Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[James Holton]

I seem to recall Wladek mentioning that he has been trying to keep 
proteindiffraction.org alive using his own personal funds, which must be 
difficult.  The NIH grant for Proteindiffraction.org was U01 HG008424, 
which had a Project End date of 2018-05-31, and no record of a renewal. 
It was part of the NIH BD2K (Big Data to Knowledge) program, but the 
website for BD2K appears to be a broken link now. The final archive.org 
of it lists an NIH Request for Information NOT-OD-16-091 in 2016, where 
the community was solicited to fill out a survey about how useful the 
program was. Did anyone here fill out that survey?


-James Holton
MAD Scientist

On 6/13/2024 12:24 PM, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne.
Greetings,
John

Emeritus Professor John R Helliwell DSc





On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:

Dear Martin,Thankyou.Unfortunately I have no explanation to offer on https://proteindiffraction.org/";>proteindiffraction.org 
currently. Greetings,John Emeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin 
Malý  wrote:





Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/";>https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html";>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Kay Diederichs]

Hi Matt,

I guess that the datasets have the same spacegroup and very similar cell 
parameters?

And that you have two similar models that you obtained by refining against the 
datasets?

What you can do is to find out which dataset gives the better model, and is 
therefore better 
(i.e. generally more useful - but maybe not in every place of the e.d. map).
To arrive at this conclusion, use the two models for a paired-refinement-type 
of comparison, i.e.

a) note Rwork_AA,Rfree_AA of model A (obtained by refinement against dataset A)
b) note Rwork_BB,Rfree_BB of model B (obtained by refinement against dataset B)
c) rigid-body-and-overall-B refine model A against dataset B to obtain 
Rwork_AB,Rfree_AB
d) rigid-body-and-overall-B refine model B against dataset A to obtain 
Rwork_BA,Rfree_BA
e) if Rfree_AB < Rfree_BB then dataset A is better than dataset B (and 
conversely)
f) check the result of e): if Rfree_BA > Rfree_AA (and conversely) then this 
confirms the result from e)

Hope that this at least is a step towards the insights you're after!

Best, Kay

On Fri, 14 Jun 2024 15:58:41 -0400, Matt Mcleod  wrote:

>I should clarify.  I am mostly concerned about the electron density map.
>
>I want to make sure that I can most closely compare the maps from two
>different quality structures, rather than the datasets themselves via CC1/2
>or other metrics.  This is more so for interpreting structural changes.
>
>For example, if there is sparse density for some particular thing
>indicating partial occupancy, how can I compare those two maps.  So for
>low-resolution datasets, maybe there is less density but is that because of
>data quality or because in that dataset there is a lower occupancy through
>some meaningful structural change (compared to higher resolution/better
>data)?
>
>On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of
>> the same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is
>> alright, but the data quality in the lower resolution bins are also not the
>> same.  Is there a way to "inject" noise into the data such that the bins
>> are more similar?
>>
>> These datasets cannot be recollected at higher resolution since they are
>> collected at increasingly high pressure, and the resolution change is
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
>> 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/
>>
>
>
>--
>*Matthew Jordan McLeod, PhD*
>*Post-Doctoral Fellow - Cornell University*
>
>
>
>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 
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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Matt Mcleod]

I should clarify.  I am mostly concerned about the electron density map.

I want to make sure that I can most closely compare the maps from two
different quality structures, rather than the datasets themselves via CC1/2
or other metrics.  This is more so for interpreting structural changes.

For example, if there is sparse density for some particular thing
indicating partial occupancy, how can I compare those two maps.  So for
low-resolution datasets, maybe there is less density but is that because of
data quality or because in that dataset there is a lower occupancy through
some meaningful structural change (compared to higher resolution/better
data)?

On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:

> Hi all,
>
> I am wondering what the best practice is to compare datasets that are of
> the same protein but different quality, for instance 2 vs. 3 A.
>
> I know that truncating the structures to the same resolution bin is
> alright, but the data quality in the lower resolution bins are also not the
> same.  Is there a way to "inject" noise into the data such that the bins
> are more similar?
>
> These datasets cannot be recollected at higher resolution since they are
> collected at increasingly high pressure, and the resolution change is
> anticorrelated with the pressure; no way to get around crystal stability.
>
> Any suggestions are appreciated,
> Matt
>
> 
>
> 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/
>


-- 
*Matthew Jordan McLeod, PhD*
*Post-Doctoral Fellow - Cornell University*



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Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[Jeffrey B Bonanno]

Correction made below - AMV in my original message should read AMX of course
__

BNL NSLS-II, FMX or AMX beamlines: overall coordinator Vivian Stojanoff

Beamline scientists
FMX Wuxian Shi or Martin Fuchs or Alexei Soares

AMX Jean Jakoncic or Edwin Lazo or Dale Kreitler

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Friday, June 14, 2024 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the "Phish Alert" button on the top right of the 
Outlook dashboard to report any suspicious emails.

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your opinion 
matters, but the NIH cannot read your mind!  I personally think it very 
important that they get an accurate picture.

Some of you might not be sure if the beamline you usually use is one of these 
"MSR" things? Well, if you read CCP4BB and have used or plan to use the ALS, 
SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, BioCAT or NE-CAT to 
collect X-ray diffraction, SAXS, XCT or, XFP data then you are one of the 
people the NIH wants to hear from.

Another way to know if you have used these resources is if any of these names 
ring a bell.  Was the person who scheduled your beam time Jane Tanamachi? Stacy 
Ortega? or Kathryn Burnett?  Then you used the ALS-ENABLE MSR.  If the beamline 
scientist who supported you was one of
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg Hura, 
Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony Rosalez, Daniil 
Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, then you used an 
MSR-supported beamline.

If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia Russi, 
Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya Marchany-Rivera, and 
Aina Cohen.

These are just to name two MSRs that I am personally familiar with. Let me know 
who I forgot.

Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of you to 
answer all 15 questions, all responses are optional. Better to have your voice 
heard that not at all.

-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:
> Dear Colleagues,
>
> Apologies for the US-centric posting, but I think this is of interest to many 
> of the bulletin board subscribers who make use of synchrotron facilities in 
> the US.
>
> NIH is seeking feedback on the Mature Synchrotron Program:
>
>
> https://gran/
> ts.nih.gov%2Fgrants%2Fguide%2Fnotice-files%2FNOT-GM-24-019.html&data=0
> 5%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7C44c31427b6784c0dc53708dc8
> c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C63853985691876247
> 3%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6
> Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uBzcefsreyYJPHwhuJmVxAYrZj0A
> Q6NPEsjtNcqmKpo%3D&reserved=0
>
> This program supports synchrotron-based user resources where the technologies 
> are at an advanced level, including Macromolecular Crystallography, 
> Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other 
> synchrotron-based techniques that generate important data, with an emphasis 
> on structural biology.
>
> Responses to the RFI will be accepted through 6/17/2024. All comments
> will be anonymous and should be submitted electronically via a web
> form at:
> https://www/.
> research.net%2Fr%2FP30_RFI&data=05%7C02%7Cjeffrey.bonanno%40einsteinme
> d.edu%7C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e
> 62025%7C0%7C0%7C638539856918767402%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
> wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&s
> data=%2Begdvk1GWC4laLwqyYGHyzKlgp%2Fb6xJfHCAKpwRORVQ%3D&reserved=0
>
> As the Director of one of the resources it has been suggested that I help 
> make the community aware of the RFI, so there is the opportunity to provide 
> feedback in a timely manner. Feel free to pass this on to any of your 
> colleagues who may be interested.
>
>Cheers,
>   Paul
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL (https://bio/
> sciences.lbl.gov%2F&data=05%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7
> C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7
> C0%7C0%7C638539856918772257%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMD
> AiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdat

Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[Jeffrey B Bonanno]

BNL NSLS-II, FMX or AMX beamlines: overall coordinator Vivian Stojanoff

Beamline scientists
FMX Wuxian Shi or Martin Fuchs or Alexei Soares
AMV Jean Jakoncic or Edwin Lazo or Dale Kreitler

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Friday, June 14, 2024 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the "Phish Alert" button on the top right of the 
Outlook dashboard to report any suspicious emails.

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your opinion 
matters, but the NIH cannot read your mind!  I personally think it very 
important that they get an accurate picture.

Some of you might not be sure if the beamline you usually use is one of these 
"MSR" things? Well, if you read CCP4BB and have used or plan to use the ALS, 
SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, BioCAT or NE-CAT to 
collect X-ray diffraction, SAXS, XCT or, XFP data then you are one of the 
people the NIH wants to hear from.

Another way to know if you have used these resources is if any of these names 
ring a bell.  Was the person who scheduled your beam time Jane Tanamachi? Stacy 
Ortega? or Kathryn Burnett?  Then you used the ALS-ENABLE MSR.  If the beamline 
scientist who supported you was one of
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg Hura, 
Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony Rosalez, Daniil 
Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, then you used an 
MSR-supported beamline.

If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia Russi, 
Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya Marchany-Rivera, and 
Aina Cohen.

These are just to name two MSRs that I am personally familiar with. Let me know 
who I forgot.

Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of you to 
answer all 15 questions, all responses are optional. Better to have your voice 
heard that not at all.

-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:
> Dear Colleagues,
>
> Apologies for the US-centric posting, but I think this is of interest to many 
> of the bulletin board subscribers who make use of synchrotron facilities in 
> the US.
>
> NIH is seeking feedback on the Mature Synchrotron Program:
>
>
> https://gran/
> ts.nih.gov%2Fgrants%2Fguide%2Fnotice-files%2FNOT-GM-24-019.html&data=0
> 5%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7C44c31427b6784c0dc53708dc8
> c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C63853985691876247
> 3%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6
> Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uBzcefsreyYJPHwhuJmVxAYrZj0A
> Q6NPEsjtNcqmKpo%3D&reserved=0
>
> This program supports synchrotron-based user resources where the technologies 
> are at an advanced level, including Macromolecular Crystallography, 
> Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other 
> synchrotron-based techniques that generate important data, with an emphasis 
> on structural biology.
>
> Responses to the RFI will be accepted through 6/17/2024. All comments
> will be anonymous and should be submitted electronically via a web
> form at:
> https://www/.
> research.net%2Fr%2FP30_RFI&data=05%7C02%7Cjeffrey.bonanno%40einsteinme
> d.edu%7C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e
> 62025%7C0%7C0%7C638539856918767402%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
> wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&s
> data=%2Begdvk1GWC4laLwqyYGHyzKlgp%2Fb6xJfHCAKpwRORVQ%3D&reserved=0
>
> As the Director of one of the resources it has been suggested that I help 
> make the community aware of the RFI, so there is the opportunity to provide 
> feedback in a timely manner. Feel free to pass this on to any of your 
> colleagues who may be interested.
>
>Cheers,
>   Paul
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL
> (https://bio/
> sciences.lbl.gov%2F&data=05%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7
> C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7
> C0%7C0%7C638539856918772257%7CUnknown%7CTWFpbGZsb3d8eyJ

[ccp4bb] Comparing datasets with different resolution/quality

[Matt McLeod]

Hi all,

I am wondering what the best practice is to compare datasets that are of the 
same protein but different quality, for instance 2 vs. 3 A.  

I know that truncating the structures to the same resolution bin is alright, 
but the data quality in the lower resolution bins are also not the same.  Is 
there a way to "inject" noise into the data such that the bins are more 
similar?   

These datasets cannot be recollected at higher resolution since they are 
collected at increasingly high pressure, and the resolution change is 
anticorrelated with the pressure; no way to get around crystal stability.

Any suggestions are appreciated,
Matt



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/

Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[James Holton]

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your 
opinion matters, but the NIH cannot read your mind!  I personally think 
it very important that they get an accurate picture.


Some of you might not be sure if the beamline you usually use is one of 
these "MSR" things? Well, if you read CCP4BB and have used or plan to 
use the ALS, SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, 
BioCAT or NE-CAT to collect X-ray diffraction, SAXS, XCT or, XFP data 
then you are one of the people the NIH wants to hear from.


Another way to know if you have used these resources is if any of these 
names ring a bell.  Was the person who scheduled your beam time Jane 
Tanamachi? Stacy Ortega? or Kathryn Burnett?  Then you used the 
ALS-ENABLE MSR.  If the beamline scientist who supported you was one of 
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg 
Hura, Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony 
Rosalez, Daniil Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, 
then you used an MSR-supported beamline.


If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia 
Russi, Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya 
Marchany-Rivera, and Aina Cohen.


These are just to name two MSRs that I am personally familiar with. Let 
me know who I forgot.


Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of 
you to answer all 15 questions, all responses are optional. Better to 
have your voice heard that not at all.


-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:

Dear Colleagues,

Apologies for the US-centric posting, but I think this is of interest to many 
of the bulletin board subscribers who make use of synchrotron facilities in the 
US.

NIH is seeking feedback on the Mature Synchrotron Program:

https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html

This program supports synchrotron-based user resources where the technologies 
are at an advanced level, including Macromolecular Crystallography, Small-Angle 
and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based 
techniques that generate important data, with an emphasis on structural biology.

Responses to the RFI will be accepted through 6/17/2024. All comments will be 
anonymous and should be submitted electronically via a web form at: 
https://www.research.net/r/P30_RFI

As the Director of one of the resources it has been suggested that I help make 
the community aware of the RFI, so there is the opportunity to provide feedback 
in a timely manner. Feel free to pass this on to any of your colleagues who may 
be interested.

   Cheers,
Paul

--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov)
Principal Investigator, Computational Crystallography Initiative, LBL 
(http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source 
(http://als-enable.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, UC Berkeley 
(http://bioeng.berkeley.edu)
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley 
(http://compbiochem.berkeley.edu)

Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul
ORCID: -0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
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Re: [ccp4bb] help with wwPDB validation warning

[Edward Berry]

This old message claims that / =  "weighted" by s.

If counting error is significant, s will be larger for stronger reflections, which are likely to 
have small I/s,  so in general /  > unweighted . As Werten points 
out.

However this seems to be the opposite of the OP's situation, if both measures 
refer to the same outer shell.
EAB
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--- Begin Message ---



b...@freesurf.fr wrote:

***  For details on how to be removed from this list visit the  ***
***  CCP4 home page http://www.ccp4.ac.uk ***




From these we calculate a weighted mean  and an error estimate of

the mean sd(), and a ratio for that unique reflection
/sd()

What is printed as Mn(I)/sd is the mean value of that ratio for all
reflections (possibly in a resolution bin) ie





Which is very different (!) from anything one could extract from a
Scalepack/HKL2000 output file, which only lists average intensity and
average sigma (in the final table at the end). The ratio of those two
numbers, i.e. /, tends to be considerably more "optimistic" than
a proper .



Werten leaves it as an exercise for the reader
to verify this. Here is my submission:

The (ratio of means) is equivalent to a weighted
(mean of ratios):

/  = sum(I)/n / sum(s)/n

 = sum (I)  / sum(s)

 = sum(s*(I/s)) / sum(s)

 =  "weighted" by s

This means /  looks like  but with more
weight given to those measurements with large s.
If the standard deviation is related to counting
error, then s is larger for strong reflections
(yes of course as a percentage it is smaller
for strong reflections, but in absolute value
it is larger).
Thus the statistic / is weighted toward
strong reflections, and will be more optimistic
than unweighted .

The next-to-last table of truncate output lists
, /, , / vs resolution.
In the critical last shells  and /
tend to be the same, perhaps because all
reflections are around the noise level and s
is dominated by background counts so that all
reflections are weighted equally.


for R-type factors (error/magnitude) the ratio of
the means (as in R-merge) is more optimistic
than the mean of the ratios (as in std deviation),
and by a much larger extent: weighted by I,
whereas "s" varies at most as the sqrt(I).
If we used the mean ratio the result would be
to horrible to contemplate, with all those weak
reflections at the noise level weighted equally
with the strong! But seriously, it makes some
sense for a statistic to be weighted toward the
strong reflections, since they contribute more
to the map. Who cares if a reflection measurement
has 70% error if it is so weak that it could be
omitted completely with no visible effect on
the map?

Ed


Best regards,

   S. Werten










--- End Message ---

Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Dear MartinHere is the weblink to our IUCr 2023 Committee on Data Workshop in Melbourne:-(IUCr) Melbourne Workshopiucr.orgPresentations are available for our speakers as you will see theirin . The IRRMC talk was given by Wladek Minor. I hope you can join us at IUCr 2026 Calgary as we progress this important theme which I am pleased to see you are enthusiastic about. Raw diffraction data archiving offers us great opportunities as a science.Greetings,John Emeritus Professor John R Helliwell DScOn 14 Jun 2024, at 17:56, Martin Malý  wrote:Dear John,Please could you give us an advice who to contact - who presented in Melbourne?I think there are more of us who are not successful in contacting their support.Thank you.MartinOn 13/06/2024 20:24, John R Helliwell wrote:Dear Gerard,Quite so. But, as this CCP4bb has also observed in emails about a month ago,there is currently no news of proteindiffraction.org to share.Certainly detailed reports of its excellent work were presented at IUCr Melbourne.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:Dear John, Is this not a matter on which internal communication within the IUCr'sCommDat (https://www.iucr.org/resources/data/commdat) would be expected tobe able to throw some light? Best wishes,    Gerard--On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:Dear Martin,Thankyou.Unfortunately I have no explanation to offer on proteindiffraction.org currently. Greetings,John Emeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin Malý  wrote:        Dear John,    Thank you for the link. It would be great if    https://proteindiffraction.org/ (IRRMC) was rescued. I    preferred this website but they stopped receiving new data sets - or    at least they do not reply to my emails for more than a year. I am    worried that the website will disappear and also all the uploaded    data sets will be gone...    Cheers,    Martin        On 12/06/2024 20:44, John R Helliwell  wrote:          Dear Colleagues,Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:-https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.htmlBest wishes,JohnEmeritus Professor John R Helliwell DScTo unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1This 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/        To unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1To unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1This 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] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Martin Malý]

Dear John,
Please could you give us an advice who to contact - who presented in 
Melbourne?
I think there are more of us who are not successful in contacting their 
support.

Thank you.
Martin

On 13/06/2024 20:24, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne.
Greetings,
John

Emeritus Professor John R Helliwell DSc





On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:

Dear Martin,Thankyou.Unfortunately I have no explanation to offer on https://proteindiffraction.org/";>proteindiffraction.org 
currently. Greetings,John Emeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin 
Malý  wrote:





Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/";>https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html";>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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[ccp4bb] CryoEM Current Practices Webinar - 06/27/2024

[Christina Zimanyi]

Dear all,
Please join the NIH supported CryoEM centers at our next CryoEM Current 
Practices webinar.

Time: Thursday, June 27, 2024 at 9 AM pacific / 12 PM eastern time

Speaker: Dr. Keerthi Gottipati, Indiana University, Bloomington

Title: Cryo-EM structure of HIV-1 Rev Response Element RNA: Structural basis of 
Rev-RRE interaction

All are welcome to attend. Registration is at no-cost, but sign-up is required:
https://us02web.zoom.us/webinar/register/WN_QwSSrdU1TrOZSKLJ0K6Gvw

Please forward this posting to anyone that may be interested.

Information about previous and future talks can be found at 
https://www.cryoemcenters.org/events/#cryoEM-webinar

Best regards,
National Center for CryoEM Access and Training



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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Clemens Vonrhein]

Dear Martin,

On Thu, Jun 13, 2024 at 10:40:43AM +0100, Martin Malý wrote:
> Thank you for the link. It would be great if https://proteindiffraction.org/
> (IRRMC) was rescued.

They are back in business since a couple of months now - at least
regarding new data appearing there.

> I preferred this website but they stopped receiving new data sets -
> or at least they do not reply to my emails for more than a year.

That's true: no luck with that for me either since last
summer. Unfortunately the website has no information (that I can find)
who to contact for support or questions - so maybe my emails just went
to the wrong addresses.

> I am worried that the website will disappear and also all the uploaded data
> sets will be gone...

Very, very possible (same happened with e.g. the original JCSG
repository with all the originally processed data and a huge amount of
meta-data gone now [1]). In that respect a site like Zeonodo.org
(backed by big players like EC, OpenAIRE, CERN etc) is much more
likely to stay up - or at least have a plan for when something new
replaces it.

Of course, something generic like Zenodo is not dealing just with MX
data and therefore doesn't provide some intrinsic template to show
more than just file downloads. But since (1) all our detectors,
beamlines and inhouse instruments now write perfect, complete and rich
meta-data into the associated image headers (or HDF5 containers), and
(2) we all deposit meta-data rich models and multi-dataset reflection
data with correct information into the PDB, this is much less
important nowadays ... right?  ;-)

Cheers

Clemens

[1] The wayback machine at archive.org comes to rescue here
... sometimes.



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[ccp4bb] CCP-EM/Diamond Icknield Workshop 4-8 November 2024 - application reminder

[Lauren Giles - STFC UKRI]

Dear all,


We would encourage anyone interested in attending the 2024 CCP-EM/Diamond 
Icknield workshop to apply soon, as we are fast approaching our maximum number 
of applicants. For more information about the workshop and how to apply, see 
below.


The 2024 CCP-EM/Diamond Icknield Workshop to be held from the 4-8th November 
2024.  This 5-day course is largely aimed at structural biologists with EM maps 
suitable for modelling building and refinement.  This course will host some of 
the leading software developers and provide ample contact time to allow 
delegates to discuss their data in detail alongside traditional lectures and 
tutorials.  This is a comprehensive course for EM model building covering 
advanced use of LocScale, ModelAngelo, Buccaneer, 
findMySequence-checkMySequence, EM_placement, Coot/Moorhen, TEMPy-REFF, ISOLDE, 
Refmac-Servalcat, Privateer, new validation tools and AlphaFold-DB & EMDB/PDBe 
updates. It will cover all aspects of modelling building including: map 
optimisation, automated model building, model fitting, medium resolution 
refinement, high resolution refinement, interactive refinement, validation and 
deposition.


The course will be held at the RAL / Diamond campus, Harwell, UK, site of the 
eBIC national facility.  Registration fee is £238.00 and accommodation can be 
booked separately at the Bear Hotel, Wantage at £78.00 per night as part of the 
registration process. Delegates are asked to meet their own travel costs.


The course is limited to 22 in-person delegates which will be selected from all 
applicants.  A maximum of 40 applicants can register interest here:

https://cvent.me/G2rx4a?RefId=Applicant+Registration


Registration of interest will close either when all places are taken or by 
Friday 12th July 2024 and the successful applicants will be informed the 
following week. Please allow 10-15 mins to fill in the registration details.


* Confirmed tutors / topics:


Tom Burnley (CCP-EM) : CCP-EM Doppio

Arjen Jakobi (TU Delft) : LocScale

Sjors Scheres (MRC-LMB) : Relion5 and ModelAngelo

Randy Read (University of Cambridge) : EM-placement

Grzegorz Chojnowski (EMBL) : FindMySequence/CheckMySequence

Maya Topf, Joseph Beton and Aaron Sweeney (CSSB Hamburg) : TEMPy-REFF, Chem-EM

Judit Debreczeni (Astrazeneca), Lucrezia Catapano (MRC-LMB) and Paul Bond 
(University of York): Coot / Moorhen

Soon Wen Hoh and Paul Bond (University of York) : Buccaneer/ModelCraft

Rob Nicholls (CCP4) and Rangana Warshamanage (CCP-EM) : Refmac/Servalcat

Tristan Croll (AltosLabs) : ISOLDE

TBC (University of York) : Privateer

PDBe (EBI) : AlphaFold-DB and 3D-Beacons

Agnel Joseph (CCP-EM) : Model validation

Kyle Morris (EBI) : EMDB deposition and validation


Best wishes,

CCP-EM team




Lauren Giles | CCP-EM Administrative Support

Scientific Computing Department
Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell
Didcot
OX11 0QX

Email: lauren.gi...@stfc.ac.uk
Zoom telephone: 01235 445059

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