[ccp4bb]
Dear Abraham, after you added all TER signal and have all rows with atom number present you can use pdbset to renumber all atoms. For this take care that you call first your TER signal ATOM (otherwise this row will be deleted). Regards Marcus - Original Message - From: protein chemistry To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, April 01, 2012 8:42 PM Subject: [ccp4bb] Dear All, I have one query regarding the atom number in the coordinates. Before i began with my coordinate submission i need to put TER cap at the end of chains/polymers, but that may lead to change in atom number for the subsequent residues/molecules. i need to know is there any way to do this or i shall leave it and submit the coordinates directly. Thanks in advance Abraham
[ccp4bb]
or you can just give the TER card an arbitrary number higher than your highest ATOM number - the PDB coordinate submission server will take care of renumbering. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 2 Apr 2012, at 09:34, Marcus Fislage wrote: Dear Abraham, after you added all TER signal and have all rows with atom number present you can use pdbset to renumber all atoms. For this take care that you call first your TER signal ATOM (otherwise this row will be deleted). Regards Marcus - Original Message - From: protein chemistry To: CCP4BB@JISCMAIL.AC.UK Sent: Sunday, April 01, 2012 8:42 PM Subject: [ccp4bb] Dear All, I have one query regarding the atom number in the coordinates. Before i began with my coordinate submission i need to put TER cap at the end of chains/polymers, but that may lead to change in atom number for the subsequent residues/molecules. i need to know is there any way to do this or i shall leave it and submit the coordinates directly. Thanks in advance Abraham
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
To my mind it just points to the fact that many scientists are generally unable to focus on one task or 'thing' at a time. i.e. very short attention spans... [before the flamer's start ‹ this is meant as a joke] Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On 4/2/12 9:47 AM, Manfred S. Weiss manfred.we...@helmholtz-berlin.de wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activit y Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear Colleagues, This is a further instance of likely scientific fraud in macromolecular crystallography, ie under formal investigation at the relevant university. Both Bernhard and the Acta D and F Editors further document aspects in their written pieces related to the need for diffraction data images availability. The call for a 'universal system' by the Editors, in their Editorial, is also what the IUCr Forum on these matters has also been discussing. A possible convergence on local raw data repositories, with each data set doi registered where it underpins a publication, detailed by the IUCr DDD WG thus far, is unlikely to be 'universal' in its global coverage. But setting standards by encouraging raw data archives in our field will afford a much needed clarity in favour of retaining raw data wherever possible. A separate issue will be, in my view, the certain expansion of current validation checks. Indeed it is the standard practice in chemical crystallography submissions to IUCr journals for Co-Editors to validate the structure determination and refinement, including omit map calculations where appropriate. Of course this is most often a much easier task in chemical crystallography, per crystal structure checked, than would be the case for macromolecular crystallography. Again I encourage colleagues to lodge their inputs at the IUCr Forum on any aspect of principle or practice in achieving diffraction raw data archiving. Best wishes, John John R Helliwell On Mon, Apr 2, 2012 at 9:47 AM, Manfred S. Weiss manfred.we...@helmholtz-berlin.de wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- Professor John R Helliwell DSc
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear Manfred, I understand your surprise and indignation, but for the sake of fairness you might also remember that I argued rather insistently at the end of last year in favour of the deposition of raw diffraction images, which is the crux of this problem. With best wishes, Gerard. -- On Mon, Apr 02, 2012 at 10:47:26AM +0200, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -- === * * * 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 * * * ===
Re: [ccp4bb] very informative - Trends in Data Fabrication
For the latest documentary on trolls in Norway see http://www.imdb.com/title/tt1740707/ The documentary describes both the classification system of Norwegian Trolls and why they are sensitive to sun light, i.e turn to stone. Depending in the species, some Trolls apparently prefer bridges and others caves. They all are attracted to christian blood though. cheers Preben On 4/1/12 10:42 PM, Ethan Merritt wrote: On Sunday, 01 April 2012, Kendall Nettles wrote: What is the single Latin word for troll? Kendall According to Google Translate, it is Troglodytarum. But I'm dubious. I thought trolls lived under bridges rather than in caves. Except for the ones who inhabit the internet, of course. Ethan -- J. Preben Morth, Ph.D Group Leader Membrane Transport Group Nordic EMBL Partnership Centre for Molecular Medicine Norway (NCMM) University of Oslo P.O.Box 1137 Blindern 0318 Oslo, Norway Email: j.p.mo...@ncmm.uio.no Tel: +47 2284 0794 http://www.jpmorth.dk
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear Kevin et al., At the risk of being flamed as well, I could not resist this opportunity for shameless self promoting During my Ph.D. I worked on a flavoprotein as well and found flavin bending angles of 10 and 19°. I even published pictures of the electron density of the flavin (J.Mol.Biol.(1989), 208:679-696) and cited a reference from 1987 reporting a flavin bending angle of 20° for another flavoprotein. In this time, one had to presonally modify the PROLSQ restraints by hand, since if something was defined as being flat, it would become flat, no matter what the electron density was trying to say. Trying since there was no Rfree, no maximum likelyhood refinement and no CCP4BB so the maps were heavily biased. Although this period is commonly referred to as the stone-age of protein crystallography, many crystal structures were solved in this time that are still valid today. Before reinventing wheels, one could look a little further back in the literature than the last 7 years. Remains the question how this incorrect FMN definition could remain in the CCP4 package for so long. We need more people like Kevin, who loudly complain about errors in the CCP4 definitions instead of just fixing one's personal definition. Cheers! Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Sunday, April 01, 2012 9:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate andinterpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map... You are right! Actually, I am not an experienced protein crystallographer. I have learnt a lot from CCP4BB. I may have paid too much attention to bonding angle and bond length, like in small molecule. This may be an example to share with you. When I worked on those nitroreductase complexed with FMN in 2009 (?), I always observed that the flavin ring presented a strange geometry after refinement. Indeed, I had used the definition of FMN from CCP4 library all the time. In some cases, the methyl group at position of either 7a or 8a was bent off the aromatic ring, if the whole the rest of flavin was restrained in a flat plane. According to my limited knowledge from organic chemistry, carbon of 7 and 8 on the flavin ring is sp2 hybridized in a coplanar manner. How could those methyl groups be bent as sp3 hybridization? Any chemistry behind? With increased resolution (1.6 ~ 1.8 Ang), I observed that the electron density map was a bent along the N5-N10 axis. The bend angle was around ~16 degree. Again, I questioned myself why it was bent? Should this be correct? According to my limited knowledge in chemistry, N10 should be sp3 configuration even if FMN is in its oxidization form, in which the flavin ring should be bent. A quick google immediately gave me a link to a very nice paper published by David W. Rodgers in 2002. http://www.jbc.org/content/277/13/11513.full.pdf+html According to this paper, Yes! In the oxidized enzyme, the flavin ring system adopts a strongly bent (16°) conformation, and the bend increases (25°) in the reduced form of the enzyme,... When I reported this in the group meeting, I was laughed and told that this is just a model bias. It was over interpreted. Nobody has such sharp vision on electron density map. If this was correct, why nobody could find this and report to CCP4 within last 7 years? Eventually, a senior team member emailed to CCP4 about this issue. Since then, the definition of FMN was updated, according to my suggestion. I was asked how did you find it?... why you believed you are so right? I really don't how to answer. Je pense donc je suis Kevin On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine. But they can't just magic funding and positions into existence... If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated. 1. All of data was correct and real,
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
OK, following on our psychological displacement: The examples Pheobe gave are mostly of collective nouns http://en.wikipedia.org/wiki/Collective_noun to be distinguished from mass nouns: http://en.wikipedia.org/wiki/Mass_noun Strictly speaking, data is not a collective noun and is the plural of datum. Use of singular form is accepted nowadays but it doesn't mean that it's correct. To quote Merriam-webster: ...Data leads its own life independent of datum... See: http://www.merriam-webster.com/dictionary/data And by the way, what do you answer to how much data did you collect? A lot? just a little? Had we asked: how complete is your data? how many frames did you collect? How many data sets? wouldn't we have got a much more informative answer? Boaz Most crystallographers use the word data as a mass noun - that is, the syntax of data follows that of gravel or mud, not that of pebble/pebbles. People who pounce on the phrase data is routinely say data collection and data processing. But note that the proper way to construct compound nouns such as those is to use the singular form - one would never say rocks collection or apples picking. So if we have to say data are then we should be discussing how (not) to fabricate a datum set. Also note that when people come back from the synchrotron, we ask how much data did you collect not how many. Much is generally used with mass nouns. That doesn't mean we can't ALSO use the word as one with discrete singular and plural forms, especially when we have a few, individual observations rather than a huge pile that blurs into an aggregate. In that case, I see nothing incorrect about discussing an individual datum and using data as the plural form. Sometimes it is the artificial, over-simplified rule that is stupid, not the native speakers of a language. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alp habetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
Re: [ccp4bb] very informative - Trends in Data Fabrication
I am surprised that James Holton was not listed as a co-author, I understand that he has been expending a great deal of effort into how to accurately fabricate data. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] very informative - Trends in Data Fabrication
If James Holton had been involved, the fabrication would not have been discovered. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Schuller Sent: Monday, April 02, 2012 2:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication I am surprised that James Holton was not listed as a co-author, I understand that he has been expending a great deal of effort into how to accurately fabricate data. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. On Mon, 2 Apr 2012, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f?r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] very informative - Trends in Data Fabrication
I thought Ethan was looking for the verb -- you know, fishing!!! On Mon, 2 Apr 2012, jens Preben Morth wrote: For the latest documentary on trolls in Norway see http://www.imdb.com/title/tt1740707/ The documentary describes both the classification system of Norwegian Trolls and why they are sensitive to sun light, i.e turn to stone. Depending in the species, some Trolls apparently prefer bridges and others caves. They all are attracted to christian blood though. cheers Preben On 4/1/12 10:42 PM, Ethan Merritt wrote: On Sunday, 01 April 2012, Kendall Nettles wrote: What is the single Latin word for troll? Kendall According to Google Translate, it is Troglodytarum. But I'm dubious. I thought trolls lived under bridges rather than in caves. Except for the ones who inhabit the internet, of course. Ethan -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Requested: Three-Day Data Fabrication Workshop
Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Guys, http://www.youtube.com/watch?v=CobZuaPMQHw second 9 in this 22 sec video -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Monday, April 02, 2012 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
On 04/02/12 11:15, Jacob Keller wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): ... --Break-out support-session with survivors: comforting words on careers after the fall There's always economics. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
I'm now preparing for the flood of 'unsubscribe ccp4bb' requests On Apr 2, 2012, at 9:15 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote: Guys, http://www.youtube.com/watch?v=CobZuaPMQHw second 9 in this 22 sec video -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard DVD Kleywegt Sent: Monday, April 02, 2012 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear Gerard, inside Germany it's apparently called German Humour. There's a Wikipedia entry for that as well. Go figure: http://en.wikipedia.org/wiki/German_humor Andreas (still living on Sunday time) On 02/04/2012 4:03, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately.
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990
Re: [ccp4bb] very informative - Trends in Data Fabrication
Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat außer Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse . Ø And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions on BB and then some, and to all those who actually read BMC and submitted errata. Best regards, BR - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 hofkristall...@gmail.com b...@hofkristallamt.org http://www.ruppweb.org/ -- Once the sun of science is standing low, even dwarfs cast tall shadows --
[ccp4bb] Postdoctoral Position Available in Structural Biophysics and Protein Engineering in Rockville, Maryland, USA
A NIH funded postdoctoral position is available at the Institute for Bioscience Biotechnology Research (IBBR) at the University of Maryland in Rockville, Maryland, USA. Several research projects are available to study the interleukin-7 signaling pathway at the structural, biochemical, and biophysical levels. Candidates must have a Ph.D. degree in biochemistry or a related field, with experience in molecular biology, bacterial/insect cell protein expression and purification. Prior experience in structural (X-ray crystallography or NMR spectroscopy) and biophysical techniques is preferred. Salary will be commensurate upon experience. For further information (http://www.ibbr.umd.edu/profiles/scott-walsh) or to apply for the position please send a cover letter, CV, and two references to Dr. Scott Walsh (email: swals...@umd.edu).
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Touche. I very humbly and sincerely hereby retract my previous post--pressured by the scientific community, I felt obligated to present something of worth to the community, and therefore completely dreamed up the whole conference. I hope I have not inconvenienced anyone who may have made arrangements for travel based on my previous posting. JPK On Mon, Apr 2, 2012 at 10:39 AM, James Kiefer kiefer.ja...@gene.com wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Dear James, On Mon, Apr 02, 2012 at 08:39:41AM -0700, James Kiefer wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. Wait a minute ... I have indeed been trying to understand what types of random processes would best model errors in actual data, but that is in order to produce better likelihood functions to refine against raw data, not to better fake errors in fabricated data ;-) - although of course ... . Your suggested title is very good! I will work on a talk, even if the Workshop never happens. With best wishes, Gerard. -- I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990 -- === * * * 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 * * * ===
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Dear Andreas, That page confirms the old adage: German humour is no laughing matter. --Gerard On Mon, 2 Apr 2012, Andreas F?rster wrote: Dear Gerard, inside Germany it's apparently called German Humour. There's a Wikipedia entry for that as well. Go figure: http://en.wikipedia.org/wiki/German_humor Andreas (still living on Sunday time) On 02/04/2012 4:03, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
And please consider the date of Sunday's posts. We take this stuff seriously. That's what's nice about science. We ferret out mischief and bring it to the public. Nothing up my sleeve - all tricks will be exposed and dealt with harshly A Buffalo view. Sent via BlackBerry by ATT -Original Message- From: Gerard DVD Kleywegt ger...@xray.bmc.uu.se Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Mon, 2 Apr 2012 17:03:42 To: CCP4BB@JISCMAIL.AC.UK Reply-To: Gerard DVD Kleywegt ger...@xray.bmc.uu.se Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. On Mon, 2 Apr 2012, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f?r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Maybe we could have the workshop in Abilene? JPK On Mon, Apr 2, 2012 at 11:25 AM, Gerard Bricogne g...@globalphasing.comwrote: Dear James, On Mon, Apr 02, 2012 at 08:39:41AM -0700, James Kiefer wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. Wait a minute ... I have indeed been trying to understand what types of random processes would best model errors in actual data, but that is in order to produce better likelihood functions to refine against raw data, not to better fake errors in fabricated data ;-) - although of course ... . Your suggested title is very good! I will work on a talk, even if the Workshop never happens. With best wishes, Gerard. -- I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990 -- === * * * 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 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] very informative - Trends in Data Fabrication
Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat auA*er Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse A* And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions on BB and then some, and to all those who actually read BMC and submitted errata. Best regards, BR - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 hofkristall...@gmail.com b...@hofkristallamt.org http://www.ruppweb.org/ -- Once the sun of science is standing low, even dwarfs cast tall shadows --
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Yep, phenix.fake_f_obs is available for use since April 22, 2011, but I made it such that it will only do the right thing in experienced hands -;) and I wouldn't teach it unless you sign a disclaimer -:) It's good for developers though who want to do fully controllable numeric experiments to test ideas. Pavel On Mon, Apr 2, 2012 at 8:39 AM, James Kiefer kiefer.ja...@gene.com wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990
Re: [ccp4bb] very informative - Trends in Data Fabrication
I like your point--somehow we should enlist the evil inclination to power our science, a la Faust. How is it that those hackers are so innovative for so little reward? I remember a Smithsonian article years ago which quoted the calculated mean $/hr rate of money counterfeiters as being ~pennies/hr, and I assume hackers would fit right in there... JPK On Sun, Apr 1, 2012 at 11:45 PM, Artem Evdokimov artem.evdoki...@gmail.comwrote: I can't resist asking: If we assume that the data fabrication techniques and the techniques for discovery of such activities should have the same sort of arms race as the development of viruses and anti-malvare software (but of course on a much more modest scale since structural biology is a relatively niche discipline) - can we then speculate further that eventually the most sophisticated fabrication techniques would be equivalent to de novo structure prediction :) It's really too bad that there's no real money in this (again, relatively speaking - not as much money as there is in software development), because if there was then the structural biology equivalent of 'virus hackers' would in reality approximate the same development trajectory as the most successful (and legitimate) protein modelers. Given the ingenuity of hackers and like-minded people in general, I sometimes wonder if this isn't a better way to develop structure prediction tools... Artem On Sun, Apr 1, 2012 at 10:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine. But they can't just magic funding and positions into existence... If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated. 1. All of data was correct and real, Hmmm... It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate and interpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map... Paul. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] very informative - Trends in Data Fabrication
I thought we had evidence for hackers doing this already. J http://www.nature.com/nature/journal/v477/n7365/full/477373e.html (no flames, please-'tis intended to be funny, not factual) Bryan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, April 02, 2012 1:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication I like your point--somehow we should enlist the evil inclination to power our science, a la Faust. How is it that those hackers are so innovative for so little reward? I remember a Smithsonian article years ago which quoted the calculated mean $/hr rate of money counterfeiters as being ~pennies/hr, and I assume hackers would fit right in there... JPK On Sun, Apr 1, 2012 at 11:45 PM, Artem Evdokimov artem.evdoki...@gmail.com wrote: I can't resist asking: If we assume that the data fabrication techniques and the techniques for discovery of such activities should have the same sort of arms race as the development of viruses and anti-malvare software (but of course on a much more modest scale since structural biology is a relatively niche discipline) - can we then speculate further that eventually the most sophisticated fabrication techniques would be equivalent to de novo structure prediction :) It's really too bad that there's no real money in this (again, relatively speaking - not as much money as there is in software development), because if there was then the structural biology equivalent of 'virus hackers' would in reality approximate the same development trajectory as the most successful (and legitimate) protein modelers. Given the ingenuity of hackers and like-minded people in general, I sometimes wonder if this isn't a better way to develop structure prediction tools... Artem On Sun, Apr 1, 2012 at 10:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine. But they can't just magic funding and positions into existence... If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated. 1. All of data was correct and real, Hmmm... It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate and interpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map... Paul. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Hm, last I checked my passport said German - still think I can make lots of fun of myself. Some Germans are epigenetically marked with humor-suppressor genes others not. Jürgen On Apr 2, 2012, at 11:03 AM, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. On Mon, 2 Apr 2012, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edumailto:schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f?r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
My favorite part of the german humor link: Some German humorists such as Loriothttp://en.wikipedia.org/wiki/Vicco_von_B%C3%BClow use seriousness as means of humor. On Apr 2, 2012, at 1:38 PM, Bosch, Juergen wrote: Hm, last I checked my passport said German - still think I can make lots of fun of myself. Some Germans are epigenetically marked with humor-suppressor genes others not. Jürgen On Apr 2, 2012, at 11:03 AM, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. On Mon, 2 Apr 2012, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edumailto:schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f?r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.dehttp://www.helmholtz-berlin.de/ Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 And the summary indicates that outside Germany = English speaking world - which probably unveals its author as American ;-) On 04/02/12 18:25, Gerard DVD Kleywegt wrote: Dear Andreas, That page confirms the old adage: German humour is no laughing matter. --Gerard On Mon, 2 Apr 2012, Andreas F?rster wrote: Dear Gerard, inside Germany it's apparently called German Humour. There's a Wikipedia entry for that as well. Go figure: http://en.wikipedia.org/wiki/German_humor Andreas (still living on Sunday time) On 02/04/2012 4:03, Gerard DVD Kleywegt wrote: Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPeed9UxlJ7aRr7hoRAh9tAKDpydssNnLTrxn51ccjsR6Sfr4azwCdHWN1 u2uFraBdBejfkNLF9nnXhCA= =OngV -END PGP SIGNATURE-
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear Phoebe, I cannot imagine myself delivering maps and coordinates (after years of work... I insist: after years of work) to a reviewer that could be, for whatever chance, my best competitor (even if I suggested to the editor not to include him/her as a reviewer... but decisions from editors are of all kind). I simply prefer not imagine this after two publications fuelled by clear, direct and strong competition. That was stressful enough, already. If I have to add to this stress the thought that my coordinates can go to the wrong hands, then I think I would just give up or, alternatively, send the work to a lower impact, fast-publishing journal and make my life easier while sending my scientific future to the low-impact bin, killing future opportunities. Competition is there. I see that data to be deposited is strictly confidential. I support the PDB to make the quality check work at the level you mention, but not a reviewer: People are nice but the world is big and competition is crazy… at least enough to make fraud or copy other's work. The latter is less difficult; by copying (simply copy and paste to my computer this nice structure that I was looking for!), there is no need to invent anything. About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. Maria On 2 April 2012 18:43, Phoebe Rice pr...@uchicago.edu wrote: Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat auA*er Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse A* And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions on BB and then some, and to all those who actually read BMC and submitted errata. Best regards, BR - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 hofkristall...@gmail.com b...@hofkristallamt.org http://www.ruppweb.org/ -- Once the sun of science is standing low, even dwarfs cast tall shadows -- -- Maria Solà Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Dear James, With all due respect, you have left out a key component to successful data fabrication in the modern age: THE MOLECULAR REPLACEMENT. Since almost all new structures have more or less close homologues in PDB, a smart fabricator should use their experimental data as a template. It will be more difficult to detect than the data built from the calculated structural factors. To prevent future fabrication attempts, we do not need submitting detector images, partially processed structural data such as unmerged structural factors would work, and they do not take that much space. The switch to the new format could be done in no time Alex On Apr 2, 2012, at 8:39 AM, James Kiefer wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990
Re: [ccp4bb] very informative - Trends in Data Fabrication
On Mon, Apr 2, 2012 at 11:00 AM, Maria Sola i Vilarrubias msv...@ibmb.csic.es wrote: About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. This will often be insufficient, I'm afraid. We generally assume good faith on the part of the authors: if the caption says the 2mFo-DFc map is shown contoured at 1.5sigma, we assume that this is an honest statement, but we also have no way of verifying it until the experimental data are available. I know of at least one case offhand where the maps could not possibly have been contoured at that level - the ligands are not misfit, they are simply not present in the crystals, and the paper is misleading (deliberately or not, I don't know). Most reviewers do not have the patience to spend weeks pursuing these issues. (Although it would certainly help if reviewers insisted that the density around ligands not be shown in isolation.) That aside, I completely understand why someone would be reluctant to share their data with potential competitors. Someone once suggested making the model and maps viewable via a web applet (AstexViewer or similar), but even that sounds like it could be prone to abuse. -Nat
Re: [ccp4bb] very informative - Trends in Data Fabrication
Artem Evdokimov wrote: I can't resist asking: If we assume that the data fabrication techniques and the techniques for discovery of such activities should have the same sort of arms race as the development of viruses and anti-malvare software (but of course on a much more modest scale since structural biology is a relatively niche discipline) - can we then I don't think this assumption holds for structure prediction, except in the extreme asymptotic limit. All of the cases of fabricated data that I've heard of were detected because the fabricated data didn't look like actual experimental data - because our models for calculating data are missing a variety of things that occur experimentally. So a hypothetical arms race might be result in a better model of the various components (and potential sources) of errors during data collection and processing. But this would be a much more interesting development in itself than any use for fabricating data. Pete speculate further that eventually the most sophisticated fabrication techniques would be equivalent to de novo structure prediction :) It's really too bad that there's no real money in this (again, relatively speaking - not as much money as there is in software development), because if there was then the structural biology equivalent of 'virus hackers' would in reality approximate the same development trajectory as the most successful (and legitimate) protein modelers. Given the ingenuity of hackers and like-minded people in general, I sometimes wonder if this isn't a better way to develop structure prediction tools... Artem On Sun, Apr 1, 2012 at 10:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine. But they can't just magic funding and positions into existence... If the coordinate is downloaded for modeling and docking, people may not check the density and model by themself. However this is not the worst case, since the original data was fabricated. 1. All of data was correct and real, Hmmm... It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. I hope and believe that this is not the case. Even basically-trained crystallographers should be able to calculate and interpret difference maps of the kind described by Bernhard. And with the EDS and PDB_REDO server, one does not even need to know how to make generate a difference map... Paul.
Re: [ccp4bb] very informative - Trends in Data Fabrication
That's very sad, but a good point. I may be a bit naive because I haven't had to worry mas uch about direct competition. However, I do find it very frustrating as a reviewer to try to pass judgement on a crystal structure based only on the standard table 1. Sometimes I'm tempted to write based on the information presented, darned if I know! Maybe 3rd-party validation through the pdb (with a report sent to the reviewers) is more appropriate? Phoebe = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 20:00:48 +0200 From: Maria Sola i Vilarrubias msv...@ibmb.csic.es Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: pr...@uchicago.edu Cc: CCP4BB@jiscmail.ac.uk Dear Phoebe, I cannot imagine myself delivering maps and coordinates (after years of work... I insist: after years of work) to a reviewer that could be, for whatever chance, my best competitor (even if I suggested to the editor not to include him/her as a reviewer... but decisions from editors are of all kind). I simply prefer not imagine this after two publications fuelled by clear, direct and strong competition. That was stressful enough, already. If I have to add to this stress the thought that my coordinates can go to the wrong hands, then I think I would just give up or, alternatively, send the work to a lower impact, fast-publishing journal and make my life easier while sending my scientific future to the low-impact bin, killing future opportunities. Competition is there. I see that data to be deposited is strictly confidential. I support the PDB to make the quality check work at the level you mention, but not a reviewer: People are nice but the world is big and competition is crazy… at least enough to make fraud or copy other's work. The latter is less difficult; by copying (simply copy and paste to my computer this nice structure that I was looking for!), there is no need to invent anything. About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. Maria On 2 April 2012 18:43, Phoebe Rice pr...@uchicago.edu wrote: Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat auA*er Dienst, is written as Bernhard - unless you are referring to some other guy with a french name Bernard. As one may extrapolate given my recent paper, I have been called names a lot worse A* And the book indeed is a bible of xtallography. Enough of this - it is becoming embarrassing. I wish I had done a more careful job proofing, as over 500 errata attest to, and we all are only seeing further because we are standing on the shoulders of giants. So once again thanks to all the contributors I have pestered with my questions
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear Phoebe, As it happens, validation through the PDB is exactly what the X-ray Validation Task Force proposed (to be honest, it was a suggestion made by George Sheldrick the last time there was a debate like this on the CCP4-BB!), and the wwPDB is currently implementing the pipeline needed to automatically produce a good validation report. A preliminary version of such a report is already available when you deposit a structure now, the IUCr journals already require this for papers describing structures, and there seems to be interest from some other journals. In the meantime, if you're refereeing a paper from a journal that doesn't require the validation report to be submitted with the paper, you can always ask them to get it from the author. Best wishes, Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 2 Apr 2012, at 20:01, Phoebe Rice wrote: That's very sad, but a good point. I may be a bit naive because I haven't had to worry mas uch about direct competition. However, I do find it very frustrating as a reviewer to try to pass judgement on a crystal structure based only on the standard table 1. Sometimes I'm tempted to write based on the information presented, darned if I know! Maybe 3rd-party validation through the pdb (with a report sent to the reviewers) is more appropriate? Phoebe = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 20:00:48 +0200 From: Maria Sola i Vilarrubias msv...@ibmb.csic.es Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: pr...@uchicago.edu Cc: CCP4BB@jiscmail.ac.uk Dear Phoebe, I cannot imagine myself delivering maps and coordinates (after years of work... I insist: after years of work) to a reviewer that could be, for whatever chance, my best competitor (even if I suggested to the editor not to include him/her as a reviewer... but decisions from editors are of all kind). I simply prefer not imagine this after two publications fuelled by clear, direct and strong competition. That was stressful enough, already. If I have to add to this stress the thought that my coordinates can go to the wrong hands, then I think I would just give up or, alternatively, send the work to a lower impact, fast-publishing journal and make my life easier while sending my scientific future to the low-impact bin, killing future opportunities. Competition is there. I see that data to be deposited is strictly confidential. I support the PDB to make the quality check work at the level you mention, but not a reviewer: People are nice but the world is big and competition is crazy… at least enough to make fraud or copy other's work. The latter is less difficult; by copying (simply copy and paste to my computer this nice structure that I was looking for!), there is no need to invent anything. About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. Maria On 2 April 2012 18:43, Phoebe Rice pr...@uchicago.edu wrote: Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
That's pretty funny, isn't it? Andreas On 02/04/2012 6:52, Jacob Keller wrote: Sorry to beat a dead horse, but: * *Antiwitz* (/anti-joke/): A short, often absurd scene, which has the recognizable structure of a joke, but is illogical or lacking a punch-line. Example: /Two thick feet are crossing the street. Says one thick foot to the other thick foot: Hello!/ Other examples: Nachts ist es kälter als draußen (At night it's colder than outside) or Zu Fuß ist es kürzer als über'n Berg (Walking is faster than over the mountain).
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
Given some of the etymological discussion, and the suggestion of economics as an alternative career, it would seem that the workshop should be held in either Italy or Greece. Lynn Ten Eyck On Apr 2, 2012, at 9:30 AM, Jacob Keller wrote: Maybe we could have the workshop in Abilene? JPK On Mon, Apr 2, 2012 at 11:25 AM, Gerard Bricogne g...@globalphasing.com wrote: Dear James, On Mon, Apr 02, 2012 at 08:39:41AM -0700, James Kiefer wrote: Dear Jacob, With all due respect, you have left out a key component to successful data fabrication in the modern age: software. It is quite obtuse not to have allocated at least one day of the workshop for practical applications of Photoshop to diffraction image generation and at least a passing coverage of whether or not Adobe Lightroom and crystallographic presets therein will be sufficiently capable of muddling the RCSB staff analysis of data feasibility checking. I would very much like to see Gerard Bricogne present a keynote lecture entitled something like, The R-Fake Parameter: A Maximum Likelihood Modulus to Define a Minimum Acceptable Data Drift Coefficient for Use in the Fabrication of Credibly Artificial Diffraction Data. Wait a minute ... I have indeed been trying to understand what types of random processes would best model errors in actual data, but that is in order to produce better likelihood functions to refine against raw data, not to better fake errors in fabricated data ;-) - although of course ... . Your suggested title is very good! I will work on a talk, even if the Workshop never happens. With best wishes, Gerard. -- I also believe that we are perhaps full of hubris as a crystallographic community, because an entire field of faked structural data has existed long before crystallographers even considered manufacturing their data. Specifically, the molecular modeling community has already surpassed us in their thinking on the subject. While we idly discuss how to properly generate false data, they have had the foresight to abandon ALL data...and even the starting coordinates in crystal structures - be they real or fictitious - and publish volumes of papers entirely unencumbered by reality or plausibility. My hat is off to them. Best regards, Jim On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990 -- === * * * 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 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Requested: Three-Day Data Fabrication Workshop
I wish to point out (because I remembered just now) that I offered a similar service after the Murthy scandal on this BB in August 2007: http://www.ruppweb.org/new_comp/frame_maker.html - and JK proposed a value-added contribution. See attached. Btw, Kim Henrick's analysis from 2007 still seems rather lucid to me. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, April 02, 2012 8:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Requested: Three-Day Data Fabrication Workshop Dear CCP4BB, due to increasing demand, it seems we should put together a workshop on data fabrication, covering the various important topics (chaired by JHo): --Images: the future of fabrication? How long can we rely on database Luddism? --Ways out: how to leave a trail of accidental data mix-ups --Publish large or small? Cost-benefit analyses of impact factor vs. risk of being discovered --Pushing the envelope: how significant is two [sic] significant --Crossing discipline boundaries: are data fabrication procedures universal? --Build a better hofkristallrat-trap: utilization of rhetorical bombast and indignation in reply letters --Break-out support-session with survivors: comforting words on careers after the fall --Session on the inextricably-related topic of grammatical pedantry, to be followed by a soccer (football?) match Greeks Vs. Latins Ample funding will be available from big pharma and other industry sectors Please submit further topics to the CCP4BB list JPK ps I can't believe no one mentioned the loathsome Latino-Greek multimer in the recent curmudgeonry postings. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** ---BeginMessage--- In response to your website, I was thinking of a startup collecting old photos of crystals (harder to computer-generate) to go with the frames--interested in a collaboration? Maybe you could just put a link on your page? JPK ==Original message text=== On Fri, 17 Aug 2007 3:24:45 pm CDT Bernhard Rupp wrote: The PDB is missing a business opportunity. If authors pay 1000s of dollars for publication in high impact journals, they might as well pay a few bucks for image deposition. If I could get my images stored reliably and perpetually for something like $20-50 a pop, I'd do it. Do you know where your favourite frames from 1998 are? Image storage is a good idea *in itself*, but as an enforcement tool it only will make the *exceedingly few* Reids more inventive. PS: Frames for sale. http://www.ruppweb.org/new_comp/frame_maker.html -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kim Henrick Sent: Friday, August 17, 2007 7:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Richard Reid and the PDB After Richard Reid more than 100 million people each year have to have their shoes examined and one effect is that older buildings like Heathrow Terminal 3 is the most painful place on earth, the cost of someone trying light their shoelaces has affect us all. The discussion on archiving image data sets - I guess that less than 1% of the image sets for PDB entries are useful to software development (and can be got privately) I guess that maybe 1 in 10,000 entries have a series problem that may require referees to look at the images (and can be accessed upon demand) The cost of disks for your PC - kitchen table disks from a supermarket, may be $1 per Gbyte on USB i/o but an archive centre required to maintain the data will probably need RAID 0/1 - RAID 10, this has high performance, and highest data protection, i.e. can tolerate multiple drive failures, but has high redundancy cost overhead, if you havent noticed a large collection of disks has failures. Look up the problems that the series of Landsat satellites have had from 1980 onwards with the problems arising out of the volume of data and the short life of computer compatible tapes and optical discs. Archiving data lacks glamour its the boring day to day rectification and storage of information, very little money gets spent on this task,for remote sensing the most significant cost is transmission/correction and archiving the data - Three semi-trailer loads of Landsat tapes were found (literally) moldering in a damp basement in Baltimore after people and funding agencies lost interest. Oh yes and detectors change every 5 years and processing software gets lost. At the EBI before we even get a single disk we pay ,000 for a cabinet - disks cost around for 300gigbytes (and not the best disks these are around the same cost for 146 Gigbytes). Disk technology changes every 5 years - an archive cost is to recover the data ever 5 years onto the next generation of hardware. Molecular
