[ccp4bb] IUCr Congress 2020 in Prague programme planning; data aspects

best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Open Access Repositories for Big Data?

that 50 Gbytes would be much better and eg thereby allow for a time resolved diffraction sequence of datasets. One week later it had increased from 5 to 50 Gbytes per data set. Greetings, John Emeritus Professor John R Helliwell DSc > On 18 Jan 2019, at 16:41, Aaron Finke wrote: >

[ccp4bb] UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response

Dear Colleagues, Thankyou for asking about the weblink to the case studies. The UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response is here:- https://www.gov.uk/government/publications/open-research-data-task-force-final-report Best wishes, John ###

[ccp4bb] General interest

Dear Colleagues, For your general interest, you can find the lecture slides that I presented at ACA 2019 in the Transactions Symposium on Data via the weblink here:- https://forums.iucr.org/viewtopic.php?f=39&t=421 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of

[ccp4bb] General interest

Dear Colleagues, The details, including all abstracts, for the IUCr Satellite at ECM32 Vienna on Data Science Skills in Publishing for Editors, Authors and Referees can be found here:- https://forums.iucr.org/viewtopic.php?f=39&t=419 Best wishes, John Emeritus Professor John R Helliwell

Re: [ccp4bb] Importance of temperature during initial crystallization screening

Dear Sergei, There is also this high temperature crystallisation study of lysozyme, up to 55 degrees C:- https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/0014-5793%2872%2980273-4 Best wishes, John Emeritus Professor John R Helliwell DSc > On 1 Aug 2019, at 10:23, Sergei Strelkov wr

[ccp4bb] General interest

mp;t=422&sid=f14add194ce5e9c146b51b6ace1ad72a Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of IUCr Committee on Data To unsubscribe from the CCP4BB list, click the following lin

Re: [ccp4bb] challenges in structural biology

Dear James, Here you go, a “grand challenge” suggestion to consider for funding from the “James Holton Foundation for structural biology research”:- “The human genome/proteome in 3-D” Greetings, John Emeritus Professor John R Helliwell DSc > On 14 Sep 2019, at 02:39, James Holton wr

Re: [ccp4bb] challenges in structural biology

llection.. Greetings! John Emeritus Professor John R Helliwell DSc https://www.crcpress.com/The-Whats-of-a-Scientific-Life/Helliwell/p/book/9780367233020 > On 18 Sep 2019, at 22:15, James Holton wrote: > > Thank you John, an excellent choice as always. Here is your trillion > dollars

Re: [ccp4bb] AW: [ccp4bb] challenges in structural biology

being interesting how the rice genome is more complicated than our genome. Best wishes, John Emeritus Professor John R Helliwell DSc > On 19 Sep 2019, at 08:35, Kollmar, Martin wrote: > > Dear John, > the „100,000 human genes“ is a long-standing myth broad forward by the > initia

[ccp4bb] General interest

Dear Colleagues, I draw your attention to my posting at the IUCr Committee on Data Public Forum ( https://forums.iucr.org/viewtopic.php?f=39&t=423 ) about the recent USA National Academies Report on Reproducibility and Replicability in Science. Best wishes, John Emeritus Professor Jo

Re: [ccp4bb] Picking water molecules at 4A structure.

> and refinement (with R/Rfree of ~ 22/27) we could see some small water like > densities...all throughout the complex. Now my query is, whether one should > pick water molecules at this low resolutions or it is totally unscientific > to do so? > > Many thanks in advance...!!! >

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

y ever used xenon? Can anyone share the starting pressure and > time for optimization? > > Thank you again, > > Bei > -- Professor John R Helliwell DSc

Re: [ccp4bb] Heavy-atom derivatives

ome papers about quick-soak, its a good method? Using platine, Hg, > Br... > > Any suggestions? Thank you so much. > > Best wishes, > > -- > Giulliana Rangel > M.S. Biotechnology Program - UNIFESP > Structural Biology Laboratory > Phone: +55 (12) 3309-9698 > 330 Talim St > ZIP CODE 12231-280 > São José dos Campos - SP/ BR > > -- Professor John R Helliwell DSc

Re: [ccp4bb] CCDs + Re: PILATUS data collection

as good as it can get? Greetings, John Prof John R Helliwell DSc On Thu, May 16, 2013 at 6:03 PM, Gerard Bricogne wrote: > Dear James, > > A week ago I wrote what I thought was a perhaps excessively long and > overly dense message in reply to Theresa's initial query, then I

[ccp4bb] The weblinks for the Daresbury Laue software source code and information

/02/00/me6120/index.html Best wishes, John Emeritus Professor John R Helliwell DSc 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 mes

[ccp4bb] Collection of articles from ISDSB2019 now published in IUCr Journals

Dear Colleagues, A collection of articles from the International Symposium on Diffraction Structural Biology 2019 held in Osaka is now online in IUCr Journals at https://journals.iucr.org/special_issues/2021/ISDSB2019 Several of these articles are open access. Best wishes, Atsushi Nakagawa, John He

Re: [ccp4bb] Analysis of NMR ensembles

/index.html which I imagine will be of keen interest. The IUCr has established a Commission on NMR Crystallography and Related Methods:- https://www.iucr.org/iucr/commissions/nmr-crystallography Best wishes, John Emeritus Professor John R Helliwell DSc > On 27 May 2021, at 10:35, Rasmus F

[ccp4bb] European Crystallography School ECS6

Dear Colleagues, I commend to you the European Crystallography School ECS6. Full details are here:- https://akcongress.com/ecs6/ Best wishes, John Emeritus Professor John R Helliwell DSc To unsubscribe from the CCP4BB

[ccp4bb] General interest: the history of the European Crystallography Schools

found here:- https://ecsx.ecanews.org/ ie replacing the x by the number. The current one ‘Budapest’ being 6. (In each the ECA website is mirrored to the local host organising team.) Greetings, John Emeritus Professor John R Helliwell DSc ECA Past President 2007 to 2010

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

Dear Andrea, https://journals.iucr.org/s/issues/2000/06/00/hi2016/index.html Greetings, John Emeritus Professor John R Helliwell DSc > On 3 Aug 2021, at 12:53, Thorn, Dr. Andrea > wrote: > >  > Dear colleagues, > I have compiled a list of papers that cover the applica

[ccp4bb] IUCr’s Committee on Data recent meeting minutes now online

Dear Colleagues, I imagine that you will be interested in the IUCr’s Committee on Data recent meeting minutes which are now online here:- https://forums.iucr.org/viewtopic.php?f=39&t=441 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman IUCr Committee on

Re: [ccp4bb] Obituary for John D. Westbrook

community. I was deeply shocked when I heard the news. I have many memories of his incisive and very helpful expert comments and suggestions in our IUCr workshops and committee meetings. John is going to be greatly missed. Yours sincerely, John Emeritus Professor John R Helliwell DSc > On

Re: [ccp4bb] (renaming chains)….water numbering aspect

with table columns labelled time, pressure or temperature. I have had mixed success retaining this explanatory table in the main text however versus being forced to put it into the Supplementary. Hope this helps, Best wishes, John Emeritus Professor John R Helliwell DSc > On 1 Nov 2

Re: [ccp4bb] renaming chains

Dear Valeh Apologies, I was solely replying to the numbering/labelling of waters observation/query of Mohamed, ie as a function of in situ parameter (time, temperature and pressure). Best wishes John Emeritus Professor John R Helliwell DSc > On 1 Nov 2021, at 18:39, Oganesyan, Va

[ccp4bb] Call for Topical review articles for Acta Cryst F Structural Biology Communications

, Mark van Raaj and Janet Newman Emeritus Professor John R Helliwell DSc 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

[ccp4bb] General interest

wishes, John Emeritus Professor John R Helliwell DSc 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 member

[ccp4bb] The second of our Topical reviews is now online Fwd: Call for Topical review articles for Acta Cryst F Structural Biology Communications

Dear Colleagues, The second of our Acta Cryst F topical reviews initiative is now online:- https://journals.iucr.org/f/issues/2022/03/00/va5045/index.html The article is open access. We welcome proposals for further topical reviews. Best wishes, John Emeritus Professor John R Helliwell DSc Guest

Re: [ccp4bb] Sad demise of Prof. M. Vijayan, MBU, IISc, India

Professor John R Helliwell DSc > On 24 Apr 2022, at 09:07, ASHISH ANILRAO DESHMUKH > <79fffa49db31-dmarc-requ...@jiscmail.ac.uk> wrote: >  > Dear All, > > With profound sorrow, we are sad to inform the demise of Prof. M. Vijayan on > the morning of 24th Apri

Re: [ccp4bb] X-ray crystallography defense questions

seems to be “What is your view on being able to predict what you have found out by Xray crystallography? Best wishes, John Emeritus Professor John R Helliwell DSc > On 14 Jun 2022, at 16:58, Jessica Besaw wrote: > >  > Hello CCP4! > > I am preparing for my Ph

Re: [ccp4bb] open review?

are currently giving this a very serious go: https://www.unesco.org/en/natural-sciences/open-science . Greetings, John Emeritus Professor John R Helliwell DSc IUCr Representative to CODATA, IUCr Representative to UNESCO’s Open Science discussions. > On 23 Jun 2022, at 02:08, James Hol

Re: [ccp4bb] open review?

-ukrn-working-together-to-create-a-new-primary-research-record-for-science/ Neither of which seem to involve funders however. No reply as yet to my direct message @HelliwellJohn to @asapbio Greetings, John Emeritus Professor John R Helliwell DSc > On 23 Jun 2022, at 14:18, John R Helliw

Re: [ccp4bb] open review?

individual nations? We know we can: the UN, International Council for Science, IUCr…… So, it probably isn’t a one size fits all idea that James has put forward… Best wishes, John Emeritus Professor John R Helliwell DSc > On 27 Jun 2022, at 19:03, Debanu Das wrote: > >  > >So,

Re: [ccp4bb] open review?

wishes, John Emeritus Professor John R Helliwell DSc > On 27 Jun 2022, at 20:16, Debanu Das wrote: > >  > Thinking about it some more, I think all the materials (patentable IP or > trade secrets, which in the US are IP and under Defense of Trade Secrets Act) > of a researche

Re: [ccp4bb] Comparing two datasets

Emeritus Professor John R Helliwell DSc > On 26 Jul 2022, at 11:40, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >  > Not only does SCALEIT do the job - it presented useful plots and an > informative log file.. > Eleanor > (You ne

[ccp4bb] Launch of IUCrData Raw Data Letters: Editorial

Dear Colleagues, I imagine you will be interested to know of the launch of IUCrData’s Raw Data Letters. The Main Editor is Dr Loes Kroon Batenburg. See https://forums.iucr.org/viewtopic.php?f=39&t=449&p=729#p729 Greetings, John Emeritus Professor John R Helliwell DSc Chair of IUCr

[ccp4bb] General interest article

Education article in J Appl Cryst. Best wishes, John Emeritus Professor John R Helliwell DSc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&a

[ccp4bb] My talk slides I have uploaded at Zenodo Re: [phenixbb] SSRL/LCLS User Meeting Registration is Open

Dear Colleagues, I have placed my SLAC 2022 Users’ Meeting (https://events.bizzabo.com/SLAC-UsersMeeting-2022) talk slides at Zenodo:- https://zenodo.org/record/7118593#.YzXNHi3TWhC All best wishes, John Emeritus Professor John R Helliwell DSc > On 19 Aug 2022, at 19:28, Mooers, Blaine

Re: [ccp4bb] hydrogens?

, John Emeritus Professor John R Helliwell DSc > On 11 Nov 2022, at 19:47, Murpholino Peligro wrote: > >  > Hi > > What is the best way to add hydrogens to a pdb file for a, probably, last > round of refinement? > > Can hydrogens be added in a pH/pka-dependent

Re: [ccp4bb] Rotation

MacCHESS, Cornell University > schul...@cornell.edu > > -- Professor John R Helliwell DSc

Re: [ccp4bb] To win or not twinning?

protein diffraction images > and understand what I am seeing. The basics like recognizing bad data and > what usually leads to deformity in the spots (for example, elliptical or > duplicated) would be of great help. > > 2 - Should I look for other space groups? What else could be tried? Is > this a case where a twin law should be used in the refinement? If yes, what > can I do to confirm the need for a twin law in the refinement? > > Thank you all in advance. > Regards, > Napo > -- Professor John R Helliwell DSc

[ccp4bb] IUCr DDDWG Workshop on "Research Data Management" will be at ACA 2017 in New Orleans

Dear Colleagues, We draw your attention to the next IUCr Diffraction Data Deposition Working Group (DDDWG) Workshop which is entitled "Research Data Management" to be held at the ACA 2017 in New Orleans. Details can be found here:- http://forums.iucr.org/viewtopic.php?f=21&t=395

[ccp4bb] Landscape report on open research data

allography features various times in the document, as does genomics and astronomy. As well as being an excellent survey I think the report brings out numerous issues within this very important topic. All best wishes, John Emeritus Professor John R Helliwell DSc

[ccp4bb] Final report of the IUCr Diffraction Data Deposition Working Group

spx?C=O-D0K8K_PcEspfxeGxZQYWhd61iTrQmoXKD0_aYD_yEP1opsEPbUCA..&URL=http%3a%2f%2fforums.iucr.org%2fviewtopic.php%3ff%3d21%26t%3d396> Yours sincerely, John Professor John R Helliwell DSc

[ccp4bb] Open Access weblink to Final report of IUCr Diffraction Data Deposition Working Group

Apologies everyone. The open access weblink is:- http://forums.iucr.org/viewtopic.php?f=21&t=396 John Emeritus Professor John R Helliwell DSc

[ccp4bb] Faraday Discussion on Photo induced processes in nucleic acids and proteins

Dear Colleagues, I draw your attention to this upcoming Faraday Discussion which i imagine will be of interest:- http://www.rsc.org/events/detail/24607/photoinduced-processes-in-nucleic-acids-and-proteins-faraday-discussion Greetings, John Emeritus Professor John R Helliwell DSc

Re: [ccp4bb] B-factor standardization

m atom oscillation, since Bave differences are neutralized. > > Does anyone can help me in finding a publication (80s or 90s) where these > BS values are used? > > Thanks! > > Oliviero > -- Professor John R Helliwell DSc

[ccp4bb] Open science, UNESCO initiative

attached short report, including several weblinks. I imagine that aspects of these UNESCO, and UN, activities may well be of interest. Best wishes, John Emeritus Professor John R Helliwell DSc To unsubscribe from the

[ccp4bb] General interest, education article

Dear Colleagues,I imagine you will find this education article of general interest Golden oldies: ten crystallography articles that we think must be readjournals.iucr.orgThe article is open access.Best wishes,John Emeritus Professor John R Helliwell DSc To unsubscribe from the CCP4BB list, click

Re: [ccp4bb] Crystallisation textbook

Dear Mike,I offer you this suggestion :-global.oup.comwhich is in the OUP and IUCr Book Series. Greetings,John Emeritus Professor John R Helliwell DScOn 14 Jul 2023, at 15:19, Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote: Hi all,   I'd

Re: [ccp4bb] Crystallisation textbook

Dear Mike,And a review of our book in Chemistry World:-Crystal clearchemistryworld.comGreetings,John Emeritus Professor John R Helliwell DScOn 14 Jul 2023, at 16:20, John R Helliwell wrote:Dear Mike,I offer you this suggestion :-global.oup.comwhich is in the OUP and IUCr Book Series. Greetings

[ccp4bb] General interest

. The book itself is also open access:- https://www.jstor.org/stable/j.ctv2gz3zp1 Best wishes, John Emeritus Professor John R Helliwell DSc To unsubscribe from the CCP4BB list, click the following link: https

Re: [ccp4bb] Patenting ligand binding?

stumbling block at least at Univ Manchester who have a keen eye for whether it might be deemed worth it. Thanks for sharing. Greetings, John Emeritus Professor John R Helliwell DSc > On 28 Jul 2023, at 08:46, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscm

[ccp4bb] General interest: Data matters session at the ACA 2023 in Baltimore

Dear Colleagues, I have placed a note about this at the IUCr Committee on Data Public Forum: https://forums.iucr.org/viewtopic.php?f=39&t=457&sid=54ca94b6a4db968acc28ab6ce91b722f including a weblink to my slides at Zenodo. Best wishes, John Emeritus Professor John R Helli

Re: [ccp4bb] Occupancy Refinement limitation

Dear Matt,I believe this study we made may well assist your evaluations:-(IUCr) Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystalsjournals.iucr.orgBest wishes,John Emeritus Professor John R

[ccp4bb] Errors in atomic coordinates and B factors in MX

for Public Input to the IUCr Committee on Data. The article itself is also open access.Best wishes,John Emeritus Professor John R Helliwell DSc To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

R Helliwell DSc > On 2 Dec 2023, at 09:15, Tim Grüne wrote: > > Hi Mark, > responsible people are resigning from X. > Cheers, > Tim > > Am 01.12.2023 23:24, schrieb Mark J. van Raaij: >> just came across this critique of that paper on Twitter: >> Th

[ccp4bb] General interest: Interoperability of crystallographic data and databases

Dear Colleagues, I imagine you will be interested in this Feature Article on the "Interoperability of crystallographic data and databases" in the current issue of IUCrJ:- https://journals.iucr.org/m/issues/2024/01/00/lt5064/index.html Best wishes, John Emeritus Professor John R Hel

Re: [ccp4bb] Crystallizing a tough target

Dear Kavya, Concanavalin A with glucoside involved 120 mg/ml protein. Details of the crystallisation are here:- https://doi.org/10.1016/0022-2836(87)90198-7 PDB code 1GIC. Best wishes, John Emeritus Professor John R Helliwell DSc > On 5 Feb 2024, at 10:27, kavyashreem wrote: > >

Re: [ccp4bb] Combating disinformation in science and other areas

John R Helliwell DScOn 13 Feb 2024, at 23:16, Focco van den Akker wrote:Dear all,   As fellow scientists specializing in structural biology, it's disheartening to witness a decline in society's trust in science; perhaps many of you have come across the remarkable book "The Dead

Re: [ccp4bb] request for applications

emittance we can get, then it passes through an undulator of alternating positive and negative ions. (A resemblance to a sodium chloride belies its its actual complexity). All best wishes, John Emeritus Professor John R Helliwell DSc > On 2 Apr 2024, at 09:03, Pete Dunten wr

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

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 Best wishes, John Emeritus Professor John R Helliwell DSc

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

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

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

developing plans that the IUCr Committee on Data will review this landscape under its new Chairman Prof Simon Coles. It would be great if you would be there.All best wishes,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 18:11, Filipe Maia wrote: Hi, https://cxidb.org is also an

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

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

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

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

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

UK and bad for the EU. Greetings,John Emeritus Professor John R Helliwell DScOn 15 Jun 2024, at 03:52, James Holton wrote: 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

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Dear Colleagues,I think this paper from 1979 is still very interesting:-Crystallographic studies of the dynamic properties of lysozymenature.comHave a great weekend,John Emeritus Professor John R Helliwell DScOn 2 Aug 2024, at 16:29, Bohdan Schneider wrote:Hello:yes, a great discussion! I second

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Dear Medhanjali,I imagine you would find this useful:-Online_DPI: a web server to calculate the diffraction precision index for a protein structurejournals.iucr.orgSee also:-sciencedirect.comBest wishes,John Emeritus Professor John R Helliwell DScOn 22 Aug 2024, at 19:08, Medhanjali Dasgupta

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Dear Medhanjali,In case of difficulty with the weblink in our J Appl Cryst Online DPI paper that I mentioned, Prof Sekar provides this one:-Diffraction Precision Index (DPI)physics.iisc.ac.inBest wishes,John Emeritus Professor John R Helliwell DScOn 23 Aug 2024, at 21:53, Medhanjali Dasgupta

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

Dear Tim, and Arpita and Doeke, Basically structure is not affected (as evidenced by our Fisher and Helliwell database survey in Acta Cryst) but kinetics is affected ie everything is slower in D2O and can thereby be toxic. Greetings John Emeritus Professor John R Helliwell DSc > On 6 Sep 2

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