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At the risk of merely echoing some of Steve's comments, I would like
to say that while journals will not necessarily use your recommended
reviewers, they will almost always honor your reasonable requests to
exclude certain reviewers. This undercuts any reason to be paranoid,
unless you think that there are many people who will unethically use
your map.<br>
Ed<br>
<br>
<div class="moz-cite-prefix">On 4/30/15 6:13 PM, Ludtke, Steven J
wrote:<br>
</div>
<blockquote cite="mid:8AF4CB4D-9F57-4C06-8D0A-22CF65911C51@bcm.edu"
type="cite">
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I'm not sure if endless echoing is going to be that worthwhile,
but I'll add that I have been involved in a couple of reviews
where not only were final maps required, but a reviewer (not me)
actually requested the raw data (or a portion of the raw data)
involved in the reconstruction! I know I am not alone in seeing
cases like this. Admittedly in these cases, the editor did seem a
bit taken aback, but still followed through after discussing with
the author.
<div class=""><br class="">
</div>
<div class="">I cannot see that one has any ground to stand upon
in refusing to submit their final map to reviewers. In theory
the paper should encompass the entire results of the study. The
fact that it isn't possible to fully represent the data in the
publication itself doesn't negate the philosophical point.
Either you are ready to release your result to the world or you
aren't. Publishing isn't about hiding things, it's about
spreading your new knowledge as widely as possible. Given the
requirement to deposit to the EMDB, at most this gives the
reviewer a brief lead on general public access. The 'hold past
publication' policy in the databases is transitioning out
anyway. The excuse that "it took me 3 years to solve the
structure and it will take me another 2 years to really dissect
the map" is fading as cryoEM is becoming a higher throughput
technique. The idea that you so mistrust your colleagues that
you would require an MTA for the review process is completely
ludicrous. If there are IP concerns about a particular result,
you should not publish it until you are ready to share with the
world. I, for one, have no problem in forgoing my anonymity in
the review process, as journals like eLife promote, but I can at
least understand the value in being permitted to remain
anonymous. If there are specific colleagues that you fear will
misuse your data, you should identify them in the cover letter
to the editor with your reasoning, and trust the ethics of the
editor.
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Apr 30, 2015, at 4:46 PM, Gabriel Lander
<<a moz-do-not-send="true"
href="mailto:glander@scripps.edu" class="">glander@scripps.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;"
class="">
I would like to echo Eva & Ed’s comments (I am
also NOT a reviewer).
<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">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?</div>
<div class="">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.</div>
<div class="">-gabe</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Apr 30, 2015, at 2:16 PM, Eva
Nogales <<a moz-do-not-send="true"
href="mailto:enogales@lbl.gov" class="">enogales@lbl.gov</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class=""><font
class="" face="Helvetica Neue">Hi
Friedrich,<br class="">
<br class="">
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</font><font
class="" face="Helvetica Neue"><font
class="" face="Helvetica Neue"> some
really terrible structures</font>. 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...)<br
class="">
<br class="">
Eva<br class="">
</font><br class="">
<div class="moz-cite-prefix">On 4/30/15 1:49
PM, Friedrich Foerster wrote:<br class="">
</div>
<blockquote
cite="mid:CALtyCEgzVd4vo8Hp+W0CsGh0jhYnFC+ONCNtDBEbRkyLr7+aEQ@mail.gmail.com"
type="cite" class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">
<div class="">dear colleagues,<br
class="">
<br class="">
</div>
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:<br
class="">
</div>
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.<br class="">
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: "<font class="" size="2">Supporting
data must be made available to
editors and peer</font><font
class="" size="2">-</font><font
class="" size="2">reviewers at
the time of</font><font class=""
size="2"> submission for the
purposes of evaluating the
manuscript.</font><font class=""
size="2"> Peer</font><font
class="" size="2">-</font><font
class="" size="2">reviewers</font><font
class="" size="2"> may be asked</font><font
class="" size="2"> to comment on
the terms of access to
materials, methods and/or data
sets</font><font class=""
size="2">"</font>.<br class="">
</div>
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.<br class="">
<br class="">
</div>
Thanks <br class="">
<br class="">
</div>
Friedrich<br class="" clear="all">
<div class=""><br class="">
-- <br class="">
<div class="gmail_signature">Dr.
Friedrich Foerster<br class="">
Max-Planck Institut fuer Biochemie<br
class="">
Am Klopferspitz 18<br class="">
D-82152 Martinsried<br class="">
<br class="">
Tel: +49 89 8578 2632<br class="">
Fax: +49 89 8578 2641<br class="">
<br class="">
<a moz-do-not-send="true"
href="http://www.biochem.mpg.de/foerster"
target="_blank" class="">www.biochem.mpg.de/foerster</a><br
class="">
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<br class="">
<pre class="moz-signature" cols="72">--
__________________________________________________________________
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: <a moz-do-not-send="true" href="http://cryoem.berkeley.edu/" class="">cryoem.berkeley.edu</a>
(510) 666-3334 Teresa Tucker, Assistant to Eva Nogales
Professor, UC Berkeley and Lawrence Berkeley Natl. Lab
__________________________________________________________________
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<pre class="moz-signature" cols="72">--
Edward H. Egelman, Ph.D.
Professor
Dept. of Biochemistry and Molecular Genetics
University of Virginia
President
Biophysical Society
phone: 434-924-8210
fax: 434-924-5069
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