[ccp4bb] Beamline scientist position at the HZB BESSY II MX-beamlines (application reference: F 2012/18), deadline 18.11. 2012
The HZB MX-team is seeking a beamline scientist to support the operations of the three MX-beamlines at BESSY-II. The initial contract will run over a period of three years. Payment will be on the basis of germans TVöD-Bund salary scheme. HZB-MX is offering state-of-the-art MX-beamlines to the international user community and is actively developing the experimental capabilities of these stations. This includes the development of long wavelength phasing methods, the in situ crystal screening using the automation platform CATS, controlled crystal dehydration by the HC1c device and the utilization of the Pilatus 6M detector, which will soon be installed at BL14.1. The successful candidate shall have a PhD in physics, biochemistry or chemistry and shall possess practical experiences in the field of X-ray crystallography, preferentially using synchrotron radiation. Furthermore proven experiences in software development i.e. using Python or other modern languages are a clear advantage. HZB is encouraging the application of female scientists. Handicapped applicants with a comparable qualification are preferred. In case of further questions contact: Dr. Uwe Mueller (e-mail: u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de), phone: +49-30-806214974) or Dr. Manfred S. Weiss (e-mail: m...@helmholtz-berlin.demailto:m...@helmholtz-berlin.de), phone: +49-30-806213149) Applications including a CV, list of publications and contact information of two referees shall be sent until 18.11. 2012 electronically and as a single pdf-file stating the application reference: “F 2012/18” within the email header to: personalabteil...@helmholtz-berlin.demailto:personalabteil...@helmholtz-berlin.de) We are looking forward for your applications. Uwe Mueller Manfred Weiss Dr. Uwe Mueller Macromolecular Crystallography (BESSY-MX) | Group leader Elektronenspeicherring BESSY II Albert-Einstein-Str. 15, D-12489 Berlin, Germany Fon: +49 30 8062 14974 Fax: +49 30 8062 14975 url: www.helmholtz-berlin.de/bessy-mxhttp://www.helmholtz-berlin.de/bessy-mx email:u...@helmholtz-berlin.demailto:u...@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 Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Re: [ccp4bb] Twinned Data
Hello, I am afraid that you aren't saying (writing) enough to describe the problem(s) you are facing... Twin fraction ? How many crystals were used to collect the diffraction data (remember that there are polar space groups, where c going up is different from c going down) etc etc. Without enough information, no advice can be provided... Fred. On 19/10/12 12:13, Iris Gawarzewski wrote: Hello everybody, I collected data to 2.8A with the space group P63 but they seems to be twinned. I tried phenix refinement with the twin law I got from Xtriage but the model looks quiet weird... Hope that somebody can help me with this problem. Kind regards, Iris ___ Iris Gawarzewski PhD student Arbeitskreis Schmitt Institut für Biochemie Geb. 26.32.03.21 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf -Germany- Tel: 0049-211-81-13577 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] imosflm, bad predictions - solved!
Hi This was indeed the issue - on this beamline (I think it's 19-ID-D at APS, but I'm waiting on confirmation of this) the phi axis rotates the opposite way to usual, so Mosflm needs to be told. (As an aside, in the most recent release we automatically check the serial number of the detector to see if it's in a list where we know this is done - but our internal list is not comprehensive [and some detectors don't record this information in a useful way...]. We'll add the detector from Jan's dataset to our list) The best way to check if this is the problem is to - (1) index in the normal way using two images. If (a) the predictions don't look right and (b) the sigma(x,y) (the column to the right of the cell dimensions) is more than you would normally expect (say, for a good looking crystal if it's more than ~0.1mm) (c) the cell is not close to what you expect then this may be the issue. (2) Index from the first image chosen by Mosflm and see if the predictions match and sigma(x,y) is much smaller than in (1b) (3) Index from the second image chosen by Mosflm and check predictions (for this image) and sigma (x,y) If (2) and (3) look good but (1) is bad, there's a good chance the phi is rotating the opposite way to that which Mosflm expects. In this case, check the setting box in the Settings - Experiment Settings - Experiment window and try (1) again - remembering that if you do this you need to repeat the spot search. The orientation of the displayed image has no bearing on the beam centre used by Mosflm as read from the image header. Some beamlines record the beam centre in the Denzo frame, some in the Mosflm frame, some in both (and possibly some do in some other frame - there's a wide choice!). In iMosflm, the image is displayed with respect to the internal Mosflm frame - so it's consistent with how we treat the images computationally. Other programs (probably?) display the image as thee detector software displays it. On 18 Oct 2012, at 22:12, Ben wrote: I had a very similar problem with data collected on a particular beamline. The issue was that I had to reverse the spindle direction in imosflm settings. Also, when I load data from this beamline into imosflm the program rotates the images by 90 degrees for some reason (this does not happen in HKL2000). Because of this rotation, the beam center that I used in HKL2000 was different than the beam center position for imosflm. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Twinned Data - more information
Hello everybody, I collected datasets with a resolution to 2.8A from 3 crystal grown in the same condition. The space group seems to be P63. Statistic of XSCALE.LP SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 10.001023 173 204 84.8% 7.4% 14.1% 1023 10.86 8.1%99.5* -280.422 156 6.004199 704 709 99.3% 11.1% 15.1% 4199 10.4312.1%99.1* -250.515 640 4.00 124012131 2137 99.7% 15.5% 15.5% 124009.9117.0%97.7* -180.6841893 3.5084291486 1486 100.0% 18.3% 18.0% 84268.1020.1%96.4*-80.7881259 3.304630 842 842 100.0% 23.0% 22.3% 46276.5925.5%94.5* -130.768 686 3.1060571121 1121 100.0% 28.3% 26.3% 60535.5031.4%93.6*-30.829 882 3.003527 664 664 100.0% 33.7% 34.2% 35244.5637.5%86.8* 60.827 502 2.903961 756 756 100.0% 48.4% 49.5% 39563.2453.8%82.7* 20.784 549 2.802140 699 862 81.1% 31.6% 37.4% 20572.5137.7%87.0* 20.789 178 total 463678576 8781 97.7% 17.2% 18.1% 462657.1519.0%98.2*-90.7306745 I tried Xtriage and got the following: merohedral twin operator twin law: h,-h-k,-l Britton plot: 0.423 H-test: 0.439 Maximum Likelihood Method: 0.457 I have a model with the sequence of my protein and did Phaser_MR (Z-score around 4... I know that this is quiet bad...). This solution I refined with phenix.refinement using the twin law from Xtriage. Rfree is around 0.44 best but the model looks weird... Greetings, Iris ___ Iris Gawarzewski PhD student Arbeitskreis Schmitt Institut für Biochemie Geb. 26.32.03.21 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf -Germany- Tel: 0049-211-81-13577
Re: [ccp4bb] PNAS on fraud
Just a few additional ideas on the significance of the presented values of the correlation coefficient. For samples of size N from a bivariate normal with correlation r, its standard deviation is approximately StDev(R) = (1 - R^2)/sqrt(N – 1) - note that it depends on the number of points used to calculate CC. One good reference is Hotelling, H. (1953). New light on the correlation coefficient and its transforms. Journal of the Royal Statistical Society, Series B, 15(2), 193-232. For the three cases mentioned in Figure 3, fraud, error and duplicates the correlation coefficients and their standard deviationa are respectively: 0.294 0.031 (almost 10 times above its standard deviation) 0.338 0.042 (also well above standard deviation) 0.119 0.045 (2.5 times above standard deviation, what the authors call 'slight' correlation) A distribution of CC is not Gaussian, which is often inconvenient. One can do a Fischer's z-transformation to obtain z-statistics z = (1/2)ln((1+R)/(1-R)) which is approximately normally distributed with standard deviation 1/sqrt(N-3) and then do z-score tests on it. For the same three cases the values of normally distributed z and their standard deviation are very similar to the values obtained from the approximation above. 0.303 0.034 0.352 0.048 0.120 0.045 With best regards, Victor On 18/10/2012 19:52, DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] Twinned Data - more information
Well, the first thing I note is that P6(3) is a polar space group. Hence what I would do myself is the following: take your crystal 'number 1' (as a reference); take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it; try to see which of the original XDS_ASCII or the reindexed XDS_ASCII file gives you the lowest R-sym values, the one with the lowest Rsym's has consistent indexing with your 'reference' crystal 1 - normally somewhere in the XDS output (forgot where) there is a reindexing card mentioned repeat with crystal 3; Then you know what is consistent w.r.t. crystal 1. So you take the 3 files that are appropriate and repeat the XSCALE scaling. It may very well be that you do not have any twinning but that you have not consistently indexed the 3 data sets. Unless you have already taken care of consistent indexing but didn't say (write) it. HTH, Fred. On 19/10/12 13:17, Iris Gawarzewski wrote: Hello everybody, I collected datasets with a resolution to 2.8A from 3 crystal grown in the same condition. The space group seems to be P63. Statistic of XSCALE.LP SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 10.001023 173 204 84.8% 7.4% 14.1% 1023 10.86 8.1%99.5* -280.422 156 6.004199 704 709 99.3% 11.1% 15.1% 4199 10.4312.1%99.1* -250.515 640 4.00 124012131 2137 99.7% 15.5% 15.5%124009.9117.0%97.7* -180.6841893 3.5084291486 1486 100.0% 18.3% 18.0% 84268.1020.1%96.4*-80.7881259 3.304630 842 842 100.0% 23.0% 22.3% 46276.5925.5%94.5* -130.768 686 3.1060571121 1121 100.0% 28.3% 26.3% 60535.5031.4%93.6*-30.829 882 3.003527 664 664 100.0% 33.7% 34.2% 35244.5637.5%86.8* 60.827 502 2.903961 756 756 100.0% 48.4% 49.5% 39563.2453.8%82.7* 20.784 549 2.802140 699 862 81.1% 31.6% 37.4% 20572.5137.7%87.0* 20.789 178 total 463678576 8781 97.7% 17.2% 18.1%462657.1519.0%98.2*-90.7306745 I tried Xtriage and got the following: merohedral twin operator twin law: h,-h-k,-l Britton plot: 0.423 H-test: 0.439 Maximum Likelihood Method: 0.457 I have a model with the sequence of my protein and did Phaser_MR (Z-score around 4... I know that this is quiet bad...). This solution I refined with phenix.refinement using the twin law from Xtriage. Rfree is around 0.44 best but the model looks weird... Greetings, Iris ___ Iris Gawarzewski PhD student Arbeitskreis Schmitt Institut für Biochemie Geb. 26.32.03.21 Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf -Germany- Tel: 0049-211-81-13577 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
[ccp4bb] Beamline scientist position at the HZB BESSY II MX-beamlines (application reference: F 2012/18), deadline 18.11.2012
The HZB MX-team is seeking a beamline scientist to support the operations of the three MX-beamlines at BESSY-II. The initial contract will run over a period of three years. Payment will be on the basis of germans TVöD-Bund salary scheme. HZB-MX is offering state-of-the-art MX-beamlines to the international user community and is actively developing the experimental capabilities of these stations. This includes the development of long wavelength phasing methods, the in situ crystal screening using the automation platform CATS, controlled crystal dehydration by the HC1c device and the utilization of the Pilatus 6M detector, which will soon be installed at BL14.1. The successful candidate shall have a PhD in physics, biochemistry or chemistry and shall possess practical experiences in the field of X-ray crystallography, preferentially using synchrotron radiation. Furthermore proven experiences in software development i.e. using Python or other modern languages are a clear advantage. HZB is encouraging the application of female scientists. Handicapped applicants with a comparable qualification are preferred. In case of further questions contact: Dr. Uwe Mueller (e-mail: u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de), phone: +49-30-806214974) or Dr. Manfred S. Weiss (e-mail: m...@helmholtz-berlin.demailto:m...@helmholtz-berlin.de), phone: +49-30-806213149) Applications including a CV, list of publications and contact information of two referees shall be sent until 18.11. 2012 electronically and as a single pdf-file stating the application reference: “F 2012/18” within the email header to: personalabteil...@helmholtz-berlin.demailto:personalabteil...@helmholtz-berlin.de) We are looking forward for your applications. Uwe Mueller Manfred Weiss Dr. Uwe Mueller Soft Matter and Functional Materials Macromolecular Crystallography (BESSY-MX) | Group leader Elektronenspeicherring BESSY II Albert-Einstein-Str. 15, D-12489 Berlin, Germany Fon: +49 30 8062 14974 Fax: +49 30 8062 14975 url: www.helmholtz-berlin.de/bessy-mxhttp://www.helmholtz-berlin.de/bessy-mx email:u...@helmholtz-berlin.demailto:u...@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 Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
[ccp4bb] Fwd: [ccp4bb] PNAS on fraud
Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While that view is unsupportable in a fundamental sense, I feel strongly that we should understand that error correction costs exponentially more, the smaller the tolerance for errors. In protein synthesis, evolution has settled on error rates of ~1 in 4000-1. Ensuring those rates is already costly in terms of NTPs hydrolyzed. NASA peer review provided me another shock: budgets for microgravity experiments were an order of magnitude higher than those for ground-based experiments, and most of the increase came via NASA's insistence on higher quality control. Informally, I've concluded that the rate of scientific fraud in all journals is probably less than the 1 in 10,000 that (mother) nature settled on. I concur with Randy. Charlie On Oct 18, 2012, at 2:43 PM, Randy Read wrote: In support of Bayesian reasoning, it's good to see that the data could over-rule our prior belief that Nature/Science/Cell structures would be worse!
Re: [ccp4bb] CCP4-6.3.0 installtion
On Oct 18, 2012, at 3:39 PM, Kip Guja k...@pharm.stonybrook.edu wrote: If the output says: /bin/bash then do source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh ccp4i If the output says: /bin/tcsh or /bin/csh then do source /Applications/ccp4-6.3.0/bin/ccp4.setup-csh ccp4i You need to replace with or with the return key.
Re: [ccp4bb] PNAS on fraud
Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While that view is unsupportable in a fundamental sense, I feel strongly that we should understand that error correction costs exponentially more, the smaller the tolerance for errors. In protein synthesis, evolution has settled on error rates of ~1 in 4000-1. Ensuring those rates is already costly in terms of NTPs hydrolyzed. NASA peer review provided me another shock: budgets for microgravity experiments were an order of magnitude higher than those for ground-based experiments, and most of the increase came via NASA's insistence on higher quality control. Informally, I've concluded that the rate of scientific fraud in all journals is probably less than the 1 in 10,000 that (mother) nature settled on. I concur with Randy. Charlie On Oct 18, 2012, at 2:43 PM, Randy Read wrote: In support of Bayesian reasoning, it's good to see that the data could over-rule our prior belief that Nature/Science/Cell structures would be worse! -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] PNAS on fraud
Hi Phillippe, If looking only at the figs. 3A,B,C in the PNAS paper alone, yes, I would agree with you that the proposed correlation is quite weak. Without the help of the trend lines, I would probably conclude that there is no correlation between the IF and number of retractions by a simple look. Of course the R squares are quite telling on the quality of the fitting already. On the other hand, the same authors had done similar analysis on a smaller pool of samples (17 journals) in an earlier study: http://iai.asm.org/content/79/10/3855.full, figure 1. It seems that when including way less journals, the trend stood out quite nicely - leading the authors to say a strong correlation in the earlier publication. I am not sure if the earlier clearer trend was a result of cherry picking, as the choice of journals looks quite normal – like a standard pool of journals one particular lab would consider to publish papers on. It would also be interesting for us on the CCP4BB to try picking only the journals that we would consider to publish structures on, and plot the RI:IF graph to see what would happen. Compared to other fields of biology, frauds in crystallography is probably easier to detect, thus we need worry less about the false negatives: the low impact papers that were fraudulent or erroneous, but nobody cared to spend their effort battling.( I think when taking consideration of this, drawing conclusions from figs. 3A,B,C would be even more dangerous.) I would also like to bring two more issues for discussion: One, in the 2011 IAI paper's fig. 1, the authors plotted Retraction Index, which is the total # of Retractions multiplied by 1000 then divided by total number of publication, whereas in the 2012 PNAS paper figures 3A,B,C, the plots simply used number of retractions to plot against the IFs. I wonder what they will look like if the figures 3A,B,C were plotted as RI vs IF – considering that many low or moderately-low IF journals publish huge numbers of papers. The second issue is, in the PNAS figures 3A,B,C, at the lower left corner, although the dots have a dense looking, the viewers have to realize that most of them only represent 1 to 3 retractions. Ten of such points contain the same number of retractions that one point at the upper halves of the panels A and B contains. Maybe simple bar graphs for numbers of retractions in each IF bin would provide more help. Also, the fact that the averaged IFs landed at ~8 and ~12 for the fraud and errors cases (fig 3D) suggests that the absolute number of retractions occurred in high IF journals is quite significant, especially considering that there are way fewer journals with IF10 than the ones with IF10 in the 200-300 journals. So in my view, maybe trying to fit a straight line to the distribution is overly idealistic, some sort of partition does exist. Zhijie -- From: DUMAS Philippe (UDS) p.du...@ibmc-cnrs.unistra.fr Sent: Friday, October 19, 2012 6:15 AM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] PNAS on fraud Le Jeudi 18 Octobre 2012 22:52 CEST, Zhijie Li zhijie...@utoronto.ca a écrit: Thank you for this funny (and yet significant) comment. But I do not see clearly whether you agree with me or with the PNAS paper For me, this conclusion in the PNAS paper is just ridiculous. Philippe D On curve fitting: http://twitpic.com/8jd081 -- From: DUMAS Philippe (UDS) p.du...@ibmc-cnrs.unistra.fr Sent: Thursday, October 18, 2012 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas
Re: [ccp4bb] PNAS on fraud
Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and indeed victimized) Ephraim Racker at Cornell by using 125Iodine to construct gel autoradiographs to support his remarkable notion of the use of phosphorylation and dephosphorylation in cell signaling. His data were entirely fictitious, but it turned out that his ideas were pregnant indeed. I still view the cross-checking he provoked in serious students of signaling as having stimulated the entire field and actually accelerated it. Both Paradies and Spector are gifted fakes. Their work deserves appreciation for the intelligence that went into the tales they told. A lay homolog was Ferdinand Waldo Demara, who had very little formal education, but who established himself as outstanding in several fields, including open heart surgery, which he performed on a Japanese sailor rescued from after a battle, and who had shrapnel very close to his heart. Apparently, the sailor lived, and Demara saved his life. His story is told in a wonderful film with Tony Curtis in the roll, called The Great Imposter. I hope I've answered your question about what I meant to say on the subject. Charlie On Oct 19, 2012, at 11:25 AM, dom.bell...@diamond.ac.ukmailto:dom.bell...@diamond.ac.uk wrote: Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While that view is unsupportable in a fundamental sense, I feel strongly that we should understand that error correction costs exponentially more, the smaller the tolerance for errors. In protein synthesis, evolution has settled on error rates of ~1 in 4000-1. Ensuring those rates is already costly in terms of NTPs hydrolyzed. NASA peer review provided me another shock: budgets for microgravity experiments were an order of magnitude higher than those for ground-based experiments, and most of the increase came via NASA's insistence on higher quality control. Informally, I've concluded that the rate of scientific fraud in all journals is probably less than the 1 in 10,000 that (mother) nature settled on. I concur with Randy. Charlie On Oct 18, 2012, at 2:43 PM, Randy Read wrote: In support of Bayesian reasoning, it's good to see that the data could over-rule our prior belief that Nature/Science/Cell
Re: [ccp4bb] PNAS on fraud
This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re: [ccp4bb] PNAS on fraud Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and indeed victimized) Ephraim Racker at Cornell by using 125Iodine to construct gel autoradiographs to support his remarkable notion of the use of phosphorylation and dephosphorylation in cell signaling. His data were entirely fictitious, but it turned out that his ideas were pregnant indeed. I still view the cross-checking he provoked in serious students of signaling as having stimulated the entire field and actually accelerated it. Both Paradies and Spector are gifted fakes. Their work deserves appreciation for the intelligence that went into the tales they told. A lay homolog was Ferdinand Waldo Demara, who had very little formal education, but who established himself as outstanding in several fields, including open heart surgery, which he performed on a Japanese sailor rescued from after a battle, and who had shrapnel very close to his heart. Apparently, the sailor lived, and Demara saved his life. His story is told in a wonderful film with Tony Curtis in the roll, called The Great Imposter. I hope I've answered your question about what I meant to say on the subject. Charlie On Oct 19, 2012, at 11:25 AM, dom.bell...@diamond.ac.ukmailto:dom.bell...@diamond.ac.uk wrote: Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While that view is unsupportable in a fundamental sense, I feel strongly that we should understand that error correction costs exponentially more, the smaller the tolerance for errors. In protein synthesis, evolution has settled on error rates of ~1 in 4000-1. Ensuring those rates is already costly in terms of NTPs hydrolyzed. NASA peer review provided me another shock: budgets for microgravity experiments were an order of magnitude higher than those for ground-based experiments, and most of the increase came via NASA's insistence on higher quality control. Informally, I've concluded that the
Re: [ccp4bb] PNAS on fraud
On Friday, October 19, 2012 10:12:44 am Colin Nave wrote: This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 A paper claiming that all papers are false, by someone named Ioannidis? I wonder if he is from Crete :-) E for channeling Epimenides Merritt -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] PNAS on fraud
This gets us more into the philosophy of science but I've always felt authors had a right to speculate in the discussion sections of their papers on what it all means. And speculate even past the information in the actual data (see for example the wonderfully prescient final lines of the Watson Crick paper). As long as the experiments are fully described and the confidence of the data is clearly spelled out. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8611 (voice) (716) 480-8615 (mobile) (716) 898-8660 (fax) deti...@hwi.buffalo.edu www.hwi.buffalo.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Friday, October 19, 2012 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re: [ccp4bb] PNAS on fraud Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and indeed victimized) Ephraim Racker at Cornell by using 125Iodine to construct gel autoradiographs to support his remarkable notion of the use of phosphorylation and dephosphorylation in cell signaling. His data were entirely fictitious, but it turned out that his ideas were pregnant indeed. I still view the cross-checking he provoked in serious students of signaling as having stimulated the entire field and actually accelerated it. Both Paradies and Spector are gifted fakes. Their work deserves appreciation for the intelligence that went into the tales they told. A lay homolog was Ferdinand Waldo Demara, who had very little formal education, but who established himself as outstanding in several fields, including open heart surgery, which he performed on a Japanese sailor rescued from after a battle, and who had shrapnel very close to his heart. Apparently, the sailor lived, and Demara saved his life. His story is told in a wonderful film with Tony Curtis in the roll, called The Great Imposter. I hope I've answered your question about what I meant to say on the subject. Charlie On Oct 19, 2012, at 11:25 AM, dom.bell...@diamond.ac.ukmailto:dom.bell...@diamond.ac.uk wrote: Dear Charlie, Do you mean that small doses of fraud should be accepted as a form of natural evolution? Or perhaps you were suggesting that genuine errors/mistakes are acceptable in 1/1 due to the high costs of spotting them? D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd:
[ccp4bb] A case of post publication fraud...Re: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud
Dear Colleagues, A different type of, post publication, fraud is the case of the discovery of streptomycin. See :- http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext I am just returned from the ICSTI Conference on Science, Law and Ethics in Washington DC representing IUCr where I learnt of this very disturbing case. I explained to the book's author and speaker Peter Pringle that, on behalf of Universities today, procedures are now in place, at least in the University of Manchester, for graduate students and supervisors to both sign within 'eprog' that they have discussed matters of authorship etiquette and rules as well as IP sharing formalities. Have a good weekend, John Prof John R Helliwell DSc On 19 Oct 2012, at 13:08, Carter, Charlie car...@med.unc.edu wrote: Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While that view is unsupportable in a fundamental sense, I feel strongly that we should understand that error correction costs exponentially more, the smaller the tolerance for errors. In protein synthesis, evolution has settled on error rates of ~1 in 4000-1. Ensuring those rates is already costly in terms of NTPs hydrolyzed. NASA peer review provided me another shock: budgets for microgravity experiments were an order of magnitude higher than those for ground-based experiments, and most of the increase came via NASA's insistence on higher quality control. Informally, I've concluded that the rate of scientific fraud in all journals is probably less than the 1 in 10,000 that (mother) nature settled on. I concur with Randy. Charlie On Oct 18, 2012, at 2:43 PM, Randy Read wrote: In support of Bayesian reasoning, it's good to see that the data could over-rule our prior belief that Nature/Science/Cell structures would be worse!
Re: [ccp4bb] PNAS on fraud
I think the real point here is that a difference exits between divergent interpretation of legitimate evidence - which is normal scientific epistemology - or whether the presented 'evidence' is in some fashion tampered with. The former is healthy procedure and (I hope) not subject of disagreement - we all have been wrong a few times at least and corrected either by better insight or new evidence (or actually useful reviews) - and the question boils down to where 'tampering' with evidence starts. Is willful neglect of contrary results tinkering? Is looking only for reinforcing data already tinkering (aka expectation and confirmation bias)? It is easy to judge in the case of poorly fabricated stuff like bet V1 or c3b, but I think the borderline cases are potentially much more damaging. Btw, I have few more references to the psychology of science Koehler JJ (1993) The Influence of Prior Beliefs on Scientific Judgments of Evidence Quality. Organizational Behavior and Human Decision Processes 56(1): 28-55. Simmons JP, Nelson LD and Simonsohn U (2011) False-Positive Psychology: Undisclosed Flexibility in Data Collection and Analysis Allows Presenting Anything as Significant. Psychological Science: DOI: 10.1177/0956797611417632. Frey BS (2003) Publishing as Prostitution? Choosing Between Ones Own Ideas and Academic Failure. Public Choice 116, 205-223 (ETHZ) Nice weekend reading. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of George DeTitta Sent: Friday, October 19, 2012 10:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This gets us more into the philosophy of science but I've always felt authors had a right to speculate in the discussion sections of their papers on what it all means. And speculate even past the information in the actual data (see for example the wonderfully prescient final lines of the Watson Crick paper). As long as the experiments are fully described and the confidence of the data is clearly spelled out. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8611 (voice) (716) 480-8615 (mobile) (716) 898-8660 (fax) deti...@hwi.buffalo.edu www.hwi.buffalo.edu -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: Friday, October 19, 2012 1:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 17:55 To: ccp4bb Subject: Re: [ccp4bb] PNAS on fraud Dom, You've opened a pandora's box here, which I won't try to contain. The short answer is both of the above. I feel it is becoming increasingly difficult as a referee to be on top of every paper I review, and as an editor it is becoming increasingly difficult to find willing referees. Both phenomena are diagnostic of the cost of eliminating fraudulent publications, which gall me pretty much as much as they do many others, but which do not drive me apoplectic, either. I've been amused over the years by the frantic efforts to bring crystallographic charlatans to justice, even as I've been angered by publication in high-impact journals of material I myself view as fraudulent, but which obviously survives peer review. On the second of your alternatives, I'll give you two examples of highly celebrated frauds that wound up moving science forward, despite their scurrilous background. The first is the story of Hasko Paradies, whose only legitimate publication, as far as I know, was a first-author paper on the crystallization of tRNA. In that paper, he was, I think, the first author to describe the use of spermine/spermidine and Mg++ ions in improving crystallization conditions. These two contributions proved useful in the actual generation by others of suitable crystals. Paradies apparently went on to make a habit of filching precession photographs from dark rooms and then presenting them elsewhere and at meetings as if he had taken them and as if they were from hot problems of the day. His story was chronicled by Wayne Hendrickson, Ed Lattman, and others in Nature many years later. He dropped out of science and became a pediatrician, I believe in Munich, where, despite not having attended medical school, he was much beloved by his patients and their families. Paradies had been an associate of my own post-doctoral mentor, Sir Aaron Klug. I've no way of knowing whether or not he actually faked the data in his report of tRNA crystallization. His crystals did not diffract in any case, which may have driven him to short cuts. The other celebrated Fraud was Mark Spector, who embarrassed (and
Re: [ccp4bb] PNAS on fraud
CCP4- intetesting topic and many off-target topics veing discussed. John Ionnandis' work, who is an epidemiologist and statistician, addresses issues in the design and interpretation of GWAS studies for SNPs and disease associations in one hand and clinical studies, especially Phase III intervention studies on the other. His primary interest is in statistic interpretation of these studies rather than 'fabrication' or purposeful introduction of erroneous information into study reports. He is a useful if controversial advocate for clarity in statistical concepts for these works. Dexter Kennedy, MD Thumbed from my iPhone On Oct 19, 2012, at 10:40 AM, Ethan Merritt merr...@u.washington.edu wrote: On Friday, October 19, 2012 10:12:44 am Colin Nave wrote: This is worth looking at as well. Suggests most papers should be retracted! http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124 A paper claiming that all papers are false, by someone named Ioannidis? I wonder if he is from Crete :-) E for channeling Epimenides Merritt -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] A case of post publication fraud...Re: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud
On Fri, Oct 19, 2012 at 2:20 PM, Jrh jrhelliw...@gmail.com wrote: Dear Colleagues, A different type of, post publication, fraud is the case of the discovery of streptomycin. See :- http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext I can't resist posting this quite interesting tangential fact that is unrelated to fraud : penicillin was discovered by Ernest Duchesne. -Bryan
[ccp4bb] off topic: a Python online course and others
Hello all, Considering that many biologists come to the field with no background in programming (like me) and want to learn a scripting language, I thought that many young members of the community might find this useful. There's an ongoing FREE online course An Introduction to Interactive Programming in Python (no computer background needed), presented by the department of computer science from Rice University. It just started and as far as the first week goes, it is very well presented and entertaining. https://www.coursera.org/course/interactivepython There's plenty of other useful courses there as well. https://www.coursera.org Anastasia Anastasia A Aksyuk IRTA fellow Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 email: anastasia.aks...@nih.gov phone: 301-451-8247
[ccp4bb] Jrh further Re: [ccp4bb] A case of post publication fraud...Re: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud
One of the hardest things for an author, and a handling Editor, is making sure that the references list of a submitted article is complete, but is an easier task now with our e-tools than in the days of the penicillin discovery. Another case is that of Einstein's special theory article of 1905 where Lorentz was not cited. Abraham Paix explored this in the biography of Einstein noting that Einstein did finally acknowledge that they, Lorentz and Einstein, had been in correspondence on the topic. Prof John R Helliwell DSc On 19 Oct 2012, at 19:43, Bryan Lepore bryanlep...@gmail.com wrote: On Fri, Oct 19, 2012 at 2:20 PM, Jrh jrhelliw...@gmail.com wrote: Dear Colleagues, A different type of, post publication, fraud is the case of the discovery of streptomycin. See :- http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext I can't resist posting this quite interesting tangential fact that is unrelated to fraud : penicillin was discovered by Ernest Duchesne. -Bryan
Re: [ccp4bb] off topic: a Python online course and others
Hi, For those starters on python programming, I strongly recommend Hanns Petter Langtangen's book A primer on scientific programming with python. It specifically targets the scientific programming, which we care about the most. The only thing I am not sure is that this book was written using python 2.6. A transition to 3.2 maybe a pain in future. Nian Huang On Fri, Oct 19, 2012 at 3:12 PM, Aksyuk, Anastasia (NIH/NIAMS) [F] anastasia.aks...@nih.gov wrote: Hello all, Considering that many biologists come to the field with no background in programming (like me) and want to learn a scripting language, I thought that many young members of the community might find this useful. There's an ongoing FREE online course An Introduction to Interactive Programming in Python (no computer background needed), presented by the department of computer science from Rice University. It just started and as far as the first week goes, it is very well presented and entertaining. https://www.coursera.org/course/interactivepython There's plenty of other useful courses there as well. https://www.coursera.org Anastasia Anastasia A Aksyuk IRTA fellow Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 email: anastasia.aks...@nih.gov phone: 301-451-8247
[ccp4bb] Salt bridge in crystallization
Dear All, A lot of 3-D crystal structures highlight the salt bridges in the structure, although some structures of them are got at high salt concentrations. Will you please explain to me why the protein salt bridge can still exist in the high salt concentration as used in the crystallization condition? I am looking forward to getting your reply. Acoot
Re: [ccp4bb] Salt bridge in crystallization
On 10/19/2012 10:37 PM, Acoot Brett wrote: Will you please explain to me why the protein salt bridge can still exist in the high salt concentration as used in the crystallization condition? You are saying it as if there is some fundamental law of nature that says that salt bridges cannot be maintained at high salt concentration. I know of no such law. The observation simply means that (mostly for entropic reasons) the free energy of the salt bridge is still lower. If you present your case as to why the salt bridges must be disrupted, we can poke holes in it :) Cheers, Ed -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
