[ccp4bb] AW: AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-08 Thread Schreuder, Herman /DE 
In this way I fully agree. To me it sounds like one of those journals that will 
publish anything without going through the trouble of peer review. However, 
this will not get Artem the coordinates he was looking for.

Best Herman

Von: Frank von Delft 
Gesendet: Dienstag, 7. April 2020 19:10
An: Schreuder, Herman /DE ; CCP4BB@JISCMAIL.AC.UK
Betreff: Re: AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!


EXTERNAL : Real sender is 
frank.vonde...@sgc.ox.ac.uk<mailto:frank.vonde...@sgc.ox.ac.uk>

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 <mailto:CCP4BB@JISCMAIL.AC.UK> 
Im Auftrag von Frank von Delft
Gesendet: Dienstag, 7. April 2020 17:19
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

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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Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Bernhard Rupp 
> go the Rupp Route:  Name and Shame!

Thanks for the character reference.

Best, BR



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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 =1 

 

 

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 =1 




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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Rajiv gandhi.s 
Any paper published should share the data publicly, it is the job of the
journal editor to ask so. If they don't want to disclose to scientific
community then, how one could trust the data  published in that paper
describes active site and key structural information. Contact the editor of
the journal, that's ideal.

On Tue, Apr 7, 2020, 10:41 PM Frank von Delft 
wrote:

> 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   *Im
> Auftrag von *Frank von Delft
> *Gesendet:* Dienstag, 7. April 2020 17:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> 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
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
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>
>
>
>
> --
>
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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Frank von Delft 
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  *Im Auftrag von 
*Frank von Delft

*Gesendet:* Dienstag, 7. April 2020 17:19
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 
<mailto:owner-ccp...@jiscmail.ac.uk>


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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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Boaz Shaanan 



Hi Artem,
Indeed it seems, as you mentioned, that you have to go ahead and determine the structure, particularly if you've gone a few steps ahead already (pure protein, crystals, data?). 
Good luck,
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel




On Apr 7, 2020 19:24, Artem Evdokimov  wrote:



Sadly, I agree: it is pretty clear that the authors did not want coordinates revealed. Therefore asking them for information is not likely to lead to getting anything. To be completely fair, it's likely not even the authors themselves, but their
 corporate policy that's responsible.


In cases like this, I normally choose not to publish, but maybe their bosses insisted. Anyway, many options to find excuses, but it looks like Artem has to go solve this structure himself.


Thank you all very much, many good responses :)

Arte,



- Cosmic Cats approve of this message







On Tue, Apr 7, 2020 at 12:06 PM Schreuder, Herman /DE <herman.schreu...@sanofi.com> 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 <CCP4BB@JISCMAIL.AC.UK>
Im Auftrag von Frank von Delft
Gesendet: Dienstag, 7. April 2020 17:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!


 

EXTERNAL : Real sender is
owner-ccp...@jiscmail.ac.uk

 

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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Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread John R Helliwell 
Dear Artem,
These sort of things are very frustrating.
I had a similar situation with a published modelled structure of low sequence 
identity to that we were working on with crystallography. ie the modelled 
structure coordinates were not, could not be, deposited nor was it attached to 
the journal article.  To write to the author would have revealed our project 
work, and my collaborator would not have agreed to making the enquiry anyway. 
The journal was reputable but their policy of not attaching the model 
coordinates to an article presumably was based on the public database policy 
and so an enquiry from me would presumably have gone straight to the author 
from the editor. We pressed on independently but we got scooped. 
In these situations is the question what is the **least worst** option?
I won’t pronounce on that choice for your challenge because there may be fine 
details, which will affect your choice.
All the best,
John 
Emeritus Professor John R Helliwell DSc




> On 7 Apr 2020, at 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
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Jurgen Bosch 
You could also crawl through patents of sausage making. If they published now 
it is likely they have patented it since it sounds as if it an incredible 
important method for adding flavors to sausages.

Jürgen 

> On Apr 7, 2020, at 12:23 PM, Artem Evdokimov  
> wrote:
> 
> Sadly, I agree: it is pretty clear that the authors did not want coordinates 
> revealed. Therefore asking them for information is not likely to lead to 
> getting anything. To be completely fair, it's likely not even the authors 
> themselves, but their corporate policy that's responsible.
> 
> In cases like this, I normally choose not to publish, but maybe their bosses 
> insisted. Anyway, many options to find excuses, but it looks like Artem has 
> to go solve this structure himself.
> 
> Thank you all very much, many good responses :)
> 
> Arte,
> 
> - Cosmic Cats approve of this message
> 
> 
> On Tue, Apr 7, 2020 at 12:06 PM Schreuder, Herman /DE 
> mailto:herman.schreu...@sanofi.com>> 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  <mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag von Frank von Delft
> Gesendet: Dienstag, 7. April 2020 17:19
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
> 
>  
> 
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> <mailto:owner-ccp...@jiscmail.ac.uk>
>  
> 
> 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
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following li

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Artem Evdokimov 
Sadly, I agree: it is pretty clear that the authors did not want
coordinates revealed. Therefore asking them for information is not likely
to lead to getting anything. To be completely fair, it's likely not even
the authors themselves, but their corporate policy that's responsible.

In cases like this, I normally choose not to publish, but maybe their
bosses insisted. Anyway, many options to find excuses, but it looks like
Artem has to go solve this structure himself.

Thank you all very much, many good responses :)

Arte,

- Cosmic Cats approve of this message


On Tue, Apr 7, 2020 at 12:06 PM Schreuder, Herman /DE <
herman.schreu...@sanofi.com> 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  *Im Auftrag von *Frank
> von Delft
> *Gesendet:* Dienstag, 7. April 2020 17:19
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> 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
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=yyLzWvA2WqYlYHjvwWG6lk3OIm5wwZN_UsYlNbf8Meo=zldJ57kosENgJpj99VYugwSVD8wrOzyvCgE4aQH58wc=>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Jurgen Bosch 
Honestly, as a Zugreister to Bavaria and now living in a Sausage Diaspora (by 
Bavarian standards), I would take any sausage available.

Educational Sausages might be the way to go. You could ask a Sausage Modeler 
who previously participated in a Sausage-CASP competition to reach out to the 
authors so he/she can compare his Sausage model with the true and only Sausage.

May the Sausage be with you V <- Spock greeting

Jürgen 

> On Apr 7, 2020, at 12:05 PM, 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  <mailto:CCP4BB@JISCMAIL.AC.UK>> Im Auftrag vonFrank von Delft
> Gesendet: Dienstag, 7. April 2020 17:19
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> <mailto:owner-ccp...@jiscmail.ac.uk>
>  
> 
> 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
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=yyLzWvA2WqYlYHjvwWG6lk3OIm5wwZN_UsYlNbf8Meo=zldJ57kosENgJpj99VYugwSVD8wrOzyvCgE4aQH58wc=>
>  
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywy

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Schreuder, Herman /DE 
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  Im Auftrag von Frank von Delft
Gesendet: Dienstag, 7. April 2020 17:19
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

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



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=yyLzWvA2WqYlYHjvwWG6lk3OIm5wwZN_UsYlNbf8Meo=zldJ57kosENgJpj99VYugwSVD8wrOzyvCgE4aQH58wc=>




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Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread V F 
> 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,

Why and how such referees and editors reach such levels in academia?


On Tue, 7 Apr 2020 at 17:18, Frank von Delft
 wrote:
>
> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Frank von Delft 

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



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1






To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] on-topic: your opinions requested!

2020-04-07 Thread Artem Evdokimov 
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



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1