[3dem] summary about the question on Resolution estimate: FSC vs PDB modeling

[Michael Chapman]

Qiu-Xing & others, ... adding to some of the excellent prior comments...

There appears wide consensus that comparison to a (homologous) PDB is preferable in (the minority of) cases, like the one discussed, where such a model is available.  Many of the challenges noted have been overcome in an objective assessment described in Chapman et al, 2013.  The algorithm is to convolute the atomic map with a Butterworth low-pass filter, least-squares refining the cut-off frequency for maximal agreement of atomic and EM maps for voxels in the neighborhood of (selected) atoms.  The result is converted to a resolution where the fitted signal falls below a threshold, so is analogous to FSC or FCR.  However it reflects attenuation of signal rather than signal:noise ratio, so might be more appropriate for assessment of information content, but less appropriate for filtering decisions etc. during processing.

This approach revealed the overestimation of resolution in the Mm-Cpn structure as later confirmed through Gold Standard assessment by the original authors.  As part of other work, Scott Stagg & colleagues compared it to other metrics over a range of resolution regimes. It is implemented as part of last year's release of RSRef.

Chapman, M.S., A. Trzynka, B.K. Chapman, 2013. Atomic modeling of cryo-electron microscopy reconstructions - Joint refinement of model and imaging parameters. J Struct Biol 182, 10-21.
Stagg, S.M., A.J. Noble, M. Spilman, M.S. Chapman, 2014. ResLog plots as an empirical metric of the quality of cryo-EM reconstructions. J Struct Biol 185, 418-26.

Michael.
Michael S. Chapman, R.T. Jones Professor of Structural Biology
Dept. Biochemistry & Molecular Biology; School of Medicine, Mail Code L224
Oregon Health & Science University
3181 Sam Jackson Park Road; Portland, OR 97239-3098
chapmami at ohsu.edu / (503) 494-1025; http://xtal.ohsu.edu/


-----Original Message-----
From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of Qiu-Xing Jiang
Sent: Thursday, March 13, 2014 4:23 PM
To: Qiu-Xing Jiang
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] summary about the question on Resolution estimate: FSC vs PDB modeling

Dear all,
Thanks for all the comments regarding my question of FSC vs PDB modeling in resolution determination. If interested, please read the paper (Nature
505:103-07) on the origin of this question. I would like to point out that the team of people working on the lectin project had a favor for using the conventional "gold-standard" FSC as a resolution estimator and conservatively using the structural information to understand the biological process, to be on a safe side.

>From different responses, there are divided opinions on using PDB modeling to replace FSC. With Dr. Egelman's lead on the development, it may soon be different. Interestingly, all three responses I received about ResMap are pretty positive. Likely more people will agree with them. We may have a good solution to the question already.

With regards.
Qiu-Xing


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