[3dem] B-factors

[Hagen, Wim J.]

Dear Henning,

You mention “ResLog B-factor”, but could that be mixing up two things?

Reslog Analysis, at least in cryoSPARC, uses reconstruction-only for the subsets of particles to build the plot, based on the poses of the particles from 3D-refinement of the full dataset.
https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/post-processing/job-reslog-analysis__;!!Mih3wA!AgY5dBQd-XhHY1O0m5MdiahCiXuZaFNiqzSWPxClQ6CMYaws6iEctqqslya3plYhyszAACzLOR0t1m9fwFWVKVud0Q$ 

The Rosenthal-Henderson B-factor plot, at least in the Relion bfactor_plot.py script, uses 3D-refinement for the subsets of particles.
https://urldefense.com/v3/__https://github.com/3dem/relion/blob/master/scripts/bfactor_plot.py__;!!Mih3wA!AgY5dBQd-XhHY1O0m5MdiahCiXuZaFNiqzSWPxClQ6CMYaws6iEctqqslya3plYhyszAACzLOR0t1m9fwFU1HQk4_g$ 

This makes the outcome of both procedures different, regardless of the units used for fitting the plotted line. Reslog Analysis still serves the quality assessments discussed in Stagg et al, but one could argue that it is not the best indicator for how many (more) particles on needs to get to a certain resolution.

Best,

Wim

From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Alexis Rohou
Sent: 19 January 2024 00:45
To: Henning Stahlberg <henning.stahlberg at epfl.ch>
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] B-factors

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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<mailto: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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