Re: [ccp4bb] Patterson map

[Eleanor Dodson]

Can you send your command file ?
And how are you displaying the Patterson map ?
>From CCP4I you can request a peak search of the map - check if the peaks
correspond to ones you would expect from your coordinates

Maybe read the map and vector positions into COOT to see?
Eleanor

On Tue, 21 Jun 2022 at 19:19, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, in P21, FFT swaps the axes around so Y will be the slowest changing
> axis i.e. along W in the Patterson, I think.
>
> How many atoms are in your model? Very hard to be sure it's not working as
> the Patterson is so very convoluted with a large model.
>
> Cheers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message 
> On 21 Jun 2022, 14:11, fuxingke < fuxingke0...@163.com> wrote:
>
>
>In ccp4, I can use "Generate Patterson Map" to generate Patterson map
> in "Map & Mask Utilities". But, I found a serious problem. When I use a set
> of data with spacegroup P21 and the position of atom is kown, the length
> of  w-axis in the Patterson map is not equal to cell parameters c. What's
> more, the position of Patterson peaks are also different from the
> interatomic vectors. The parameter is as below.
>   Why the Patterson map is different? How can I avoid this problem？Is
> there any other better method to calculate the Patterson map?
> [image: 0]
>
> I'm looking forward to your reply.
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
>
> --
>
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Re: [ccp4bb] Solubility of Aluminum Fluoride

[Dr. Kevin M Jude]

I posted the following to ccp4bb in 2017 in response to a similar question 
about ADPBeF4. For AlF4 you’ll increase the NaF stoichiometrically:

reagent[stock] (mM)final concentration (mM)volume (µl)
BeCl2  100090  9
NaF750 450 60
ADP, pH 8  100 30  30
H2O1
total volume   100

To prepare ADP:Be:F (1:3:15)
Prepare BeCl2 stock in the fume hood due to release of Cl2 gas
thoroughly mix BeCl2 and NaF
Add ADP
dilute with H2O to final volume
This is done at room temperature and the reactions are fast. Careful mixing 
(and adjusting the pH of the ADP beforehand) are important because the BeCl2 
stock will precipitate at neutral or elevated pH, and the BeFx solution is 
quite acidic.


From: CCP4 bulletin board  on behalf of Firdous Tarique 

Date: Tuesday, June 21, 2022 at 5:13 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Solubility of Aluminum Fluoride
Thanks for your input. To avoid precipitation what about doing something like 
this? For example, as we know: AlCl3 + 3NaF = AlF3 + 3NaCl

Therefore, adding 100mM AlCl3 plus 300mM NaF to get 100mM of AlF3 solution, 
then directly using this 100 mM stock of AlF3 for the final dilution, say 1 or 
2 mM in the reaction mix ? Or it is recommended to use AlCl3 and NaF hoping to 
form AlF3 in the reaction mix.

Best

Faisal


On Tue, Jun 21, 2022 at 2:08 PM Guillaume Gaullier 
mailto:guillaume.gaull...@univ-tlse3.fr>> 
wrote:
Hi Firdous,

I have read a fair amount of papers about ATP-dependent chromatin remodelers in 
which ADP-BeF3 is often cited. It is made as follows (quoting from one of these 
papers): "ADP-BeF3 was prepared as a 10x stock (10 mM ADP, 30 mM BeSO4, 150 mM 
NaF, 10 mM MgCl2), freshly before use."

So the trick is to get all you need from a mixture of soluble compounds, 
instead of from only one poorly soluble salt. Not sure this will work the same 
with Al instead of Be, but it’s easy enough to try: use any known-soluble salt 
of Al instead of this BeSO4, and see if it works. NaF is extremely toxic, so 
use adequate protective measures (PPE, hood, etc.).

Good luck,

Guillaume



On 21 Jun 2022, at 19:38, Firdous Tarique 
mailto:kahkashantari...@gmail.com>> wrote:

Hi

Sorry for the off topic question but can anybody please suggest how to dissolve 
Aluminium Fluoride in water ? I know it has little solubility in water but have 
seen people using AF3 for their structural studies (ADP + AF3 as ATP analogue). 
Is there any other solvent where they have made AF3 solution or is there some 
trick to dissolve it in water?.

Thanks

Firdous



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Re: [ccp4bb] Solubility of Aluminum Fluoride

[Dr. Kevin M Jude]

Sorry, I should have said ADPBeF3 (not ADPBeF4), and increase the NaF 
proportion for ADPAlF4. Which in practice means reducing the concentrations of 
everything else due to limited solubility of NaF.

From: CCP4 bulletin board  on behalf of Dr. Kevin M Jude 

Date: Wednesday, June 22, 2022 at 9:10 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Solubility of Aluminum Fluoride
I posted the following to ccp4bb in 2017 in response to a similar question 
about ADPBeF4. For AlF4 you’ll increase the NaF stoichiometrically:

reagent[stock] (mM)final concentration (mM)volume (µl)
BeCl2  100090  9
NaF750 450 60
ADP, pH 8  100 30  30
H2O1
total volume   100

To prepare ADP:Be:F (1:3:15)
Prepare BeCl2 stock in the fume hood due to release of Cl2 gas
thoroughly mix BeCl2 and NaF
Add ADP
dilute with H2O to final volume
This is done at room temperature and the reactions are fast. Careful mixing 
(and adjusting the pH of the ADP beforehand) are important because the BeCl2 
stock will precipitate at neutral or elevated pH, and the BeFx solution is 
quite acidic.


From: CCP4 bulletin board  on behalf of Firdous Tarique 

Date: Tuesday, June 21, 2022 at 5:13 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Solubility of Aluminum Fluoride
Thanks for your input. To avoid precipitation what about doing something like 
this? For example, as we know: AlCl3 + 3NaF = AlF3 + 3NaCl

Therefore, adding 100mM AlCl3 plus 300mM NaF to get 100mM of AlF3 solution, 
then directly using this 100 mM stock of AlF3 for the final dilution, say 1 or 
2 mM in the reaction mix ? Or it is recommended to use AlCl3 and NaF hoping to 
form AlF3 in the reaction mix.

Best

Faisal


On Tue, Jun 21, 2022 at 2:08 PM Guillaume Gaullier 
mailto:guillaume.gaull...@univ-tlse3.fr>> 
wrote:
Hi Firdous,

I have read a fair amount of papers about ATP-dependent chromatin remodelers in 
which ADP-BeF3 is often cited. It is made as follows (quoting from one of these 
papers): "ADP-BeF3 was prepared as a 10x stock (10 mM ADP, 30 mM BeSO4, 150 mM 
NaF, 10 mM MgCl2), freshly before use."

So the trick is to get all you need from a mixture of soluble compounds, 
instead of from only one poorly soluble salt. Not sure this will work the same 
with Al instead of Be, but it’s easy enough to try: use any known-soluble salt 
of Al instead of this BeSO4, and see if it works. NaF is extremely toxic, so 
use adequate protective measures (PPE, hood, etc.).

Good luck,

Guillaume




On 21 Jun 2022, at 19:38, Firdous Tarique 
mailto:kahkashantari...@gmail.com>> wrote:

Hi

Sorry for the off topic question but can anybody please suggest how to dissolve 
Aluminium Fluoride in water ? I know it has little solubility in water but have 
seen people using AF3 for their structural studies (ADP + AF3 as ATP analogue). 
Is there any other solvent where they have made AF3 solution or is there some 
trick to dissolve it in water?.

Thanks

Firdous



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[ccp4bb] Instruct-ERIC online training course "Instruct-ing Structural Biologists Towards Integration"

[Enrico Ravera]

Dear all,

Instruct-ERIC offers a range of workshops delivered at Instruct Centres (
https://instruct-eric.eu/instruct-training-events-annual).
In this framework, the  CERM/CIRMMP Italy centre is organizing the online
course "Instruct-ing Structural Biologists Towards Integration" - from July
18th to 21st 2022.

Info and registration can be found at: https://bit.ly/instruct-ing
During three practical sessions (9:00-13:00 CEST) the participants will be
trained on different software for integrating multiple types of Structural
Biology experimental data.
On the final day (13:00-19:00 CEST), renowned researchers in the field will
present examples of studies for which Integration of different techniques
proved to be the only way to achieve their goals. Psychological aspects of
science communication and the philosophical implications of integrative
approaches will also be discussed.

Keynote speakers:
•Lucia Banci
•Alexandre Bonvin
•Frank Neese
•David Stuart
•Andrej Sali
•Angela Gronenborn
•Sandra Mitchell

The organizing Committee

Max Bonomi (Institut Pasteur - CNRS)
Enrico Ravera (Instruct-ERIC CERM/CIRMMP Centre and University of Florence)
Dina Schneidman-Duhovny (Hebrew University of Jerusalem)
Christian Tarchi (University of Florence)


Enrico Ravera, Ph.D.
Associate Professor of Chemistry
CERM and Department of Chemistry,
University of Florence
Via L. Sacconi 6,
50019 Sesto Fiorentino
Florence, Italy
http://www.cerm.unifi.it/people/enrico-ravera




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Re: [ccp4bb] Solubility of Aluminum Fluoride

[Patrick Loll]

Kevin and Guillaume said it all quite well. I just want to stress one thing, 
namely that these solutions are metastable, and will eventually precipitate 
(hours to days). 

In the case of the beryllium salts, the precipitation is due to slow formation 
of metal hydroxide species. I have no direct experience with the aluminum 
variants, but since aluminum is notorious for forming goopy hydroxides, I would 
guess that the same issue pertains. So make the solution right before using, 
try not to use a pH too far above neutrality, and be very cautious about (for 
example) putting any of these solutions into an FPLC. 

Pat

> On 22 Jun 2022, at 12:15 PM, Dr. Kevin M Jude  wrote:
> 
> Sorry, I should have said ADPBeF3 (not ADPBeF4), and increase the NaF 
> proportion for ADPAlF4. Which in practice means reducing the concentrations 
> of everything else due to limited solubility of NaF.
>  
> From: CCP4 bulletin board  on behalf of Dr. Kevin M 
> Jude 
> Date: Wednesday, June 22, 2022 at 9:10 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Solubility of Aluminum Fluoride
> 
> I posted the following to ccp4bb in 2017 in response to a similar question 
> about ADPBeF4. For AlF4 you’ll increase the NaF stoichiometrically:
>  
> reagent[stock] (mM)final concentration (mM)volume (µl)
> BeCl2  100090  9
> NaF750 450 60
> ADP, pH 8  100 30  30
> H2O1
> total volume   100
> 
> To prepare ADP:Be:F (1:3:15)
> Prepare BeCl2 stock in the fume hood due to release of Cl2 gas
> 
> thoroughly mix BeCl2 and NaF
> Add ADP
> dilute with H2O to final volume
> 
> This is done at room temperature and the reactions are fast. Careful mixing 
> (and adjusting the pH of the ADP beforehand) are important because the BeCl2 
> stock will precipitate at neutral or elevated pH, and the BeFx solution is 
> quite acidic.
>  
>  
> 
---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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Re: [ccp4bb] Patterson map

[Ian Tickle]

Hi, from the FFT documentation:

AXIS   


*In general DO NOT change the axis order unless you are in P1 or are very
sure you know what you are doing! This is permitted if your map is being
calculated using the routines for P1 or P222, but not otherwise.*

   are the letters X, Y and Z in the appropriate order.
Note that many of the FFT space-group specific routines have FIXED axis
orders. In general these are Y,X,Z for those which have rotation axes along
c, and are best output with z-sections (all space-groups with space-group
number greater than 18 (P21212)).

For P1, the monoclinic space-groups, and space-groups 16 (P 2 2 2), 17 (P 2
2 21) and 18 (P 21 21 2), the required axis order is Z,X,Y, which gives
y-sections.

If this keyword is left out (the recommended procedure), and the map is
calculated in FFT space-group P1 (the FFTBIG default) then the standard
order for TRUE space-group is used, *i.e.* Z,X,Y for P1, the monoclinic
space-groups, and space-groups 16, 17 and 18; for all higher symmetry
space-groups the standard axis ordering will be Y,X,Z.

Otherwise, note that any axis permutation must make sense in the
space-group used for the FFT, *e.g.* the P21 FFT (sg4) always generates a
21 axis along the section axis, through the origin. Axis permutation is
only permitted in a few space-groups and should probably by cyclic: 1, 2,
19, 21, 23, 47. In space-group 19, only cyclic permutations are valid,
*i.e.* Y,X,Z (default); Z,Y,X; or X,Z,Y; others will give WRONG ANSWERS.

Cheers

-- Ian

On Tue, 21 Jun 2022, 14:12 fuxingke,  wrote:

>In ccp4, I can use "Generate Patterson Map" to generate Patterson map
> in "Map & Mask Utilities". But, I found a serious problem. When I use a set
> of data with spacegroup P21 and the position of atom is kown, the length
> of  w-axis in the Patterson map is not equal to cell parameters c. What's
> more, the position of Patterson peaks are also different from the
> interatomic vectors. The parameter is as below.
>   Why the Patterson map is different? How can I avoid this problem？Is
> there any other better method to calculate the Patterson map?
> [image: 0]
>
> I'm looking forward to your reply.
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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[ccp4bb] open review?

[James Holton]

Greetings all,

I'd like to ask a question that I expect might generate some spirited 
discussion.


We have seen recently a groundswell of support for openness and 
transparency in peer review. Not only are pre-prints popular, but we are 
also seeing reviewer comments getting published along with the papers 
themselves. Sometimes even signed by the reviewers, who would have 
traditionally remained anonymous.


My question is: why don't we also do this for grant proposals?

I know this is not the norm. However, after thinking about it, why 
wouldn't we want the process of how funding is awarded in science to be 
at least as transparent as the process of publishing the results? Not 
that the current process isn't transparent, but it could be more so. 
What if applications, and their reviewer comments, were made public? 
Perhaps after an embargo period?  There could be great benefits here. 
New investigators especially, would have a much clearer picture of 
format, audience, context and convention. I expect unsuccessful 
applications might be even more valuable than successful ones. And yet, 
in reality, those old proposals and especially the comments almost never 
see the light of day. Monumental amounts of work goes into them, on both 
sides, but then get tucked away into the darkest corners of our hard drives.


So, 2nd question is: would you do it? Would you upload your application 
into the public domain for all to see? What about the reviewer comments? 
If not, why not?  Afraid people will steal your ideas? Well, once 
something is public, its pretty clear who got the idea first.


3rd question: what if the service were semi-private? and you got to get 
comments on your proposal before submitting it to your funding agency? 
Would that be helpful? What if in exchange for that service you had to 
review 2-3 other applications?  Would that be worth it?


Or, perhaps, I'm being far too naiive about all this. For all I know 
there are some rules against doing this I'm not aware of.  Either way, 
I'm interested in what this community thinks. Please share your views!  
On- or off-list is fine.


-James Holton
MAD Scientist



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Re: [ccp4bb] open review?

[Herbert J. Bernstein]

Dear James,
  I think open reviews would be a major improvement in the grants review
process.  Most grant reviews are done carefully and honestly, but I have
seen some that were clearly written carelessly and dishonestly that would
not
have been submitted if the reviewers knew they would have to publicly
stand behind what they said.  Sunlight is an excellent disinfectant.
  Good suggestion.
  Regards,
Herbert

On Wed, Jun 22, 2022 at 9:09 PM James Holton  wrote:

> Greetings all,
>
> I'd like to ask a question that I expect might generate some spirited
> discussion.
>
> We have seen recently a groundswell of support for openness and
> transparency in peer review. Not only are pre-prints popular, but we are
> also seeing reviewer comments getting published along with the papers
> themselves. Sometimes even signed by the reviewers, who would have
> traditionally remained anonymous.
>
> My question is: why don't we also do this for grant proposals?
>
> I know this is not the norm. However, after thinking about it, why
> wouldn't we want the process of how funding is awarded in science to be
> at least as transparent as the process of publishing the results? Not
> that the current process isn't transparent, but it could be more so.
> What if applications, and their reviewer comments, were made public?
> Perhaps after an embargo period?  There could be great benefits here.
> New investigators especially, would have a much clearer picture of
> format, audience, context and convention. I expect unsuccessful
> applications might be even more valuable than successful ones. And yet,
> in reality, those old proposals and especially the comments almost never
> see the light of day. Monumental amounts of work goes into them, on both
> sides, but then get tucked away into the darkest corners of our hard
> drives.
>
> So, 2nd question is: would you do it? Would you upload your application
> into the public domain for all to see? What about the reviewer comments?
> If not, why not?  Afraid people will steal your ideas? Well, once
> something is public, its pretty clear who got the idea first.
>
> 3rd question: what if the service were semi-private? and you got to get
> comments on your proposal before submitting it to your funding agency?
> Would that be helpful? What if in exchange for that service you had to
> review 2-3 other applications?  Would that be worth it?
>
> Or, perhaps, I'm being far too naiive about all this. For all I know
> there are some rules against doing this I'm not aware of.  Either way,
> I'm interested in what this community thinks. Please share your views!
> On- or off-list is fine.
>
> -James Holton
> MAD Scientist
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>



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Re: [ccp4bb] open review?

[Ronnie Berntsson]

Hi James,

I agree that it’sa good suggestion. In Sweden when you apply to any of the 
publicly funded grant agencies the application is automatically in the public 
domain.  This means that anyone can ask to see your proposal and the agency is 
obliged to send it out to the people asking for it. I’ve used this a couple of 
times to look at grant proposals within my field as a learning experience. 

Best wishes,
Ronnie

Sent from my iPhone

> On 23 Jun 2022, at 03:09, James Holton  wrote:
> 
> Greetings all,
> 
> I'd like to ask a question that I expect might generate some spirited 
> discussion.
> 
> We have seen recently a groundswell of support for openness and transparency 
> in peer review. Not only are pre-prints popular, but we are also seeing 
> reviewer comments getting published along with the papers themselves. 
> Sometimes even signed by the reviewers, who would have traditionally remained 
> anonymous.
> 
> My question is: why don't we also do this for grant proposals?
> 
> I know this is not the norm. However, after thinking about it, why wouldn't 
> we want the process of how funding is awarded in science to be at least as 
> transparent as the process of publishing the results? Not that the current 
> process isn't transparent, but it could be more so. What if applications, and 
> their reviewer comments, were made public? Perhaps after an embargo period?  
> There could be great benefits here. New investigators especially, would have 
> a much clearer picture of format, audience, context and convention. I expect 
> unsuccessful applications might be even more valuable than successful ones. 
> And yet, in reality, those old proposals and especially the comments almost 
> never see the light of day. Monumental amounts of work goes into them, on 
> both sides, but then get tucked away into the darkest corners of our hard 
> drives.
> 
> So, 2nd question is: would you do it? Would you upload your application into 
> the public domain for all to see? What about the reviewer comments? If not, 
> why not?  Afraid people will steal your ideas? Well, once something is 
> public, its pretty clear who got the idea first.
> 
> 3rd question: what if the service were semi-private? and you got to get 
> comments on your proposal before submitting it to your funding agency? Would 
> that be helpful? What if in exchange for that service you had to review 2-3 
> other applications?  Would that be worth it?
> 
> Or, perhaps, I'm being far too naiive about all this. For all I know there 
> are some rules against doing this I'm not aware of.  Either way, I'm 
> interested in what this community thinks. Please share your views!  On- or 
> off-list is fine.
> 
> -James Holton
> MAD Scientist
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
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Re: [ccp4bb] open review?

[Frank von Delft]

I suspect funders will worry about it becoming even harder to find 
reviewers - they're already hard to flush out, if I'm not mistaken, and 
might become even more reclusive if they run the risk of being pilloried 
in public.


If that sounds theoretical:  even in this community, for all its 
collegiality and friendliness, we pillory one another in public and 
print just about our /data/.


Frank


On 23/06/2022 02:08, James Holton wrote:

Greetings all,

I'd like to ask a question that I expect might generate some spirited 
discussion.


We have seen recently a groundswell of support for openness and 
transparency in peer review. Not only are pre-prints popular, but we 
are also seeing reviewer comments getting published along with the 
papers themselves. Sometimes even signed by the reviewers, who would 
have traditionally remained anonymous.


My question is: why don't we also do this for grant proposals?

I know this is not the norm. However, after thinking about it, why 
wouldn't we want the process of how funding is awarded in science to 
be at least as transparent as the process of publishing the results? 
Not that the current process isn't transparent, but it could be more 
so. What if applications, and their reviewer comments, were made 
public? Perhaps after an embargo period? There could be great benefits 
here. New investigators especially, would have a much clearer picture 
of format, audience, context and convention. I expect unsuccessful 
applications might be even more valuable than successful ones. And 
yet, in reality, those old proposals and especially the comments 
almost never see the light of day. Monumental amounts of work goes 
into them, on both sides, but then get tucked away into the darkest 
corners of our hard drives.


So, 2nd question is: would you do it? Would you upload your 
application into the public domain for all to see? What about the 
reviewer comments? If not, why not?  Afraid people will steal your 
ideas? Well, once something is public, its pretty clear who got the 
idea first.


3rd question: what if the service were semi-private? and you got to 
get comments on your proposal before submitting it to your funding 
agency? Would that be helpful? What if in exchange for that service 
you had to review 2-3 other applications?  Would that be worth it?


Or, perhaps, I'm being far too naiive about all this. For all I know 
there are some rules against doing this I'm not aware of. Either way, 
I'm interested in what this community thinks. Please share your 
views!  On- or off-list is fine.


-James Holton
MAD Scientist



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