[3dem] Resolution estimate: FSC vs PDB modeling

[Edward Egelman]

I feel compelled to respond to this, as I am the "senior colleague". The 
paper under discussion appeared recently in Nature (2014), Mukherjee et 
al. Let me correct the record. If one compares the map (EMDB-5795) with 
the atomic model (4MTH) all correlation disappears at better than about 
16 Angstroms, so the statement that there was strong correlation at 9.2 
to 15 Angstroms is wrong. I urge others to make this comparison 
themselves. This led me to raise questions about the 9.2 Angstrom 
resolution claim for the map. As far as I can see, after more than 20 
emails exchanged with Dr. Jiang before the submission of the paper, this 
resolution claim was simply fraudulent. That was why I asked for my name 
to be removed from this paper! I would welcome, however, for the cryo-EM 
field to move to a "reality-based" standard of resolution, and this 
paper provides a good basis for discussing why such a standard is needed.
Regards,
Ed Egelman

On 3/12/14, 8:47 AM, Qiu-Xing Jiang wrote:
> Dear colleagues,
> This has been a topic discussed in a couple of map validation papers. 
> I have a scenario encountered in a recent project and would like some 
> input from those interested.
> We had a filament complex reconstruction, made of a small protein 
> whose crystal structure contains mainly loops held together in the 
> core by three pairs of disulfide bonds. At the time of resolution 
> estimation, we used two independent maps calculated from either 
> randomly selected halves or top/bottom halves to calculate FSC as 
> usual in SPIDER. The FSC0.5 of the former gives 9.2 angstroms, which 
> is more conservative than the FSC0.143 of the latter, and was used as 
> a nominal estimate.
>
> The other opinion  from a senior colleague was PDB modeling, whose 
> operations are to dock the X-ray structures of individual units into 
> the map (assuming no change), filter the resulted PDB model to 
> different resolutions, and visually determine at which resolution the 
> map calculated from the PDB model and the experimental density map 
> match the best(at certain thresholds), and could then be used for 
> resolution estimate. When we were operating this procedure, we knew 
> that our filaments had lipids associated and our map was not good 
> enough to resolve the loops on the surface of the individual units in 
> the filament. To make  the two maps match well to our eyes, we had to 
> filter both to 12-15 angstroms, which would then say the resolution 
> was 12-15 A. The calculated cross-correlation between the map from the 
> pdb model and the experimental map was high at 9.2-15 range, but we 
> were not sure whether it would be decisively meaningful.
>
> We had debates and disagreements on which to report. At the end we 
> decided to use FSC0.5 as usual, and refrained from interpreting the 
> map with mutations at the subunit interface due to the experience of 
> PDB modeling. I  wonder if some of you had similar experience, and 
> more generally whether PDB modeling is suitable to replace FSC.
>
> Thanks for sharing your experience.
>
> Best regards,
>
> Qiu-Xing
>
>
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>
> UT Southwestern Medical Center
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>
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-- 
Edward H. Egelman, Ph.D.
Professor
Dept. of Biochemistry and Molecular Genetics
University of Virginia

President-Elect
Biophysical Society

phone: 434-924-8210
fax: 434-924-5069
egelman at virginia.edu
http://www.people.virginia.edu/~ehe2n

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