[3dem] Reliable cryo-EM Resolution Estimation with Modified FSC

[Penczek, Pawel A]

Dear All,

The currently prevalent single-particle resolution assessment methodology is based on Fourier Shell Correlation (FSC).  However, its use remains controversial as the outcome is subjective, mainly due to the necessity to use smooth-edged masks, which introduce artifacts and make it difficult to support the outcome by statistical analysis.

In the article Reliable cryo-EM Resolution Estimation with Modified FSC (mFSC) that just appeared on IUCrJ site (https://urldefense.com/v3/__https://doi.org/10.1107/S2052252520011574__;!!Mih3wA!U-Ahz68KwuVPUNP6BMZ1CSsJVoTLABdO9IdUnCsBWHrnzowqgjv-nocb8Rbi2ha_jw$ <https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1107_S2052252520011574&d=DwMDaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=8P5zavyLYwIWiwPar72EogSpE8PJtfj-B0muENTEnAI&s=Ntn8H-2368avF171GWdLgm2KBTbOhp7T_0jw6Yj8P-U&e=>) I addressed these deficiencies and modified the way FSC is computed.  As a result, the proposed mFSC is free from mask-induced artifacts and thus only binary masks outlining region of interest are used.  Moreover, this modification makes it possible to compute the number of degrees of freedom associated with mFSC coefficients and thus assess the resolution using one-sided Confidence Interval (CI). The use of statistical test prevents users from accepting unreliable results that may stem from using excessively small regions of interest, as in local resolution analysis.  The mFSC program is available at https://urldefense.com/v3/__http://sparx-em.org/sparxwiki/sxresolution__;!!Mih3wA!U-Ahz68KwuVPUNP6BMZ1CSsJVoTLABdO9IdUnCsBWHrnzowqgjv-nocb8RZ6sdpyyg$ .

The mFSC is particularly effective in addressing a number of problems:

  *   Since there are no mask-induced artifacts, it is possible to assess resolution by entirely eliminating solvent regions, i.e., to use masks that coincide with the structure itself

  *   I show that local resolution analysis is of limited value as the spatial resolvability of the outcome is poor. Instead, I suggest using mFSC to compute resolution of biologically relevant segments of the structure or even its secondary elements, such as helices.

  *   mFSC makes it possible to compute artifact-free resolution curves for helical structures (for which standard FSC in most cases fails due to reciprocal space artifacts)

  *   The Confidence Interval-based mFSC all but eliminates subjectiveness of resolution assessment.



Regards,


Pawel A. Penczek, Ph.D.
Professor
Department of Biochemistry and Molecular Biology
The University of Texas - McGovern Medical School
MSB 6.220
6431 Fannin
Houston, TX 77030
USA

phone: 713-500-5416
fax: 713-500-6297
pawel.a.penczek at uth.tmc.edu
https://urldefense.com/v3/__http://www.uth.tmc.edu/bmb/faculty/pawel-penczek.html__;!!Mih3wA!U-Ahz68KwuVPUNP6BMZ1CSsJVoTLABdO9IdUnCsBWHrnzowqgjv-nocb8RZcF7IYlA$ 
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