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

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 >

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 th

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

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 "b

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 struc

Re: [ccp4bb] very informative - Trends in Data Fabrication

On Mon, Apr 2, 2012 at 11:00 AM, Maria Sola i Vilarrubias 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

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

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 ar

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

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

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

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 Loriot 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

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 "h

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,

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,

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 t

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

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 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 fabricat

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 AT&T -Orig

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/

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 practi

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 arrangemen

[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 bi

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:CCP4

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

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

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 boa

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

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

[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-u

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

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

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 infor

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

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 o

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.

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 o

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,

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 i

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

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 pheno

[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,

[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 chem