[3dem] B-factors

[Alexis Rohou]

Dear Henning,

Thanks for bringing this to our attention.

I for one hadn't picked up on this discrepancy until you pointed it out. I
had assumed that all ResLog plots always used Å^2 units. To my mind this is
the only dimensionality that makes sense if we're going to use the "B
factor" concept and wording (in analogy to temperature factors) to describe
incoherent averaging in our reconstructions. I would have thought we'd
always want to give B factors in units of Å^2, following the logic outlined
in R&H2003.

Perhaps Scott and/or co-authors could comment as to why they moved from Å^2
to Å.

Cheers,
Alexis

PS. My understanding of this topic is summarized in section 4.7 of this
2021 book <https://urldefense.com/v3/__https://iopscience.iop.org/book/edit/978-0-7503-3039-8__;!!Mih3wA!EInZgiJTGjny9OeUYvfegswag6cL2aI9L5BOih5sIGlIEB17fQvaYylR2PG7ZLpVAOQHO6FMdGAZKrb0iw$ >. I
regret that I didn't notice this discrepancy in the units at the time of
writing - my text makes the assumption that all ResLog plots use 1/Å^2.
Despite this omission, readers who are not familiar with the topic in
question may still find it a useful introduction. I'd be happy to share
preprints if you do not have access to the final publication.



On Thu, Jan 18, 2024 at 6:27 AM Henning Stahlberg <henning.stahlberg at epfl.ch>
wrote:

>
> Dear Colleagues,
>
> There are two B-factors used in cryo-EM:
>
> Rosenthal and Henderson, JMB (2003) discuss the Guinier plot, where the
> amplitude falloff beyond 10A resolution can be fitted with a B-factor that
> has the unit "Angstromˆ2".
> They also discuss the dependency of the resolution d (in Angstroem) on the
> number # of particles, and provide the basis for a ResLog B-factor, which
> is obtained from the slope of 1/dˆ2 as a function of ln(#).  The numbers of
> particles needed to reach a resolution "d" is then obtained with:
> # = (1/Nasym) * (<S>/<N>)ˆ2 * (30 pi) / (N_e * sigma_e * d) * exp(B / (2 *
> dˆ2))
> The B-factor also in this case is defined as in Angstromˆ2.
>
> Stagg et al., JSB (2014) define a dependency of the resolution d from
> ln(#), with
> d = constant * ln(#) + constant.
> So, here, “d” is linear, not to the square. Their ResLog B-factor is then
> presumably obtained from the first "constant" in that equation, therefore
> in Angstrom,  not Angstromˆ2.
> This is also implemented in CryoSPARC, which also plots 1/d as a function
> of ln(#).
> But other papers, such as Yip et al. and Holger Stark, Nature (2020)
> discuss the ResLog B-factor in Aˆ2 again.
>
> It is interesting for a map to provide all three, the FSC 0.143, the
> Sharpening B-factor in Aˆ2, and the Reconstruction ("ResLog") B-factor in
> Aˆ2.
>
> But, what is the most commonly used definition of the ResLog B-factor, A
> or Aˆ2 ?
>
> Best wishes,
>
> Henning.
>
> Henning Stahlberg
> Laboratory of Biological Electron Microscopy
> Institute of Physics, School of Basic Sciences, EPFL, and
> Dep. of Fund. Microbiology, Faculty of Biology and Medicine, UNIL,
> Cubotron, BSP421, 1015 Lausanne, Switzerland
>
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>
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