I meant: complain to the editor for accepting a paper without released
coordinates. We as a community fought and won that battle >20 years ago
- so we have the weight of history on our side.
On 07/04/2020 17:05, Schreuder, Herman /DE wrote:
Dear Frank,
here I disagree. I think it is bad practice to complain to the editors
or start naming and shaming before asking the authors first. Only if
they do not want to cooperate, it would be time to bring the
flame-throwers in position.
However, I think the situation is more subtle and that that is the
reason Artem wrote his email: He wants the data, but does not want to
reveal his identity to his competitors, who apparently made a
significant effort not to reveal any useful details.
Here I would let me guide by the (perceived) commercial interest: if
it is not gigantic, then I would contact the authors to prevent a
wasteful duplication of research efforts.
If there is a significant commercial interest, it would probably be
better not to contact them and go the hard way of solving the
structure yourself. A thing to consider is also what would happen if
the authors still would refuse: they know the identity of the
competitor and you still do not have the data.
An alternative may be to ask an academic friend who also works on
sausage esterases to inquire with the authors…
Good luck with your decision!
Herman
*Von:* CCP4 bulletin board <[email protected]> *Im Auftrag von
*Frank von Delft
*Gesendet:* Dienstag, 7. April 2020 17:19
*An:* [email protected]
*Betreff:* [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
*EXTERNAL : *Real sender is [email protected]
<mailto:[email protected]>
Write to the editor - that's their job.
Though they may also see it as their job to ignore emails like yours
because that's far easier than dealing with them.
Alternatively, go the Rupp Route: Name and Shame! ;)
On 07/04/2020 16:08, Artem Evdokimov wrote:
Dear CCP4ers,
I would like to solicit your thoughts on the following (this is a
real situation, but salient details are changed):
Imagine that you're an industrial scientist in a small company,
working on the Bavarian Sausage (Weisswurst) Esterase project. The
overall structure is previously unknown, with no good homologs in
the PDB, trying to model is "OK not great" so the structure is
really needed...
Then, you find an article from a large commercial competitor, that
somehow managed to solve the Stadtwurst (Saxony Sausage) Esterase
structure (which is a very close homolog to the one you need!).
Sounds good - but as you read the paper you realize that the
authors managed to find a journal that allowed them to publish
their work without disclosing neither the coordinates of the
model, nor even the crystallization conditions of the protein -
all that's available is a tantalizing still picture of the active
site in surface mode, with a ball-and-stick ligand positioned such
that it is impossible to say what it interacts with.
So you sit and ponder - whether to write to the Editor, or maybe
to contact the authors directly (but then they would know that
you're working on this, which is not necessarily great since
you're competing), or to just buck up and do the structure on your
own (which feels a bit wasteful). Then, you realize that your
friends at CCP4 have a lot of wisdom to offer, so you sit down and
pen an email...
Any thoughts?
Artem
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