[3dem] sharing em maps during peer-review process

Thu Apr 30 15:17:15 PDT 2015

dear all,

thank you very much for sharing your experiences. we will then certainly
also follow the example of others in the field.
just to answer gabe's point about one potential way of misuse: a
high-resolution map of course greatly facilitates model building. however,
the resulting model will also be the best explanation for lower resolution
data, one just would not have found this solution. it may take a pretty
good reviewer to figure out that the lower resolution data do not justify
the correct biological conclusions.
So let us just adhere the ethical principles we should and share the data.

cheers

friedrich

On Thu, Apr 30, 2015 at 11:46 PM, Gabriel Lander <glander at scripps.edu>
wrote:

> I would like to echo Eva & Ed’s comments (I am also NOT a reviewer).
> Given that the EM field hasn’t really settled on a robust methodology to
> statistically assess the accuracy & validity of a density (yes we have gold
> standard FSC, local resolution plots, tilt-pair validation, etc. but these
> are not 100% foolproof, & there are ways to inflate resolution
> nonetheless), we generally rely on our eyes to ascertain the quality of map.
>
> I’m sure your density doesn’t fall into this category of “inaccurate”
> structure determination, so I’m curious what you think a reviewer might do
> with your density to misuse it?
> I agree with Ed that all densities should be uploaded with a submitted
> manuscript, and I am happy to do this for any manuscripts we send out.
> -gabe
>
>
> On Apr 30, 2015, at 2:16 PM, Eva Nogales <enogales at lbl.gov> wrote:
>
>  Hi Friedrich,
>
> We got the same request and we provided the map and model as a Chimera
> session to the editor and reviewer. I understand your point, but we have to
> trust the system and understand where the reviewers may be coming from. We
> do know of more than one example where having had such access  may have
> precluded publication of some really terrible structures. It will be
> interesting to hear what others think (and I have no doubt the reviewer(s)
> that asked for your and our maps is/are within the list reading this
> email...)
>
> Eva
>
> On 4/30/15 1:49 PM, Friedrich Foerster wrote:
>
>    dear colleagues,
>
>  i would be interested in experiences / suggestions / views of others in
> the field on  the following issue that may be of interest to many of us:
>  the editor of our manuscript forwarded the request of a peer-reviewer to
> access the cryo-em map of our beloved complex. this has never happened to
> us, but to our surprise the editor did not consider the request to be
> unusual.
> of course, we share the point that the map would be of great help in
> judging the interpretation of the data. however, we also feel very
> uncomfortable sending the condensed result of lengthy research to an
> anonymous colleague, who could theoretically make considerable misuse of
> it. nevertheless, the policy of the journal seems to let us little choice: "Supporting
> data must be made available to editors and peer-reviewers at the time of
> submission for the purposes of evaluating the manuscript. Peer-reviewers
> may be asked to comment on the terms of access to materials, methods
> and/or data sets".
>  in any case we would be curious whether others indeed got similar
> requests and how they dealt with it. a good solution for (paranoid?) people
> like us could be a good web-based viewer that lets others view our map, but
> i would not know of such a tool.
>
>  Thanks
>
>  Friedrich
>
> --
> Dr. Friedrich Foerster
> Max-Planck Institut fuer Biochemie
> Am Klopferspitz 18
> D-82152 Martinsried
>
> Tel: +49 89 8578 2632
> Fax: +49 89 8578 2641
>
> www.biochem.mpg.de/foerster
>
>
>
> _______________________________________________
> 3dem mailing list3dem at ncmir.ucsd.eduhttps://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> --
> __________________________________________________________________
>
> Eva Nogales
> Howard Hughes Medical Institute
> Molecular and Cell Biology Department
> QB3, Stanley Hall 708C
> University of California, Berkeley
> Berkeley, CA 94720-3220
>
> Phone: (510) 642-0557		Fax: (510) 666-3336			
> URL: cryoem.berkeley.edu(510) 666-3334		Teresa Tucker, Assistant to Eva Nogales
>
> Professor, UC Berkeley and Lawrence Berkeley Natl. Lab
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-- 
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster
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