Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography
James, This is correct. To my knowledge, the only result of BD2K initiative which is still alive (barely) is proteindiffraction.org. I know that PDBj is planning to pick-up the data but they do not have funds to keep the entire system alive, i.e. check of netadata, processing, doi handlig, etc. Best regards Wladek On 6/14/2024 10:52 PM, 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. 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 <martin.maly...@email.cz> 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1";>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB";>www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk";>www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/";>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=1"; target="_blank">https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 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 ofwww.jiscmail.ac.uk/CCP4BB, a mailing list hosted bywww.jiscmail.ac.uk, terms & conditions are available athttps://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=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 https://minorlab.org US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography
Dear Martin, I am the one who presented in Melbourne. When you contact support, please send cc to wla...@minorlab.org. Just for your information, proteindiffraction.org is not supported by NIH since 2018. Best regards Wladek On 6/14/2024 1:55 PM, 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. 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 href="https://proteindiffraction.org/";>proteindiffraction.org currently. Greetings,John dir="ltr">Emeritus Professor John R Helliwell DScdir="ltr">On 13 Jun 2024, at 10:41, Martin Malý <martin.maly...@email.cz> wrote:dir="ltr"> Dear John, Thank you for the link. It would be great if href="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: cite="mid:025c572c-c078-40d5-9fca-e697aba6b...@gmail.com"> 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:- href="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 To unsubscribe from the CCP4BB list, click the following link: href="https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1";>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of class="moz-txt-link-abbreviated" href="http://www.jiscmail.ac.uk/CCP4BB";>www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by href="http://www.jiscmail.ac.uk";>www.jiscmail.ac.uk, terms & conditions are available at href="https://www.jiscmail.ac.uk/policyandsecurity/";>https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: href="https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1"; target="_blank">https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 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/ 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/ -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 https://minorlab.org US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 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/
[ccp4bb] reproducibility workshop on April 7th
Please look at IRRMC (proteindiffraction.org) meeting WEB page: https://bioreproducibility.org/media/irrmc_conference/ If you are interested, please register to the meeting. Please note that meeting is a part of the US National Committee for Crystallography workshop series on exploring structural database use in crystallography. So, you have an opportunity to register to other meetings but please remember that our is IRRMC meeting. Meeting start on 11:00 EST (East Coast), 8:00 PST(West Coast), 15:00 UK time, 16:00 European time and 12:00am Tokyo time (sorry). Best regards Wladek -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 http://minorlab.org US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 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/
[ccp4bb] Symposium on Understanding Biology through Structure, May 13-17, 2017, Santa Fe
Dear Colleagues, As a member of the organizing committee of "Understanding Biology through Structure", I'd like to encourage you to come to Santa Fe May 13-17 to attend this exciting Symposium. In addition to an exceptional set of talks including X-ray crystallography, cryo-EM, biochemical and biophysical methods, the Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. The meeting website is at https://conferences.newmexicoconsortium.org/conferences/ubts_17 and the program can be seen at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Looking forward to seeing you there, Wladek Minor -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] HKL2000 and incompleteness
Try to increase profile fitting radius. WM --Original Message-- From: Ted Erickson Sender: CCP4 bulletin board To: CCP4BB@JISCMAIL.AC.UK ReplyTo: Ted Erickson Subject: Re: [ccp4bb] HKL2000 and incompleteness Sent: Apr 11, 2009 7:56 PM >So before I lose it because of HKL2000, I have two questions, and I'd appreciate any answers to either: >1. Can there be another reason for incompleteness that I am missing (other than blind region at higher res., overlaps, overloads, and "not enough many frames")? Another explanation for incompleteness could be due to crystal packing that results in an asymmetric diffraction pattern. The discrepancy between HKL2000 and mosflm maybe a result of the resolution cutoff, however, this is only a speculation. Ted www.P212121.com Sent via BlackBerry by AT&T
Re: [ccp4bb] images
Dear All, I would like to inform you that two SG centers: Center for Structural Genomics of Infectious Diseases - CSGID http://www.csgid.org and Seattle Structural Genomics Center for Infectious Diseases - SSGCID http://ssgcid.org/home/Target_Status.asp set-up the server at University of Virginia that will have diffraction images for all deposits from these two centers. Anybody in the World can have an access after simple registration. At the moment there are only two data sets available: 3ftt - that started whole discussion 3e4f but soon we should have all (??) of them. Also JCSG has their server with many datasets of JCSG structures. Hopefully this policy will proliferate. Wladek At 11:27 AM 3/12/2009, Garib Murshudov wrote: Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs "observed" statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for mistakes. They are doing their best to produce and deposit. There should be a proper mechanism to reduce the number of mistakes. You should agree that situation is now much better than few years. 2) A fundamental problem: What are observed data? I agree with you (Gerard) that images are only true observations. All others (intensities, amplitudes etc) have undergone some processing using some assumptions and they cannot be considered as true observations. The dataprocessing is irreversible process. I hope your effort will be supported by community. I personally get excited with the idea that images may be available. There are exciting possibilities. For example modular crystals, OD, twin in general, space group uncertaintly cannot be truly modeled without images (it does not mean refinement against images). Radiation damage is another example where after processing and merging information is lost and cannot be recovered fully. You can extend the list where images would be very helpful. I do not know any reason (apart from technical one - size of files) why images should not be deposited and archived. I think this problem is very important. regards Garib On 12 Mar 2009, at 14:03, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/ sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of "data" is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ======= Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] 3ftt and gremlins
Dear Eleanor and Gerard, PDB testing is performed on MTZ file and can not detect conversion errors. Wladek At 10:03 AM 3/12/2009, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of "data" is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: > It would be possible for the deposition sites to run a few simple tests to > at least find cases where intensities are labelled as amplitudes or vice > versa - the truncate plots of moments and cumulative intensities at least > would show something was wrong. > > Eleanor > -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ======= Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] 3ftt and gremlins
Eleanor, Please note that so far CIF structure factors files were not sent by deposition site for verification to authors. I spoke with Helen and John last Saturday and they promised me to change that policy. Alternatively, one can check his/hers new deposit on every Wednesday morning. Best regards Wladek At 05:22 AM 3/12/2009, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor Wladek Minor wrot Dear All, I just received information from Michael Gao (PDB) that updated sf file which is scheduled to be released on March 17, 2009 to replace the current incorrect sf file. Wladek Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] 3ftt and gremlins
Dear All, I just received information from Michael Gao (PDB) that updated sf file which is scheduled to be released on March 17, 2009 to replace the current incorrect sf file. Wladek Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
[ccp4bb] 3ftt and gremlins
Dear Michael, As we already wrote to Helen and John, structure factors for our deposit (PDB ID 3FTT and RCSB ID RCSB051033) were mis-processed. Currently, what was pointed on CCP4BB, instead of experimental amplitudes and sigmas PDB reports calculated amplitudes and phases. Most probably our deposited mtz file was wrongly processed because of non-standard labels for some data (F_set1 instead of F and SIGF_set1 instead of SIGF). Could you send me as soon as possible information on processing of our data file and correct our deposit? If it is necessary I will send you file with structure factors. I am including letter that I have sent to Helen and John on Saturday morning: Dear Helen and John, Following our conversation in the morning, please look into the problem with conversion of our MTZ data (for the 3ftt deposit) into structure factor CIF files. Apparently, instead of Fobs and sigmas, the Fcalc and phases are in the CIF file. To avoid these problems in the future, I propose that the CIF file containing structure factors is sent to authors for approval together with other files. I hope that we can resolve that quickly, taking into account the current discussion on the ccp4 bulletin board. I will copy you with discussion on ccp4 bulletin board initiated by Gerard. Best regards Wladek Best regards, Wladek Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
