[ccp4bb] very informative - Trends in Data Fabrication

really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-fact

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

then send the links. Best regards, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Saturday, March 31, 2012 8:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] very informative - Trends in Data Fabrication really fascinating, bringing back

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

I don't model zero occupancy in my model. But can't the refinement programs just treat those atoms with zero occupancy as missing atoms? Nian Huang On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen wrote: > really fascinating, bringing back the discussion for a repository for your > collected fr

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

Sent: Saturday, March 31, 2012 11:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication I don't model zero occupancy in my model. But can't the refinement programs just treat those atoms with zero occupancy as missing atoms? Nian Huang O

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

the allegations. " From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Sent: Saturday, March 31, 2012 12:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication This is an unreso

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

Reading the paper from Dr. Hofkristallrat a.D. and the editorial in ActaF, I must say that besides the rather reasonable demand for journals to include crystallography experts as referees, "Table 1" would have fooled me as referee. A validation report of the VTF style might not had helped either

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

Nice paper ! I really wish PDB could have some people to review those important structures, like paper reviewer. 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 fabrica

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

Given a data set (Fobs or Iobs) and atomic model it is not trivial at all to tell whether they are real or fabricated. I looked into this problem for quite some time at some point, and developed my set of criteria that thoroughly attempt to distinguish between fake and real, but they can only be i

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

informative - Trends in Data Fabrication Reading the paper from Dr. Hofkristallrat a.D. and the editorial in ActaF, I must say that besides the rather reasonable demand for journals to include crystallography experts as referees, "Table 1" would have fooled me as referee. A validation rep

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

gt; From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis > Perrakis [a.perra...@nki.nl] > Sent: Sunday, April 01, 2012 7:59 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication > > Reading the paper from Dr. Hofk

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

.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Anastassis Perrakis [a.perra...@nki.nl<mailto:a.perra...@nki.nl>] Sent: Sunday, April 01, 2012 7:59 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Reading the pap

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

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

Btw, > "Table 1" would have fooled me as referee. Not if the bulk solvent parameters would be reported or validated. See recommendations. Best, BR

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

>> I still believe Prof. Dr. Hofkristallrat außer Dienst, is written as >> Bernhard - unless you are referring to some other guy with a >> french name >> Bernard. And the book indeed is a bible of xtallography. >>Jürgen ausser Dienst ... now I get it ... my German is a lot worse than just spelli

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

actors against reduced occupancy, and other (almost always purely > cosmetic but still confusing or inconsistent) practices. > > Best, BR > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Nian Huang > Sent: Saturday, March 31, 2012 11:29 AM > To: CCP4BB@JISCMAIL

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

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 doc

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

On Sat, Mar 31, 2012 at 6:08 PM, Kevin Jin wrote: > I have seen several stories like this. Here is an open letter to Nature. > > http://www.jinkai.org/AAD/AAD_letter_2_nature.html > I'd like to understand this better : please explain precisely, on this forum, the connection being made between th

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 ...”

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

Je pense donc je suis Kevin Cogito ergo erro. BR

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

What is the single Latin word for troll? Kendall On Apr 1, 2012, at 3:06 PM, "Kevin Jin" mailto:kevin...@gmail.com>> wrote: “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 describ

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

Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis. David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk Webs : http:/

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

orcus impudens From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kendall Nettles Sent: Sunday, April 01, 2012 1:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication What is the single Latin word for troll? Kendall On

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

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.

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

David Briggs a écrit : Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis. Should we say "Alea data est" or "Alea data sunt" ? Philippe DUMAS

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

http://trololololololololololo.com/ Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis. David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk ==

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

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 relati

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] very informative - Trends in Data Fabrication

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.

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] very informative - Trends in Data Fabrication

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

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] very informative - Trends in Data Fabrication

[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 ot

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

Date: Mon, 2 Apr 2012 08:41:02 -0700 >From: CCP4 bulletin board (on behalf of "Bernhard Rupp >(Hofkristallrat a.D.)" ) >Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication >To: CCP4BB@JISCMAIL.AC.UK > > Robbie has restored the PDB_REDO of 3k78 > &

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] very informative - Trends in Data Fabrication

onday, 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 rem

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

Original message > >Date: Mon, 2 Apr 2012 08:41:02 -0700 > >From: CCP4 bulletin board (on behalf of > "Bernhard Rupp (Hofkristallrat a.D.)" ) > >Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication > >To: CCP4BB@JISCMAIL.AC.UK

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] 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

ago.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 > (o

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

ooks/2008/9780854042722.asp > > > Original message ---- >> Date: Mon, 2 Apr 2012 20:00:48 +0200 >> From: Maria Sola i Vilarrubias >> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication >> To: pr...@uchicago.edu >> Cc: CCP4BB@jiscmail

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

3 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message >Date: Mon, 2 Apr 2012 08:41:02 -0700 >From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> (on behalf of "Bernhard Rupp (Hofkristallrat a.D.)" mailto:hofkristall...@g

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

t: Tuesday, April 03, 2012 9:31 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication The sad situation is that more and more scientists are becoming desperate (for funding or tenure or both) and are told 'pu

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

I think that to review a paper containing a structure derived from crystallographic data should indeed involve the referee having access to coordinates and to the electron density. Without this access it is not possible to judge the quality and very often even the soundness of statements in the pa

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

Hi I was thinking about the last statement in the Acta editorial - "It is important to note, however, that in neither of these cases was a single frame of data collected. Not one.". This brought me back to the images.. To date there is no "global" acceptance that original diffractiom images

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

Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the be

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

The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committ

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

Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more re

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

I don't agree, if we know a referee is dishonest we should try and ruin his whole career, not just prevent him from scooping us in this one case. 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. (+

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

In fact, I would put it even stronger, if we know a referee is being dishonest, it is our duty to make sure he is removed from science, blacklisted from the journal etc. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-280

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

Dear Colleagues, One thing that would help is avoiding misappropriated priority of research results would be to join the math and physics community in their robust use of open-access preprints in arXiv. Such public preprints establish reliable timelines for research credit and help to ensu

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

tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein [y...@bernstein-plus-sons.com] Sent: Wednesday, April 04, 2012 4:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data

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

On the topic of MX fraud : could not an encryption algorithm be applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe entry? has anyone proposed such an idea before? for example (admittedly this is a mess): * a detector parameter - perhaps the serial number - is used as a public

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

I'm not sure how encryption can solve a problem of "truth or falsity". Public key encryption only says that the message that is decrypted using the public key must have been encrypted by someone who knows the private key. A person can use their private key to encrypt a lie as well as the truth.

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

Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin

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

I read the first part of the page you linked to. I'm not sure what the decent into troll etymology says about the CCP4BB community--especially in response to your seemingly innocent post. My understanding is that the goal of the CCP4BB is to educate and not belittle the naivety of other members

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

On Tue, Apr 3, 2012 at 5:16 PM, Dale Tronrud wrote: > I'm not sure how encryption can solve a problem of "truth or falsity". AFAIU any given checksum will tell you if a file is corrupted or not. My brain decided to interpret that as true or false. and >  A person can use their private key t

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

skill of presentation is at least as important in Science as being right. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data

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

The skill of presentation is at least as important in Science as being > right. > > ** ** > > Best, BR > > ** ** > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Kevin > Jin > *Sent:* Tuesday, April 03, 2012 3:34 PM &

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

AIL.AC.UK>] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. htt

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

; ** ** >> >> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of >> *Kevin Jin >> *Sent:* Tuesday, April 03, 2012 3:34 PM >> >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* Re: [ccp4bb] very informative - Trends in Data Fa

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

03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin -- Kevin Ji

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

Hi, Regarding the online image file storage issue, I just googled "cloud storage" and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will fe

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

On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote: > I would also consider looking into adding an RSS feed to your site so that > those people interested in your articles can be informed without spamming the > boards. Why continue to punish him? Adding an RSS feed means installing and configu

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

James makes an important point. I've come to regret my joke as showing poor manners. I hesitate to add to more email that no one cares about, but I do think it is important to contribute the idea that the positive tone of this forum needs to be protected. I apologize, and suggest my comments s

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

No James, you're not alone - astonishing petty pile-on (bullying?) on this board the last few days. Wikipedia says: "In Internet slang , a *troll* is someone who posts inflammatory,^[2]

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

Then everyone's data can be lost at once in the next cloud failure. Progress! "The hardware failed in such a way that we could not forensically restore the data. What we were able to recover has been made available via a snapshot, although the data is in such a state that it may have little

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

People who raise their voices for a prolonged storage of raw images miss a simple fact that the volume of collected data increases proportionally if not faster than the cost of storage space drops. I just had an opportunity to collect data with the PILATUS detector at SSRL and say you that monst

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

@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Then everyone's data can be lost at once in the next cloud failure. Progress! "The hardware failed in such a way that we could not forensically restore the data. What we were able to recover has

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

Dear 'aales...@burnham.org', Re the pixel detector; yes this is an acknowledged raw data archiving challenge; possible technical solutions include:- summing to make coarser images ie in angular range, lossless compression (nicely described on this CCP4bb by James Holton) or preserving a sufficient

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

Dear Colleagues, Clearly, no system will be able to perfectly preserve every pixel of every dataset collected at a cost that can be afforded. Resources are finite and we must set priorities. I would suggest that, in order of declining priority, we try our best to retain: 1. raw data that

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

FYI, every NSF grant proposal now must have a data management plan that describes how all experimental data will be archived and in what formats. I'm not sure how seriously these plans are monitored, but a plan must be provided nevertheless. Is anyone NOT archiving their original data in some way?

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

I would say everybody keeps probably too many junk datasets around - at least I do. And I run into the trouble of having to buy new TB plates every now and then. I think on average per year my group acquires currently ~700 GB of raw images (compressed), now if we were to only keep the useful dat

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

Dear John, Thank you for a very informative letter about the IUCr activities towards archiving the experimental data. I feel that I did not explain myself properly. I do not object archiving the raw data, I just believe that current methodology of validating data at PDB is insufficiently robust

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

We do the remote access data collections from here, and retrieving raw data from a synchrotron is becoming a full time job for a synchrotron spokesperson at a large lab. I tried to read those CDs with the archived data once. One of disks failed. SSRL is nice enough to store the images for a whil

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

This discussion has been interesting, and it's provided an interesting forum for those interested in dealing with fraud in science. I've not contributed anything to this thread, but the message from Alexander Aleshin prodded me to say some things that I haven't heard expressed before. 1. The

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

CP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald E Stenkamp Sent: Thursday, April 05, 2012 1:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication This discussion has been interesting, and it's provided an interesting forum for those interested in dealing wit

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

ary data is generally considered bad form... > > @AlexA: Arguing with the PDB is not really useful. They did not generate > the bad data. > > Best, BR > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald > E Stenkamp

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

Ojweh > c) Discarding your primary data is generally considered bad form... Agreed, but it is a big burden on labs to maintain archives of their raw data indefinitely. Even IRS allows to discard them after some time. But you DO have to file in the first place, right? How long to keep is an

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

Alright, if the image deposition is the only way out, then I am for it, but please make sure that synchrotrons will do it for me... On Apr 5, 2012, at 7:58 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: > Ojweh > >> c) Discarding your primary data is generally considered bad form... > Agree

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

How should they ? They have no clue which of the 20 datasets was actually useful to solve your structure. If you ask James Holton he has (suggested) to go back to the archived data after a certain time and try to solve the undeposited structures then :-) [Where is James anyhow ? Haven't seen a p

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

Did you play as a child a game called "a broken phone"? It is when someone tells something quickly to a neighbor, and so on until the words come back to the author. Very funny game. My original thesis was that downloading/depositing the raw images would be a pain in the neck for crystallograph

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

Dear Ron, Re (3):- Yes of course the investigator has that responsibility. The additional point I would make is that the employer has a share in that responsibility. Indeed in such cases the employer university convenes a research fraud investigating committee to form the final judgement on continu

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

Dear John, Your points are well taken and they're consistent with policies and practices in the US as well. I wonder about the nature of the employer's responsibility though. I sit on some university committees, and the impression I get is that much of the time, the employers are interested

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

Ron makes an excellent point. Many institutions devote far more energy to limiting risk than to doing the right thing. This leads administrators to a frightening, but logical conclusion: The less science we do, the less chance of our doing something that could invite a penalty on the university.

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

As famously observed by the Yes Minister teamthe dream outcome for any organization: http://www.youtube.com/watch?v=x-5zEb1oS9A&feature=youtube_gdata_player J Sent from my iPhone On 07/04/2012, at 3:16 AM, Patrick Loll wrote: > Ron makes an excellent point. Many institutions devote far mo

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

Dear Ron, Quite so, and who cannot laugh at the Yes Minister perfect hospital ward operating theatre sketch ( Thankyou James W). Anyway:- Let's not get too hung up on one detail of your point 3. Your various points, including point 3, added several missing elements in this CCp4bb thread. Over

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

I doubt many people completely fail to archive data but maintaining data archives can be a pain so I'm not sure what the useful age of the average archive is. Do people who archived to tape keep their tapes in a format that can be read by modern tape drives? Do people who archived data to a ha

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

On 4/2/2012 6:03 AM, herman.schreu...@sanofi.com wrote: If James Holton had been involved, the fabrication would not have been discovered. Herman Uhh. Thanks. I think? Apologies for remaining uncharacteristically quiet. I have been keeping up with the discussion, but not sure how much diff

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

Since I was the person who started "a public outcry to "do something"", I shell explain myself to my critics. Similarly to all of you, I do not care much about those few instances of structure fabrication. I might put too much emphases on them to initiate the discussion, but they are, indeed, on

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

>You never know when a forgotten slip of the mouse when using AutoDep ten years ago will come back to haunt you. On the paper James refers to and found the data, added mystery was that the postdoc who may have slipped disappeared w/o much of trace and the PI died. Dan was the only survivor. Still

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

On 8 Apr 2012, at 21:18, aaleshin wrote: > What I suggested with respect to the PDB data validation was adding some > additional information that would allow to independently validate such > parameters as the resolution and data quality (catching of model fabrications > would be a byproduct of

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

Thank you Phil, for clarification of my point, but it appears as cheating in a current situation, when an author has to fit a three dimensional statistics into a one-dimentional table. Moreover, many of journal reviewers may never worked with the low-resolution data and understand importance of

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

onday, April 09, 2012 6:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Thank you Phil, for clarification of my point, but it appears as cheating in a current situation, when an author has to fit a three dimensional statistics into a one-di

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

> > > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of aaleshin > [aales...@burnham.org] > Sent: Monday, April 09, 2012 6:47 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] very informat

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

On 04/09/12 12:32, Boaz Shaanan wrote: How about such a footnote to Table 1: "The resolution of data is 3A in the a direction, 3.5A in b direction and 5A in the c direction" Wouldn't this do the trick? Usually there's a requirement for a table of statistics, including completeness and R in

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

It is a wonderful server indeed, but its default setting cuts the resolution at 3 sigma (if I remember correctly). It is too stringent in my opinion. Also, it is not clear to me whether to submit all data to the highest resolution point, or the data that come from the server? But then again, the

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

On Apr 9, 2012, at 11:47 AM, aaleshin wrote: > Thank you Phil, for clarification of my point, but it appears as cheating in > a current situation, when an author has to fit a three dimensional statistics > into a one-dimentional table. Moreover, many of journal reviewers may never > worked with

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

Hi Alex, It is not clear to me how to report the resolution of data when it is 3A > in one direction, 3.5A in another and 5A in the third. > can't be easier I guess: just switch from characterizing data sets with one single number (which is suboptimal, at least, as Phil pointed out earlier) and

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

Hi Pavel, Reporting the table that you suggested would create more red flags for the reviewers and readers than explaining how to understand the resolution of my data. We need more studies into this issue (correlation between the resolution of anisotropic data and model quality). And there shoul

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

Alex, I think you are mixing two things here: presenting statistics that characterizes the data and its interpretation. Looking at data completeness as a single number tells something but not a lot, while looking at these metrics per resolution reveals a whole lot more information (for example, d

  1   2   >