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Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening.

Abstract：

:The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.

journal_name

J Struct Biol

journal_title

Journal of structural biology

authors

Vilas JL,Vargas J,Martinez M,Ramirez-Aportela E,Melero R,Jimenez-Moreno A,Garduño E,Conesa P,Marabini R,Maluenda D,Carazo JM,Sorzano COS

doi

10.1016/j.jsb.2020.107447

subject

Has Abstract

pub_date

2020-03-01 00:00:00

pages

107447

issue

3

eissn

1047-8477

issn

1095-8657

pii

S1047-8477(20)30001-0

journal_volume

209

pub_type

杂志文章

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