[ccp4bb] X-ray equipment available
Full Rigaku R-axis IIC Image Plate X-ray diffraction system We would like to offer a complete macromolecular diffraction system free of charge to anyone prepared to pay (up-front) the shipping costs from our laboratory to theirs. The system consists of a R-axis IIC area detector, Rigaku RU-200BH rotating anode X-ray generator with Yale mirrors together with an Oxford cryosystems 600 series cryostream and associated dewars. The system includes a purpose built enclose made of lead-rated perspex, obviating the need for a walk in enclosure. The footprint of the X-ray generator cabinet 810cm (D) x 1100cm (W) x 900cm (H), the footprint of the radiation enclosure is 1400cm (D) x 1750cm (W) x 1000cm (H). The weight of the X-ray generator is (550kg) and the HV transformer (450kg), RaxisIIC (150kg), enclosure (80kg) and table (80kg). We wish to give away the whole system and not break it down to parts, so requests should be for the complete system. Please contact Marty Rajaratnam (Randall division of Cell and Molecular Biophysics, King’s College London) email r.rajarat...@kcl.ac.ukmailto:r.rajarat...@kcl.ac.uk if you are interested in acquiring this system. With best wishes _ Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
[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/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B. Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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/ inline: sigma_rmgif.gif
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hi Fellow BBers, I wish to point out that a) this is not an April fools joke, b) but on the other hand it shows (a little buried in the recommendations, and misspelled AFTER proofing) that people who properly do catalogue and preserve images actually can fix deposition errors (compliments to Daniel Minor and James Holton for first finding 2002 images and then reprocessing/depositing the Fobs) c) Due to the unusually high interest in reprints, I probably need to talk to Chester if one of these copies with the cover page authorizing author distribution is available, and 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 the discussion for a repository for your collected frames. Jürgen
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 jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen *Acta Cryst.* (2012). F*68*, 366-376 doi:10.1107/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421 * * Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergenB. Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B. *Abstract:* Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small *R* value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical tools, including the application of Diederichs plots, *R*[image: [sigma]] plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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/ sigma_rmgif.gif
Re: [ccp4bb] very informative - Trends in Data Fabrication
This is an unresolved problem, and no real satisfactory solution exists, because the underlying reasons for zero occupancy can be different. For people who understand this and look at electron density, it is not a problem. For users who rely on some graphics program displaying only atom coordinates, it can be. The same holds for manipulation of B-factors, trading high B-factors 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.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 On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421 http://dx.doi.org/10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20 B. B. Rupp Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78 3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78 3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4 1fm4). A variety of analytical tools, including the application of Diederichs plots, R[sigma] plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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 tel:%2B1-410-614-4742 Lab: +1-410-614-4894 tel:%2B1-410-614-4894 Fax: +1-410-955-2926 tel:%2B1-410-955-2926 http://web.mac.com/bosch_lab/ image001.gif
Re: [ccp4bb] very informative - Trends in Data Fabrication
Very interesting Response to Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen doi:10.1107/S1744309112008433 a quote from the response: Author Schwarzenbacher admits to the allegations of data fabrication and deeply apologizes to the co-authors and the scientific community for all the problems this has caused . Note added in proof: subsequent to the acceptance of this article for publication, author Schwarzenbacher withdrew his admission of 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 unresolved problem, and no real satisfactory solution exists, because the underlying reasons for zero occupancy can be different. For people who understand this and look at electron density, it is not a problem. For users who rely on some graphics program displaying only atom coordinates, it can be. The same holds for manipulation of B-factors, ‘trading’ high B-factors 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.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 On Sat, Mar 31, 2012 at 10:26 AM, Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421 Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B. Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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: +1-410-614-4742tel:%2B1-410-614-4742 Lab: +1-410-614-4894tel:%2B1-410-614-4894 Fax: +1-410-955-2926tel:%2B1-410-955-2926 http://web.mac.com/bosch_lab/
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 in refereeing - in this case. Alarm bells could had rung possibly if the PDB was re-refining all submitted structures and look for 'too good to be true' improvements (sorry Robbie ... we are not there yet to improve things SO much!). Saving the images in a repository would had been equally unlikely to have helped (they would had submitted some data ... unless these were systematically validated and cross-matched to the CRYST data cards no alarm bells either - even if running PDB_REDO in all submissions appears a tad unrealistic, re-processing all images and matching them to CRYST records seems more troublesome at the present moment). A thing that could had helped, would had been if our biology colleagues who want a structure for their story would had valued more the structural contribution by scrutinising the data (a corresponding author must scrutinise all data before accepting responsibility - and not when questioned throw the hands up waving 'it was not me ...'). Maybe ourselves as a community could also help by making our colleagues aware that crystallographic work is a tad more than 'and the author in the middle of the paper just contributed a structure' and explain them that if they want to be using structures for their publications they should be always prepared to engage in close and real collaborations where both sides accept responsibility for the data of each other, as it happens in many fruitful collaborations between biologists and crystallographers (such as these I had the privilege to engage with collaborators that criticised my data, as I did theirs ...). regards to all - Tassos (and please, no 1st April joke with fraud cases !)
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 fabricated. The worst case is: 1. All of data was correct and real, 2. The key structural evidence ( 1%) was not presented or excluded in the discussion. 3. Then the paper was reviewed by some famous people, and then published on those top level journals. 4. Eventually, it is cited in our textbook for years. For the most of cases, reviewer and reader will mainly rely on graphics displaying only. It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. Recently, 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 hope you experts will also check the coordinate files for verification. Sincerely, Kevin On Sat, Mar 31, 2012 at 8:26 AM, Bosch, Juergen jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen *Acta Cryst.* (2012). F*68*, 366-376 doi:10.1107/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421 * * Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergenB. Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B. *Abstract:* Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small *R* value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical tools, including the application of Diederichs plots, *R*[image: [sigma]] plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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/ -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/ sigma_rmgif.gif
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 indicative but never conclusive (as one can utilize each of the criteria in generating a fake data / structure making it therefore obsolete). Pavel On Sat, Mar 31, 2012 at 3:08 PM, Kevin Jin kevin...@gmail.com wrote: 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 fabricated. The worst case is: 1. All of data was correct and real, 2. The key structural evidence ( 1%) was not presented or excluded in the discussion. 3. Then the paper was reviewed by some famous people, and then published on those top level journals. 4. Eventually, it is cited in our textbook for years. For the most of cases, reviewer and reader will mainly rely on graphics displaying only. It will be very difficult for people to check the density and coordinated if he/she is not a well-trained crystallographer. Recently, 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 hope you experts will also check the coordinate files for verification. Sincerely, Kevin On Sat, Mar 31, 2012 at 8:26 AM, Bosch, Juergen jubo...@jhsph.edu wrote: really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen *Acta Cryst.* (2012). F*68*, 366-376 doi:10.1107/S1744309112008421http://dx.doi.org/10.1107/S1744309112008421 * * Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergenB. Rupphttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Rupp,%20B. *Abstract:* Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small *R* value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4). A variety of analytical tools, including the application of Diederichs plots, *R*[image: [sigma]] plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. .. 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/ -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/ sigma_rmgif.gif
Re: [ccp4bb] very informative - Trends in Data Fabrication
Bernard went to a lot of work to verify that this structure was wrong, so we should also thank him for his efforts. It is good to see someone who has a hunch follow that up and let the rest of us know about it. Thanks Bernard! Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au 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. 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 in refereeing - in this case. Alarm bells could had rung possibly if the PDB was re-refining all submitted structures and look for 'too good to be true' improvements (sorry Robbie ... we are not there yet to improve things SO much!). Saving the images in a repository would had been equally unlikely to have helped (they would had submitted some data ... unless these were systematically validated and cross-matched to the CRYST data cards no alarm bells either - even if running PDB_REDO in all submissions appears a tad unrealistic, re-processing all images and matching them to CRYST records seems more troublesome at the present moment). A thing that could had helped, would had been if our biology colleagues who want a structure for their story would had valued more the structural contribution by scrutinising the data (a corresponding author must scrutinise all data before accepting responsibility - and not when questioned throw the hands up waving 'it was not me ...'). Maybe ourselves as a community could also help by making our colleagues aware that crystallographic work is a tad more than 'and the author in the middle of the paper just contributed a structure' and explain them that if they want to be using structures for their publications they should be always prepared to engage in close and real collaborations where both sides accept responsibility for the data of each other, as it happens in many fruitful collaborations between biologists and crystallographers (such as these I had the privilege to engage with collaborators that criticised my data, as I did theirs ...). regards to all - Tassos (and please, no 1st April joke with fraud cases !)
Re: [ccp4bb] very informative - Trends in Data Fabrication
Keeping Bernard's book as reference, it is the best way. Kevin On Sat, Mar 31, 2012 at 4:56 PM, Tom Peat tom.p...@csiro.au wrote: Bernard went to a lot of work to verify that this structure was wrong, so we should also thank him for his efforts. It is good to see someone who has a hunch follow that up and let the rest of us know about it. Thanks Bernard! Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au 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. 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 in refereeing - in this case. Alarm bells could had rung possibly if the PDB was re-refining all submitted structures and look for 'too good to be true' improvements (sorry Robbie ... we are not there yet to improve things SO much!). Saving the images in a repository would had been equally unlikely to have helped (they would had submitted some data ... unless these were systematically validated and cross-matched to the CRYST data cards no alarm bells either - even if running PDB_REDO in all submissions appears a tad unrealistic, re-processing all images and matching them to CRYST records seems more troublesome at the present moment). A thing that could had helped, would had been if our biology colleagues who want a structure for their story would had valued more the structural contribution by scrutinising the data (a corresponding author must scrutinise all data before accepting responsibility - and not when questioned throw the hands up waving 'it was not me ...'). Maybe ourselves as a community could also help by making our colleagues aware that crystallographic work is a tad more than 'and the author in the middle of the paper just contributed a structure' and explain them that if they want to be using structures for their publications they should be always prepared to engage in close and real collaborations where both sides accept responsibility for the data of each other, as it happens in many fruitful collaborations between biologists and crystallographers (such as these I had the privilege to engage with collaborators that criticised my data, as I did theirs ...). regards to all - Tassos (and please, no 1st April joke with fraud cases !) -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
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 On Mar 31, 2012, at 11:05 PM, Kevin Jin wrote: Keeping Bernard's book as reference, it is the best way. Kevin On Sat, Mar 31, 2012 at 4:56 PM, Tom Peat tom.p...@csiro.aumailto:tom.p...@csiro.au wrote: Bernard went to a lot of work to verify that this structure was wrong, so we should also thank him for his efforts. It is good to see someone who has a hunch follow that up and let the rest of us know about it. Thanks Bernard! Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.aumailto:tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis [a.perra...@nki.nlmailto:a.perra...@nki.nl] Sent: Sunday, April 01, 2012 7:59 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: 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 in refereeing - in this case. Alarm bells could had rung possibly if the PDB was re-refining all submitted structures and look for 'too good to be true' improvements (sorry Robbie ... we are not there yet to improve things SO much!). Saving the images in a repository would had been equally unlikely to have helped (they would had submitted some data ... unless these were systematically validated and cross-matched to the CRYST data cards no alarm bells either - even if running PDB_REDO in all submissions appears a tad unrealistic, re-processing all images and matching them to CRYST records seems more troublesome at the present moment). A thing that could had helped, would had been if our biology colleagues who want a structure for their story would had valued more the structural contribution by scrutinising the data (a corresponding author must scrutinise all data before accepting responsibility - and not when questioned throw the hands up waving 'it was not me ...'). Maybe ourselves as a community could also help by making our colleagues aware that crystallographic work is a tad more than 'and the author in the middle of the paper just contributed a structure' and explain them that if they want to be using structures for their publications they should be always prepared to engage in close and real collaborations where both sides accept responsibility for the data of each other, as it happens in many fruitful collaborations between biologists and crystallographers (such as these I had the privilege to engage with collaborators that criticised my data, as I did theirs ...). regards to all - Tassos (and please, no 1st April joke with fraud cases !) -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/ .. 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] 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 --
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
