Re: [ccp4bb] SciVee - YouTube for scientist
Hi all, Great idea! As being relatively new to the field, I definitely find this idea appealing. Actually hearing the talks would indeed be quite educational. Cheers, Ronnie Berntsson On Aug 23, 2007, at 10:57 AM, Clemens Vonrhein wrote: Hi Eleanore, On Tue, Aug 21, 2007 at 12:56:40PM +0100, Eleanor Dodson wrote: 5) The need for crystallographic education for readers and students Just discovered SciVee (YouTube for scientists) at http://www.scivee.tv/ which is operated in partnership with the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). Maybe if those webcasts of the last few CCP4 study weekends are still available (and speakers permit), these could be placed there as a supplement to the usual Acta D issue? Hearing a talk might be even more educational than going through a Acta D paper for people new or unfamiliar with crystallographic methods. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** Ronnie Berntsson -- Ph.D. Student Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands
[ccp4bb] Postdoctoral positions in crystallography in Stockholm, Sweden
Dear group members, I would like to bring following the openings to your attention: ANNOUNCEMENT TITLE: Postdoctoral positions in crystallography in Stockholm, Sweden DEADLINE FOR APPLICATIONS: 25 October 2007 TYPE OF POSITION: Post-Doc(s) INSTITUTION/DEPARTMENT: Center for Infectious Medicine, Department of Medicine, Karolinska University Hospital in Huddinge, Karolinska Institutet CONTACT PERSON: Adnane Achour, Center for Infectious Medicine, c/o Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Department of Medicine F59, Karolinska University Hospital Huddinge, Karolinska Institutet S-141 86 Stockholm, Sweden. e-mail address: [EMAIL PROTECTED], Phone: +46-8-5248 6232, Fax: +46-8-30 42 76, website: http://www.medhs.ki.se/cim/ DESCRIPTION/REQUIREMENTS: Two postdoctoral positions are available for a period of two years at the Center for Infectious Medicine, Karolinska Institutet in Stockholm, Sweden. We are looking for enthusiastic individuals to join the laboratory of Assoc. Prof. Adnane Achour. The candidates should be good team-players. They will be mainly responsible for protein crystallography as well as the determination and interpretation of three-dimensional structures of different protein targets and protein-protein complexes. Good knowledge of protein crystallization, data collection and structural refinement is desirable. No knowledge of immunology is required. A variety of projects concerned with structural aspects of immunology are available. We combine structural and functional approaches in order to understand central immunological phenomena such as virus evasion from immune recognition (Achour et al, Immunity, 2002; Malard-Velloso et al, J. Immunology, 2004; Cerboni et al, Eur. J. Immunology, 2006; Achour et al, J. Mol. Biol. 2006; Thilo et al, J. Biol. Chem., 2007) and the role of molecular mimicry in the induction of autoimmune diseases and allergic responses (Sandalova et al, J. Biol. Chem. 2005; Kaiser et al, J. Biol. Chem. 2003; Kaiser et al, J. Mol. Biol. 2007). A large set of other projects is already well established. APPLICATION PROCEDURE: The application should include a CV (including in particular any experience relevant to the position announced) as well as the names and contact details of 2 references. The applicants should also submit a list of publications and submitted manuscripts. begin:vcard n:Achour;Adnane fn:Adnane Achour tel;fax:+46-8-30 42 76 tel;work:+46-8-5248 6232 url:http://www.medhs.ki.se/cim/medhs_eng.asp?Id=12tabell=medhs_english org:Center for Infectious Medicine;Department of Medicine, F59 adr:;;Karolinska University Hospital Huddinge;Stockholm;;141 86;Sweden version:2.1 email;internet:[EMAIL PROTECTED] title:Associate Professor end:vcard
Re: [ccp4bb] The importance of USING our validation tools
Mischa, I don't think that the field of nanotechnology crumbled when allegations against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature) turned out to be true. I don't think that nobody trusts biologists anymore because of Eric Poehlman (17 falsified grants, 10 papers with fabricated data, 12 month in prison). We are still excited to hear about stem cell research despite of what Hwang Woo-suk did or didn't do. What recent events demonstrate is that in macromolecular crystallography (and in science in general) mistakes, deliberate or not, will be discovered. Ed. Mischa Machius wrote: Due to these recent, highly publicized irregularities and ample (snide) remarks I hear about them from non-crystallographers, I am wondering if the trust in macromolecular crystallography is beginning to erode. It is often very difficult even for experts to distinguish fake or wishful thinking from reality. Non-crystallographers will have no chance at all and will consequently not rely on our results as much as we are convinced they could and should. If that is indeed the case, something needs to be done, and rather sooner than later. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353 -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] The importance of USING our validation tools
Dear colleagues, 1) I think Ajees et al. should make available the raw diffraction images of the structure in paper that has caused so much literary commotion, unless they haven't already done so. Perhaps simply put them in an open ftp server? As I imagine, unless I have missed something, these diffraction images were obtained with grant money, so they should be available to the community. Isn't it? This would allow other scientists to evaluate them as much as they wanted and publish many more papers about the validity or falsehood of the conclusions drawn in the original and (now) infamous Ajees et al. paper. That's how Science -in my opinion- ought to be. 2) I agree that depositing raw images in the PDB or elsewhere would be a great thing for everybody - I usually and happily deposit all the structure factors that I've used to obtain and refine a structure -. However, raw images are becoming larger and larger with the newer and fancier detectors and this trend might not stabilize in quite a while. Although disk space is becoming as well cheaper as time goes by, I think the ratio between these two factors is still unpractical for huge storage purposes. Unless a major development in data storage is accomplished. As an anecdote: during a trip to a synchrotron in the American Midwest, a single dataset (1 degree x 360) was something like 27GB of raw images!!! We managed to collect 1.5 TB of data in about 2 days (having to run -of course always in a hurry- to the nearest computer store to get a few more external hard-drives to backup and take with us all our data). Albeit of being a great option for many of us, I insist. I cannot imagine the burden that storing so much data would be for the PDB or any public database. Not only for taking care of the amount of disk space or storage support required, but as people have mentioned here taking care of them (curating them, since disks do crash, as we know, and optical media get irremediably scratched) would be a tremendous and likely expensive endeavor. 3) Perhaps, we should responsibly store the data ourselves, nicely stored in media that should allow us to retrieve it after many years (quite a task by itself already; forget the clay tablets though). As probably many of us have done for quite some time. And when asked, send the data to anyone who is interested. But... don't they have already problems accessing the tapes from the first lunar landing? 4) In any case, we should not forget the subject of storing and accessibility of the crystallographic raw images in a public database. Perhaps more journals should accept open letters about this subject, which is important as well as complicated, and create a much larger discussion than this one. All the best, Jordi __ Jordi Benach, PhD MX Beamline Scientist ALBA Synchrotron Light Facility Edifici Ciències. Mòdul C-3 Central Campus Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona, SPAIN Phone: +34 93 592 4333 FAX: +34 93 592 4302 E-mail: [EMAIL PROTECTED] __
Re: [ccp4bb] crystal with precipitation
Hi Shivesh I had something like this recently and found that changing the pH stopped the precipitation and the size of the crystals improved. If the crystals are large enough even if there is ppt present I would still try and collect data on them. This is likely not the case for you or you wouldn't be writing in:) hope this helps Rob Dear all I am trying to crystallize a 7kDa protein using MPD as a precipitant at 16C.I have got small florets at 55-65% of MPD in 3-4 days.The problem is that the drop is precipitating in one day only and the crystals are coming with precipitation.I have added 5% glycerol and 100mM of Nacl as an additive with the mother liquor to avoid precipitation.But,the precipitation is still there.The volume of the mother liquor is 500 microlt.The drop size is 2+2.I welcome all the suggestions regarding avoiding the precipitation.Thanx is advance. Shivesh kumar -- Robert J.Gruninger B.Sc. PhD Student Department of Chemistry Biochemistry University of Lethbridge, 4401 University Dr. Lethbridge, AB, Canada, T1K 3M4 Phone:(403)329-2746 Fax:(403)329-2057
[ccp4bb] ccp4 pack_images program?
Sorry for the repost, but I think my question got lost in the earlier thread. I've found $CCP4/x-windows/ipdisp/src/pack_c.c, pack_f.f and so forth, but they apparently don't build by default, and when I try to, I get You need to make mosflm-bits in the library for the image-packing stuff exit 1 make: *** [$CCP4/lib/libccp4.a(pack_c.o)] Error 1 I have no idea what mosflm-bits refers to and can't seem to find anything. Any suggestions how to build this? It seems it would be good to have available if we are all going to put our images on our web-servers. Thanks. Bill Scott
Re: [ccp4bb] diffraction images images/jpeg2000
Well, I know it's not the definitive source of anything, but the wikipedia entry on JPEG2000 says: The PNG (Portable Network Graphics) format is still more space-efficient in the case of images with many pixels of the same color, and supports special compression features that JPEG 2000 does not. So would PNG be better? It does support 16 bit greyscale. Then again, so does TIFF, and Mar already uses that. Why don't they use the LZW compression feature of TIFF? The old Mar325 images were compressed after all. I think only Mar can answer this, but I imagine the choice to drop compression was because the advantages of compression (a factor or 2 or so in space) are outweighed by the disadvantages (limited speed and limited compatibility with data processing packages). How good could lossless compression of diffraction images possibly be? I just ran an entropy calculation on the 44968 images on /data at the moment at ALS 8.3.1. I am using a feature of Andy Hammersley's program FIT2D to compute the entropy. I don't pretend to completely understand the algorithm, but I do understand that the entropy of the image reflects the maximum possible compression ratio. For these images, the theoretical maximum compression ratio ranged from 1.2 to 4.8 with mean 2.7 and standard deviation 0.7. The values for Huffmann encoding ranged from 0.95 to 4.7 with mean 2.4 and standard deviation 1.0. The correlation coefficient between the Huffmann and theoretical compression ratio was 0.97. I had a look at a few of the outlier cases. As one might expect, the best compression ratios are from blank images (where all the high-order bits are zero). The #1 hardest-to-compress image had many overloads, clear protein diffraction and a bunch of ice rings. So, unless I am missing something, I think the best we are going to get with lossless compression is about 2.5:1. At least, for individual frames. Compressing a data set as a video sequence might have substantial gains since only a few pixels change significantly from frame-to-frame. Are there any lossless video codecs out there? If so, can they handle 6144x6144 video? What about lossy compression? Yes yes, I know it sounds like a horrible idea to use lossy compression on scientific data, because it would change the values of that most precious of numbers: Fobs. However, the question I have never heard a good answer to is HOW MUCH would it change Fobs? More practically: how much compression can you do before Fobs changes by more than the value of SIGFobs? Diffraction patterns are inherently noisy. If you take the same image twice, then photon counting statistics make sure that no two images are exactly the same. So which one is right? If the changes in pixel values from a lossy compression algorithm are always smaller than that introduced by photon-counting noise, then is lossy compression really such a bad idea? The errors introduced could be small when compared to errors in say, scale factors or bulk solvent parameters. A great deal can be gained in compression ratio if only random noise is removed. I remember the days before MP3 when it was lamented that sampled audio files could never be compressed very well. Even today bzip2 does not work very well at all at compressing sampled audio (about 1.3:1), but mp3 files can be made at a compression ratio of 10:1 over CD-quality audio and we all seem to still enjoy the music. I suppose the best lossy compression is the one that preserves the features of the image you want and throws out the stuff you don't care about. So, in a way, data-reduction programs are probably the best lossy compression we are going to get. Unfortunately, accurate external information is required (such as the beam center convention!), so the interface to this compression algorithm still a little more complicated than pkzip. ;) Nevertheless, there are still only about 40-50 formats of diffraction images floating around (30 operating beamlines, a few in-house vendors and some history). I would like to collect them all. So, if anybody out there has a lysozyme data set (or even just a single image) from anywhere but ALS 8.3.1, please let me know how I can get a copy of it! -James Holton MAD Scientist Harry Powell wrote: Hi Just to add to this. imgCIF (or CBF, which amounts to pretty well the same thing) has fast and efficient compression built in, and has been developed with protein crystallography (particularly) in mind. There are even (a few) detectors out there which will write these instead of (or as well as) the manufacturer's native format, saving the user the trouble of conversion. If you're looking for a standard format for storing image data in, I wouldn't look any further, since (in principle) imgCIF/CBF can store all the image information you (or a fussy^H^H^H^H^H conscientious reviewer who could be bothered to re-process your dataset) would want
Re: [ccp4bb] ccp4 pack_images program?
Hi Bill, It seems it would be good to have available if we are all going to put our images on our web-servers. Probably easier to either just bzip2 the images (which works reasonably well but is somewhat slow) or use one of the imgCIF jiffy programs to do this, which will correctly retain the header information. The pack subroutines you refer to deal with the pixel array that is the image but do not address the problem of safe storage of the header. Plus of imgCIF is some data reduction packages can reduce the data straight from the compressed files. The minus is that it is not obvious that other programs can do this and that all settings in the cbf lib can be treated equivalently (e.g. compression) The plus of bzip2 is that it leaves the image essentially unharmed, and you don't need any special programs. The minus is you have to unpack before processing. Usually you get something like a factor of 3 in size for bzip2, with the compression taking typically 1s/image. Two things though if people are going to do this for real: (1) ensure the result is in manageable chunks - a 5GB tarball is no use to anyone as many programs can't download more than 2^32 bytes, noone wants to download 720 images individually (2) compute md5sums for the files so the end user can check they have downloaded correctly I guess any script-smith could put together a couple of commands to prepare the data for www download... not difficult really. Cheers, Graeme
Re: [ccp4bb] crystal with precipitation
Sorry - this may have been mentioned previously, but have you tried banging in some glycerol (5-10%)? J shivesh kumar [EMAIL PROTECTED] wrote: Dear all I welcome all the suggestions regarding my crystals which is coming with the precipitation.The pI of the protein is 4.2 and the drop precipitates with MPD as low as 30% within 4-5 hrs.I am trying the pH ranging from 3.6-5.2 at 16C.There is no precipitation at 20% of MPD.Also,at high conc,the protein precipitates.The crystals are coming as florets as I mentioned with 2+2.Should I go for higher pH like uptp 8.5 or so.crystals are not growing bigger in size so that I can mount.Should I try changing the temperature.Ican use 4C and 16C.Right now I am keeping plates at 16C.I am concentrating the protein through lyophilization.As soon I pool it for Gel filtration,majority of it get precipitated,not soluble protein.Is there any method to make the protein stable? I appreciate all the informative suggestions.Thanx in advance and thanx everybody who has suggested the various options. Shivesh kumar -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
Re: [ccp4bb] crystal with precipitation
I agree to this last suggestion. For one of my protein, I had to add at least 10 % of glycerol in my buffers to keep my protein stable while purifying. For crystallization, I diluted it to 20 % glycerol (vapour diffusion method) which allowed it to be stable in the crystallization drop and eventually leading to crystallization. (well, again it depends from protein to protein). Another thing you could try for bigger crystals is to increase your protein concentration, (if it is stable enough) and set up at 4 C (rather than 16 C). Hope this helps, Manish Sorry - this may have been mentioned previously, but have you tried banging in some glycerol (5-10%)? J shivesh kumar [EMAIL PROTECTED] wrote: Dear all I welcome all the suggestions regarding my crystals which is coming with the precipitation.The pI of the protein is 4.2 and the drop precipitates with MPD as low as 30% within 4-5 hrs.I am trying the pH ranging from 3.6-5.2 at 16C.There is no precipitation at 20% of MPD.Also,at high conc,the protein precipitates.The crystals are coming as florets as I mentioned with 2+2.Should I go for higher pH like uptp 8.5 or so.crystals are not growing bigger in size so that I can mount.Should I try changing the temperature.Ican use 4C and 16C.Right now I am keeping plates at 16C.I am concentrating the protein through lyophilization.As soon I pool it for Gel filtration,majority of it get precipitated,not soluble protein.Is there any method to make the protein stable? I appreciate all the informative suggestions.Thanx in advance and thanx everybody who has suggested the various options. Shivesh kumar -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile) * Manish B. Shah, PhD. Postdoctoral Fellow Hauptman-Woodward Medical Research Institute 700 Ellicott Street Buffalo, NY 14203. *
Re: [ccp4bb] ccp4 pack_images program?
Is there any advantage to bzip2-ing the individual images rather than making one bzip2-ed tarball with tar cvfj? Yes. If you have folks sending you images by sftp or e-mail, then you don't have ensure a tarball of Giga or Tera bytes works. You can send the smaller multiple files and restart upon failure. Jim
[ccp4bb] alternate indexing / cubic space group
Hello All, I have a question about some data with which I have been grappling. The crystal appears to be primitive cubic(p23). Are there alternate ways to index cubic data? I ask this question without regard to anomalous data. I have looked at several datasets in Xtriage. I wanted to merge data from two crystals together and I looked to see if it were necessary to reindex to do it properly. Here is what xtriage has to say. Merging analysis between datasets from 2 different crystals(These datasets are non-anomalous datasets, ie Bijvoet pairs have been merged). Reference analyses The following reindexing operators have been found: - | Operator | Correlation | matches (%) | choice | - | h,k,l| 0.000 | 89.6|| | -h,l,k | 0.722 | 91.4| --- | - I'd have thought that there was a single indexing possibilty for the cubic space group in the absence of a consideration of the anomalous signal. And I'd accept that I were wrong if I hadn't looked at some other data. So to cloud my thinking, I decided to look at the output from Xtriage for datasets from the same crystal collected 180 degrees apart. In this case the data were processed with HKL2000 with the same indexing setup, ie the crystal rotx,y,z reference zone etc and starting phis of x and x+180 were used. The data in this case is again treated as non-anomalous too. Reference analyses The following reindexing operators have been found: - | Operator | Correlation | matches (%) | choice | - | h,k,l| -0.007 | 91.0|| | -h,l,k | 0.719 | 92.7| --- | - What's going on here? I processed these two wedges at different times, but I kept all of the parameters consistent. Are there two choices of indexing? this doesn't seem possible, given that the indexing set-up was the same. or does denzo arbitrarily choose the configuration upon initial indexing irrelevant of what I tell it? I think not. Or might this show that my space group is of lower symmetry(rhombohedral or orthorhombic) than p23, with or without some possible pseudo-symmetry? In addition, I have other crystals of a similar complex(one protein has a single aa mutation) which are I23 with similar(2% difference) in cell constants. Same set-up as case 2, datasets from the same crystal collected 180 degrees apart, data were processed with HKL2000 with the same indexing setup, ie the crystal rotx,y,z reference zone etc and starting phis of x and x+180 were used. The data in this case is again treated as non-anomalous too. This data was processed at the same time. Reference analyses The following reindexing operators have been found: - | Operator | Correlation | matches (%) | choice | - | h,k,l| 0.945 | 59.7| --- | | -h,l,k | 0.110 | 58.4|| - This is what I'd have expected for case 2 as well. Lastly, for the P23(nor the I23 case for that matter) case, Xtriage doesn't indicate twinning. In each case, I can get a molecular replacement solution which has very reasonable near identical packing, my search model is 100% identical to one of the 2 proteins in the crystal. Unfortunately I don't see the second protein in the maps. It is about 20 percent the size of the other protein. The obvious answer is the second protein isn't there but I feel that it should be there because I get a nice Se fluorescence signal from the crystals, and the missing protein is the only one that is labeled. So I'm looking at possibilities of a misassigned space group, etc to get over the hump. I hope all of this doesn't sound like mindless drivel. Any comments on any or all of this? Thanks in advance. todd
Re: [ccp4bb] The importance of USING our validation tools
I've been reading the contributions on this topic with much interest. It's been very timely in that I've been giving 3rd year u/g lectures on protein X-ray structures and their validation over the past week. As part of the preparation for the lectures, I searched the PDB for structures with high solvent content. To my surprise, I found 376 crystal structures with solvent content 75% (about 1% of all crystal structures) and 120 structures with solvent content 80% (about 0.3% of all crystal structures) However, there were only 3 other structures that (like 2HR0) had 80% AND Rcryst Rfree less than 20%. All three structures are solved to better than 3A Resolution. One is from a weak data set from a virus crystal, the other two PDB files report very strong crystallographic data. The Rmerge values are more typical than for 2HR0 and none of the three appear to have the geometry or crystal contact problems of 2HR0. My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. There are another 15 structures with solvent content 75-80% and Rcryst/Rfree 20%. I didn't check them in any detail, just to see that the structure was consistent with a high solvent content. Any thoughts? Cheers, Jenny
Re: [ccp4bb] SciVee - YouTube for scientist
Hi all, Great idea! As being reasonably new to the field, I would definitely welcome those videos. Not that I don't read Acta D papers, but it is always nice to hear the talks directly, and would certainly be quite educational. Cheers, Ronnie Berntsson -- Ph.D. Student Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands On Aug 23, 2007, at 10:57 AM, Clemens Vonrhein wrote: Hi Eleanore, On Tue, Aug 21, 2007 at 12:56:40PM +0100, Eleanor Dodson wrote: 5) The need for crystallographic education for readers and students Just discovered SciVee (YouTube for scientists) at http://www.scivee.tv/ which is operated in partnership with the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). Maybe if those webcasts of the last few CCP4 study weekends are still available (and speakers permit), these could be placed there as a supplement to the usual Acta D issue? Hearing a talk might be even more educational than going through a Acta D paper for people new or unfamiliar with crystallographic methods. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] The importance of USING our validation tools
In the cases you list, it is clearly recognized that the fault lies with the investigator and not the method. In most of the cases where serious problems have been identified in published models the authors have stonewalled by saying that the method failed them. The methods of crystallography are so weak that we could not detect (for years) that our program was swapping F+ and F-. The scattering of X-rays by bulk solvent is a contentious topic. We should have pointed out that the B factors of the peptide are higher then those of the protein. It appears that the problems occurred because these authors were not following established procedures in this field. They are, as near as I can tell, somehow immune from the consequences of their errors. Usually the paper isn't even retracted, when the model is clearly wrong. They can dump blame on the technique and escape personal responsibility. This is what upsets so many of us. It would be so refreshing to read in one of these responses We were under a great deal of pressure to get our results out before our competitors and cut corners that we shouldn't have, and that choice resulted in our failure to detect the obvious errors in our model. If we did see papers retracted, if we did see nonrenewal of grants, if we did see people get fired, if we did see prison time (when the line between carelessness and fraud is crossed), then we could be comforted that there is practical incentive to perform quality work. Dale Tronrud Edwin Pozharski wrote: Mischa, I don't think that the field of nanotechnology crumbled when allegations against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature) turned out to be true. I don't think that nobody trusts biologists anymore because of Eric Poehlman (17 falsified grants, 10 papers with fabricated data, 12 month in prison). We are still excited to hear about stem cell research despite of what Hwang Woo-suk did or didn't do. What recent events demonstrate is that in macromolecular crystallography (and in science in general) mistakes, deliberate or not, will be discovered. Ed. Mischa Machius wrote: Due to these recent, highly publicized irregularities and ample (snide) remarks I hear about them from non-crystallographers, I am wondering if the trust in macromolecular crystallography is beginning to erode. It is often very difficult even for experts to distinguish fake or wishful thinking from reality. Non-crystallographers will have no chance at all and will consequently not rely on our results as much as we are convinced they could and should. If that is indeed the case, something needs to be done, and rather sooner than later. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Re: [ccp4bb] The importance of USING our validation tools
- Original Message - From: Jenny Martin [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 23, 2007 5:46 PM Subject: Re: [ccp4bb] The importance of USING our validation tools My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. You must be thinking about Mark van Raaij's T4 short tail fibre structures. Yes, the disorder in those crystals is extreme. There are ~100-150 A thick disordered layers between the ~200 A thick layers of ordered structure. The diffraction pattern does not show any anomalies (as far as I can remember from 6 years ago). The spots are round, there are virtually no spots not covered by predictions, and the crystals diffract to 1.5A resolution. The disordered layers are perpendicular to the threefold axis of the crystal. The molecule is a trimer and sits on the threefold axis. It appears that the ordered layers somehow know how to position themselves across the disordered layers. I agree here with Michael Rossmann that in these crystals the ordered layers are held together by faith. Mark integrated the dataset in lower space groups, but the disordered stuff was not visible anyway. He will probably add more to the discussion. Petr Any thoughts? Cheers, Jenny
Re: [ccp4bb] The importance of USING our validation tools
Another example of a structure with intervening layers of weak electron density at 1.75 A resolution is Pb2+ bound calmodulin that Mark Wilson solved in my laboratory: M.A. Wilson and A.T. Brunger, / Acta Cryst./D59, 1782-1792 (2003), PDB ID 1NOY. The intervening layers are not entirely disordered since PB2+ positions show up in difference maps in these layers, so it could indicate motion around these positions rather than complete disorder. However, apart from the Pb2+ positions, the electron density in these layers is weak and un-interpretable. Apart from the weak layers, the structure behaves completely normal, i.e., we observe the expected bulk solvent contribution at low resolution, and the B-factor distributions are as expected. Axel Petr Leiman wrote: - Original Message - From: Jenny Martin [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 23, 2007 5:46 PM Subject: Re: [ccp4bb] The importance of USING our validation tools My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. You must be thinking about Mark van Raaij's T4 short tail fibre structures. Yes, the disorder in those crystals is extreme. There are ~100-150 A thick disordered layers between the ~200 A thick layers of ordered structure. The diffraction pattern does not show any anomalies (as far as I can remember from 6 years ago). The spots are round, there are virtually no spots not covered by predictions, and the crystals diffract to 1.5A resolution. The disordered layers are perpendicular to the threefold axis of the crystal. The molecule is a trimer and sits on the threefold axis. It appears that the ordered layers somehow know how to position themselves across the disordered layers. I agree here with Michael Rossmann that in these crystals the ordered layers are held together by faith. Mark integrated the dataset in lower space groups, but the disordered stuff was not visible anyway. He will probably add more to the discussion. Petr Any thoughts? Cheers, Jenny -- Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web:http://atb.slac.stanford.edu Email: [EMAIL PROTECTED] Phone: +1 650-736-1031 Fax:+1 650-745-1463
