugo Balasco,

First, the misalignment correction with relion_wrapper is similar to a regular RELION refinement. You can perform any post-processing or continue with anisotropy correction using spisonet.py reconstruct.

Second, if you are using spisonet.py reconstruct, the results are corrected half-maps. You can perform post-processing on these maps using either RELION or cryoSPARC, and you may also manually test different B-factors. Based on my knowledge, sharpening results from RELION and cryoSPARC are similar. Automatic modeling tools like ModelAngelo should work well with spIsoNet-generated maps. Other tools, such as deep enhancers, are also applicable.

The local resolution estimation tools should provide accurate results, but be aware that the FSC for spIsoNet-generated maps is not gold-standard unless you use the --independent argument with spisonet.py reconstruct. Finally, if you plan to deposit spIsoNet-generated half-maps, you may need to include the pre-correction maps as well, even though spIsoNet is "conservative" due to its self-supervised nature.

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Vitor Hugo Balasco Serrão]

Thank you, Yuntao. This is very useful and I'll try to follow these steps.

Best,

Vitor Hugo Balasco Serrão, Ph.D.

Research Specialist

Biomolecular Cryo-Electron Microscopy Facility

Department of Chemistry and Biochemistry

University California - Santa Cruz

1156 High St - Santa Cruz, CA - 95060

Phone: +1 831/4007378

vbal...@ucsc.edu