Re: [ccp4bb] very informative - Trends in Data Fabrication
In fact, I would put it even stronger, if we know a referee is being dishonest, it is our duty to make sure he is removed from science, blacklisted from the journal etc. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 19:13, Maria Sola i Vilarrubias wrote: Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more results for the reviewer to be able to submit its own paper (with new ideas) in time, or copy a structure from the figures, or ask for experiments that only the reviewer can do so he/she is included in the paper, or submit as fast as possible in another journal with an extremely short delay of acceptance (e.g. 10 days, without revision?, talking to the editorial board?) things like this. Well, it is not question of making a full list, here!. The whole problem comes from publishing first, from competition. The hope with fraud with X-ray data is that it seems to be detectable, thanks to valuable people that develop methods to detect it. But it is very difficult to demonstrate that your work, ideas or results have been copied. How do you defend from this? And how after giving to them the valuable PDB? Finally, how many crystallographers are in the world? 5000? The concept of ethics can change from one place to another and, more than this, there is the fact that the reviewer is anonymous. I try to respond to my reviewers the best I can and I really trust their criteria, sometimes a bit too much, indeed. I think they all have done a very nice job. But some of the stories from above happened to me or close to me and I feel really insecure with the idea of sending a manuscript, the X-ray data and the PDB, altogether, to a reviewer shielded by anonymity. It's too risky: with an easy molecular replacement someone can solve a difficult structure and publish it first. And then the only thing left to the bad reviewer is to change the author's list! (and for the true author what is left is to feel like an idiot). In my humble opinion, we must be strict but not kill ourselves. Trust authors as we trust reviewers. Otherwise, the whole effort might be useless. Maria Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es On 3 April 2012 16:58, Mark J van Raaij mjvanra...@cnb.csic.es wrote: The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I have witnessed authors being hesitant to complain about possible violations and journals not always taking complaints seriously enough. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 16:45, Bosch, Juergen wrote: Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them - that's how I found out about the identity of the reviewer - as it couldn't be changed by the journal. I agree though that it shouldn't happen and I hope it only happens in very few cases. Jürgen On Apr 3, 2012, at 9:10 AM, Dyda wrote: I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. .. Jürgen Bosch Johns Hopkins University Bloomberg
Re: [ccp4bb] Substitution to glycerol during crystallogenesis
Glycerol is known to be able to reduce nucleation. This might be countered by an increase in protein concentration. Vera, L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11: 2755–2762. Enrico. On Tue, 03 Apr 2012 13:49:50 +0200, Toby Longwood toby.longw...@gmail.com wrote: Dear all, My question is related to a sample preparation. I’m working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] simple solution to - Trends in Data Fabrication
Hi James, My previous message on this matter remains unnoticed, but I also suggested a very simple solution to the data fraud: the crystallographers should submit to PDB partially processed data, like unmerged partial reflections. These files are much smaller than the images, and only a few people in the world are capable to forge them. This simple solution would kill any attempt to fabricate crystallographic data. Alex On Apr 3, 2012, at 7:11 AM, James Whisstock wrote: Hi I was thinking about the last statement in the Acta editorial - It is important to note, however, that in neither of these cases was a single frame of data collected. Not one.. This brought me back to the images.. To date there is no global acceptance that original diffractiom images must be deposited (though I personally think there should be). Many of the arguments around this issue relate to the time and space required to house such data. However (and apologies if this has already been raised and I have missed it), if our sole intent is to ascertain that there's no trouble at t'mill then deposition of a modest wedge of data and / or a 0 and 90, while not ideal, may be sufficient to provide a decent additional check and balance, particularly if such images, headers etc were automatically analysed as part of the already excellent validation tools in development. I'm sure there are a number of clever ways (that could be unadvertised or kept confidential to the pdb) that could be used to check off sufficient variables within such data such that it should (?) be very difficult to falsify images without triggering alarm bells. Of course this would probably then drive those that are truly bonkers to attempt to fabricate realistically noisy false diffraction images, however I would hope that such a scheme might make things just a little more difficult for those with fraudulent intent, particularly if no one (apart from the developers) knows precisely how and what the checking software checks! While it seems sad that it's come to this cell biologists and biochemists have had to deal with more and more sophisticated versions of the photoshopped western for years. Accordingly, most high profile journals run figures through commercial software that does a reasonable job of detection of such issues. J Sent from my iPhone On 03/04/2012, at 11:10 PM, Dyda d...@ulti.niddk.nih.gov wrote: I think that to review a paper containing a structure derived from crystallographic data should indeed involve the referee having access to coordinates and to the electron density. Without this access it is not possible to judge the quality and very often even the soundness of statements in the paper. I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. Unfortunately however, there is another serious issue. After a very troubling experience with a paper I reviewed, I discussed this issue with journal editors. What they said was that they already have a hell of time to find people who agree to referee, by raising the task level (asking refs to look at coords and density) they feared that no one would agree. Actually, perhaps many have noticed the large number of 5 liner referee reports saying really not much about a full length research article. People simply don't have the time to put the effort in. So I am not sure how realistic is to ask even more, for something that at some level, is pro bono work. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] zinc fingre
Yes, Rajesh, I completely agree with Pius. There is absolutely nothing wrong in asking a question on ccp4bb. The suggestion 'read a book and search on-line information sources' is a good one on any subject. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pius Padayatti Sent: Tuesday, April 03, 2012 11:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] zinc fingre Hi Rajesh, First of all you did the right thing to ask people here about our doubts. There is nothing wrong in asking questions. The board is for asking questions realted to crystallography (all aspects). Padayatti On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear Colleagues, One thing that would help is avoiding misappropriated priority of research results would be to join the math and physics community in their robust use of open-access preprints in arXiv. Such public preprints establish reliable timelines for research credit and help to ensure timely access to new results by the entire community. Fully peer-reviewed publications in real journals are still desirable, but to make this work, our journals would have to be willing to accept papers for which such a preprint system has been used. To understand the complexity of the issue, see http://nanoscale.blogspot.com/2008/01/arxiv-and-publishing.html I believe the IUCr is willing to accept papers that are posted on a preprint server (somebody correct me if I am wrong). It works for the math and physics community. Perhaps it would work for the crystallographic community. On 4/3/12 1:28 PM, Mark J van Raaij wrote: In fact, I would put it even stronger, if we know a referee is being dishonest, it is our duty to make sure he is removed from science, blacklisted from the journal etc. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 19:13, Maria Sola i Vilarrubias wrote: Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more results for the reviewer to be able to submit its own paper (with new ideas) in time, or copy a structure from the figures, or ask for experiments that only the reviewer can do so he/she is included in the paper, or submit as fast as possible in another journal with an extremely short delay of acceptance (e.g. 10 days, without revision?, talking to the editorial board?) things like this. Well, it is not question of making a full list, here!. The whole problem comes from publishing first, from competition. The hope with fraud with X-ray data is that it seems to be detectable, thanks to valuable people that develop methods to detect it. But it is very difficult to demonstrate that your work, ideas or results have been copied. How do you defend from this? And how after giving to them the valuable PDB? Finally, how many crystallographers are in the world? 5000? The concept of ethics can change from one place to another and, more than this, there is the fact that the reviewer is anonymous. I try to respond to my reviewers the best I can and I really trust their criteria, sometimes a bit too much, indeed. I think they all have done a very nice job. But some of the stories from above happened to me or close to me and I feel really insecure with the idea of sending a manuscript, the X-ray data and the PDB, altogether, to a reviewer shielded by anonymity. It's too risky: with an easy molecular replacement someone can solve a difficult structure and publish it first. And then the only thing left to the bad reviewer is to change the author's list! (and for the true author what is left is to feel like an idiot). In my humble opinion, we must be strict but not kill ourselves. Trust authors as we trust reviewers. Otherwise, the whole effort might be useless. Maria Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es On 3 April 2012 16:58, Mark J van Raaijmjvanra...@cnb.csic.es wrote: The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I have witnessed authors being hesitant to complain about possible violations and journals not always taking complaints seriously enough. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 16:45, Bosch, Juergen wrote: Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them -
Re: [ccp4bb] Substitution to glycerol during crystallogenesis
Florian Schmitzberger wrote: Dear Toby, I don't think there is a basic problem using glycerol in crystallization. Glycerol will affect the vapour pressure (if it is not present in the well/precipitant solution) and 10 % glycerol is ~ 1.3 molar concentration. During equilibration the drops may increase in volume, decreasing the protein concentration. Thus, when using glycerol I think it is generally beneficial to start with a high protein concentration. Perhaps, you can concentrate your protein sample further. It sounds like you are encouraging the OP to crystallize by reverse vapor diffusion. Unless there is reason to believe that diluting the droplets will push the protein toward saturation (salting-in region?), it would seem better to skip the reservoir, seal the wells and crystallize by batch method. Even more sensible, (as you parenthetically hint) add the same concentration glycerol to the reservoir solution to compensate and crystallize by normal forward vapor diffusion. And if you are lucky you can use the glycerol-containing reservoir solution as artificial mother liquor if you need it for mounting crystals or mixing cryoprotectant solutions. Still, it makes sense to use higher protein or PEG to counteract the tendency of glycerol to increase solubility/decrease nucleation. I have on several occasions observed immediate precipitation upon mixing protein solution (containing glycerol) and precipitant solution; drops then cleared up after a short period of time (and crystals eventually formed). In this case, the crystallization experiment starts in the supersaturated zone, and moves towards an undersaturated concentration, traversing the (metastable) zone where nucleation and crystallization can happen (rather than the other way around, which seems the more traditional approach with crystallization by vapour diffusion). Enrico Stura published a recent article, describing an effect of glycerol on crystallization. Vera,L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11 :2755–2762. You could replace glycerol with ethylenglycol or a small molecular weight PEG (e.g. 400), which may also have a stabilizing effect on your complex. Regards, Florian On Apr 3, 2012, at 7:49 AM, Toby Longwood wrote: Dear all, My question is related to a sample preparation. I’m working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby
[ccp4bb] Who is using 64-bit Linux?
The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Who is using 64-bit Linux?
We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom 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 Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] very informative - Trends in Data Fabrication
I agree with Herbert that a pre-print setup is one way to establish priority and get useful comments for an author. And I know this has been discussed before, but another way is to remove the anonymous aspect of the review, as this would achieve the same as the community pre-print distribution (at least in many ways). I would be happy to give my name when reviewing, as I feel it is my job to improve the paper, and I can still face my colleagues after the exercise. cheers, tom 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 Herbert J. Bernstein [y...@bernstein-plus-sons.com] Sent: Wednesday, April 04, 2012 4:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear Colleagues, One thing that would help is avoiding misappropriated priority of research results would be to join the math and physics community in their robust use of open-access preprints in arXiv. Such public preprints establish reliable timelines for research credit and help to ensure timely access to new results by the entire community. Fully peer-reviewed publications in real journals are still desirable, but to make this work, our journals would have to be willing to accept papers for which such a preprint system has been used. To understand the complexity of the issue, see http://nanoscale.blogspot.com/2008/01/arxiv-and-publishing.html I believe the IUCr is willing to accept papers that are posted on a preprint server (somebody correct me if I am wrong). It works for the math and physics community. Perhaps it would work for the crystallographic community. On 4/3/12 1:28 PM, Mark J van Raaij wrote: In fact, I would put it even stronger, if we know a referee is being dishonest, it is our duty to make sure he is removed from science, blacklisted from the journal etc. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 19:13, Maria Sola i Vilarrubias wrote: Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more results for the reviewer to be able to submit its own paper (with new ideas) in time, or copy a structure from the figures, or ask for experiments that only the reviewer can do so he/she is included in the paper, or submit as fast as possible in another journal with an extremely short delay of acceptance (e.g. 10 days, without revision?, talking to the editorial board?) things like this. Well, it is not question of making a full list, here!. The whole problem comes from publishing first, from competition. The hope with fraud with X-ray data is that it seems to be detectable, thanks to valuable people that develop methods to detect it. But it is very difficult to demonstrate that your work, ideas or results have been copied. How do you defend from this? And how after giving to them the valuable PDB? Finally, how many crystallographers are in the world? 5000? The concept of ethics can change from one place to another and, more than this, there is the fact that the reviewer is anonymous. I try to respond to my reviewers the best I can and I really trust their criteria, sometimes a bit too much, indeed. I think they all have done a very nice job. But some of the stories from above happened to me or close to me and I feel really insecure with the idea of sending a manuscript, the X-ray data and the PDB, altogether, to a reviewer shielded by anonymity. It's too risky: with an easy molecular replacement someone can solve a difficult structure and publish it first. And then the only thing left to the bad reviewer is to change the author's list! (and for the true author what is left is to feel like an idiot). In my humble opinion, we must be strict but not kill ourselves. Trust authors as we trust reviewers. Otherwise, the whole effort might be useless. Maria Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es On 3 April 2012 16:58, Mark J van Raaijmjvanra...@cnb.csic.es wrote: The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I
Re: [ccp4bb] Who is using 64-bit Linux?
Whatever you do, make sure you have enough bottled water before the next doomsday: http://en.wikipedia.org/wiki/Year_2038_problem I am using 64-bit linux almost exclusively for some time now. XRD software works fine, no lingering issues that I can report. ia32-libs do the trick for 32-bit binaries. On Tue, 2012-04-03 at 15:57 -0400, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] very informative - Trends in Data Fabrication
On the topic of MX fraud : could not an encryption algorithm be applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe entry? has anyone proposed such an idea before? for example (admittedly this is a mess): * a detector parameter - perhaps the serial number - is used as a public key. the detector parameter is shared among beamlines/companies/*pdb. specifically, the experimentor requests it at beamtime. * experimentor voluntarily encrypts something, using GPLv3 programs, small but essential to the deposition materials, like the R-free set indices (or please suggest something better), using their private key. maybe symmetric cipher would work better for this. or the Free R set indices are used to generate a key. * at deposition time, the *pdb unencrypts the relevant entry components using their private key related to the detector used. existing deposition methods pass or fail based on this (so maybe not the Free R set). * why do this : at deposition time, *pdb will have a yes-or-no result from a single string of characters. can be a stop-gap measure until images can be archived easily. all elements of the chain are required to be free and unencumbered by proprietary interests. importantly, it is voluntary. this will prevent entries such as Schwarzenbacher or Ajees getting past deposition - so admittedly, not many. references: http://en.wikipedia.org/wiki/RSA_(algorithm) http://en.wikipedia.org/wiki/Diffie-Hellman_key_exchange -Bryan
Re: [ccp4bb] Who is using 64-bit Linux?
I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i, coot, and shelxcde beta executables run fine. There were issues with the coot package installation due to unresolved dependencies and my ignorance thereof, but I think a working RHEL62-64 compatible package is available now, the coot wiki has latest info. I could not get Xtalview running, probably some xterm thing beyond my grasp, which also screws up the latest hkl2mapV0.3, V0.2 runs fine. Free intel ifort runs great. The great part about the VM ware installation is that I also got it running on a win7-64 8GB laptop by simply copying the virtual RHEL machine (files). That alone saved a few day's work. Also the Unity feature of VMware is a blast. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Tuesday, April 03, 2012 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
[ccp4bb] Trueblood Award Nominations
Dear Colleagues, on behalf of the selection committee I'd like to draw your attention to the the Trueblood award: http://www.amercrystalassn.org/content/pages/main-award-descriptions This will next be awarded in 2013, however nominations are sought now so that the winner can be announcement this Summer. The award will be presented at the 2013 ACA meeting. Please follow this link to obtain the nomination form: http://www.amercrystalassn.org/documents/ACAnomNEW.pdf Note that the deadline for nominations is May 1st, which should be sent to mar...@hwi.buffalo.edu. Here is a summary of the award: Kenneth N. Trueblood Award To recognize exceptional achievement in computational or chemical crystallography. The award is established in memory of Professor Kenneth N. Trueblood, UCLA 1949-1998, who was a major force in the early use of computers and the development of crystallographic computer programs. He applied these programs to the examination of chemical and molecular details of many structures at the frontiers of research. His contribution to the famous work on vitamin B12 is one example. Professor Trueblood was a leader in the development of techniques for analysis of anisotropic motion and was also a superb teacher and a lucid author. Established in 2001, the award will be given every three years and consist of an honorarium of $1,500 and up to $1,500 in travel expenses to accept the award. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ] --
[ccp4bb] core rmsd in coot
When superimposing 2 structures in coot, I get a core rmsd in the output. What does this mean? Which residues are included in the core rmsd? Are these all the residues that have equivalent residues in the moving and reference molecule? Yrsyla -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
Re: [ccp4bb] Who is using 64-bit Linux?
We have been using 64 bit Linux for several years. I'm not aware of any lingering issues with the 64 bit-ness. Linux is always sprinkling in a few new bugs, but I don't know of any current issues with 32 bit vs. 64 bit. On 04/03/12 15:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] very informative - Trends in Data Fabrication
I'm not sure how encryption can solve a problem of truth or falsity. Public key encryption only says that the message that is decrypted using the public key must have been encrypted by someone who knows the private key. A person can use their private key to encrypt a lie as well as the truth. I don't quite follow your prescription, but if you are saying that the beamline gives the depositor a code when they collect data that proves data were collected, how does the beamline personal know the contents of the crystal? Couldn't one simply collect HEWL and then deposit any model they like? The beamline could encrypt all images with their private key, and the data integration program could decrypt the images using the public key. That way when a depositor presents a set of images it could be proved that those images came, unmodified, from that beamline. The images would still have to be deposited, however. (And this provides no protection against forgeries of home source data sets.) Dale Tronrud On 04/03/12 13:19, Bryan Lepore wrote: On the topic of MX fraud : could not an encryption algorithm be applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe entry? has anyone proposed such an idea before? for example (admittedly this is a mess): * a detector parameter - perhaps the serial number - is used as a public key. the detector parameter is shared among beamlines/companies/*pdb. specifically, the experimentor requests it at beamtime. * experimentor voluntarily encrypts something, using GPLv3 programs, small but essential to the deposition materials, like the R-free set indices (or please suggest something better), using their private key. maybe symmetric cipher would work better for this. or the Free R set indices are used to generate a key. * at deposition time, the *pdb unencrypts the relevant entry components using their private key related to the detector used. existing deposition methods pass or fail based on this (so maybe not the Free R set). * why do this : at deposition time, *pdb will have a yes-or-no result from a single string of characters. can be a stop-gap measure until images can be archived easily. all elements of the chain are required to be free and unencumbered by proprietary interests. importantly, it is voluntary. this will prevent entries such as Schwarzenbacher or Ajees getting past deposition - so admittedly, not many. references: http://en.wikipedia.org/wiki/RSA_(algorithm) http://en.wikipedia.org/wiki/Diffie-Hellman_key_exchange -Bryan
Re: [ccp4bb] Who is using 64-bit Linux?
Hi Roger CCP4 and Mosflm work fine in my testing - I do builds for Linux and Macs, both 32 and 64 bits. I wouldn't expect to see a difference in performance (and don't see anything significant in practice). One thing - I think you will need to install 32-bit compatibility libraries for some of the code that is dynamically linked and has been built as 32-bit, e.g. I think ActiveTcl distros might need them (for iMosflm). On 3 Apr 2012, at 20:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Who is using 64-bit Linux?
Fedora and RHEL 64-bit work well and run pretty much all the standard programs (CCP4/Coot/Phenix/CNS/SHELX). By installing the relevant 32-bit libraries you can also run older programs if need be. On a related note, XtalView will work on Fedora/RHEL if you install/compile the appropriate XView library files. For more info, check out: http://www.physionet.org/physiotools/xview/ Hope that helps, Kip On Tue, 3 Apr 2012 17:01:30 -0400 David Schuller dj...@cornell.edu wrote: We have been using 64 bit Linux for several years. I'm not aware of any lingering issues with the 64 bit-ness. Linux is always sprinkling in a few new bugs, but I don't know of any current issues with 32 bit vs. 64 bit. On 04/03/12 15:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Application deadline approaching: CCP4 summer school at APS, in USA
Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School From data collection to structure refinement and beyond is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world's leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
Re: [ccp4bb] very informative - Trends in Data Fabrication
Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin
Re: [ccp4bb] very informative - Trends in Data Fabrication
On Tue, Apr 3, 2012 at 5:16 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: I'm not sure how encryption can solve a problem of truth or falsity. AFAIU any given checksum will tell you if a file is corrupted or not. My brain decided to interpret that as true or false. and A person can use their private key to encrypt a lie as well as the truth. [...] I don't quite follow your prescription, ...I admitted it is a mess - and sorry to mix up the various algorithms. also I must emphasize I do not have a clear picture of how encryption would work here. can I step back - it *seems* that following facts point to a checksum of sorts for a *pdb entry: * random number generator seed * randomly chosen Free R set * integer indices of the Free R set * detector things - serial number, or fingerprint of sorts - known to *pdb only. ... by checksum of sorts for a *pdb entry, what that means is an easy way to verify if all parts of the entry originated with diffraction images. detector things indicates that I am wondering if something besides an SN on a detector would be useful. ... so a scenario that comes to mind is the deposition team runs the checksum (or whatever), and gets the Free R set (for example). they run the battery of tests. they find that refinement is a disaster. they go check the detector specs they have, etc., etc., there were no images used. The beamline could encrypt all images with their private key, and[...] it could be proved that those images came, unmodified, from that beamline. would encryption of images significantly increase the integration time? Also, I am not following the image deposition forum elsewhere. ... anyways, this sounds like it was just an excercise. Thanks anyway. Regards, -Bryan
Re: [ccp4bb] Who is using 64-bit Linux?
Roger, My lab is using 64 bit distros of SUSE and Linux Mint and hasn't had any compatibility issues that I can recall. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu Date:Tue, 3 Apr 2012 15:57:40 -0400 From:Roger Rowlett rrowl...@colgate.edu Subject: Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] zinc fingre
Hi Rajesh, Have you looked at how well conserved these Cys/His residues are? Is the spacing similar to known zinc fingers? Might be good things to consider if you suspect a zinc finger in your protein, of course you probably know this already. Best, Peter
Re: [ccp4bb] very informative - Trends in Data Fabrication
Orcus, if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. The skill of presentation is at least as important in Science as being right. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin
Re: [ccp4bb] ccp4i project display
Hi, If it is under a UNIX-like system, I would probably make a new user for myself, say, projects_2012, etc.. It is not perfect, but it is a simple solution. Zhijie From: wtempel Sent: Tuesday, April 03, 2012 9:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ccp4i project display Dear colleagues, likely some of you have experienced that with 100s of ccp4i projects, the menu (limited to 25 lines?) exceeds the horizontal limitations of the computer display. Are there any suggestions how to handle this many projects? Added difficulty: I expect that were I to eliminate selected old projects from the list, I would have to return to said old project the following day. Thank you in advance, Wolfram Tempel
Re: [ccp4bb] very informative - Trends in Data Fabrication
Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Orcus, ** ** if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. ** ** The skill of presentation is at least as important in Science as being right. ** ** Best, BR ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Kevin Jin *Sent:* Tuesday, April 03, 2012 3:34 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] very informative - Trends in Data Fabrication ** ** Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin ** ** -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
Re: [ccp4bb] very informative - Trends in Data Fabrication
Trollus maximus perhaps ? But it could have different meanings e.g. in German there is something going south if it went down the orcus :-) Don't worry to much and relax. Jürgen On Apr 3, 2012, at 8:22 PM, Kevin Jin wrote: Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: Orcus, if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. The skill of presentation is at least as important in Science as being right. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin -- Kevin 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
Might I suggest looking to Sean Seaver and the P212121.com as an example of a a successful crystallographer science blogger though the site has shifted more towards a consumable supplier in recent years. I would also consider looking into adding an RSS feed to your site so that those people interested in your articles can be informed without spamming the boards. The gods of the interwebz have blessed us with the gift of RSS so that we may be made aware of when someone might be yelling something potentially interesting into the void (that and to bring us silly pictures of cats covered in phonetically spelled captions when we have a failed experiment). It is my hope that this will not discourage you from taking every opportunity to improve your writing skills but help you find a more appropriate means of disseminating your product. Cheers, Katherine On Tue, Apr 3, 2012 at 7:22 PM, Kevin Jin kevin...@gmail.com wrote: Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Orcus, ** ** if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. ** ** The skill of presentation is at least as important in Science as being right. ** ** Best, BR ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Kevin Jin *Sent:* Tuesday, April 03, 2012 3:34 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] very informative - Trends in Data Fabrication ** ** Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin ** ** -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
Re: [ccp4bb] very informative - Trends in Data Fabrication
My intent with the troll joke was to give a humorous reminder that a little self promotion is ok, but a couple times a day is annoying. Orcus means troll, as in Internet troll, meaning one who subverts the intended use of the site and is annoying people. You have made a number of on topic posts that were very nice, but also a number that were clearly off topic and viewed as self promotion, with links to your consulting service. A couple times a day is a bit much. No one wants to be rude, so we try to humor you into toning it down a little. Compared to many Internet forums, this is likely one of the nicer responses you could expect. all the best, Kendall On Apr 3, 2012, at 8:22 PM, Kevin Jin kevin...@gmail.commailto:kevin...@gmail.com wrote: Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: Orcus, if you put yourself persistently into the face of guys who play hard, you need to learn to take a few hits and shake it off. Maybe a little retrospection on why your postings might perhaps possibly maybe perceived as somewhat self-promoting and ungracious could be helpful. The skill of presentation is at least as important in Science as being right. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kevin Jin Sent: Tuesday, April 03, 2012 3:34 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hi, Regarding the online image file storage issue, I just googled cloud storage and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will feel really sorry to learn that there are some monsters called crystallographers living on our planet. In our lab, some pre-21st century data sets were stored on tapes, newer ones on DVD discs and IDE hard drives. All these media have become or will become obsolete pretty soon. Not to mention the positive relationship of getting CRC errors with the medium's age. Admittedly, it may become quite a job to upload all image files that the whole crystallographic community generates per year. But for individual labs, I think clouding data might become something worth thinking of. Zhijie
[ccp4bb] modelling a flexible peptide
Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] modelling a flexible peptide
Hi Intekhab, With 6 copies of the complex in ASU, NCS averaging might give you a better map. Uppsala software factory has everything you need to do that: http://xray.bmc.uu.se/usf/. Check the RAVE package. Particularly, have a look at the average.csh script listed in the RAVE package page in the related freebies section. That is a script made by Gerard Kleywegt and Tom Taylor for doing N cylcles of map averaging. You can modify it for your own use. I owe my own thanks to the authors too. Zhijie From: intekhab alam Sent: Tuesday, April 03, 2012 9:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] modelling a flexible peptide Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Re: [ccp4bb] very informative - Trends in Data Fabrication
On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote: I would also consider looking into adding an RSS feed to your site so that those people interested in your articles can be informed without spamming the boards. Why continue to punish him? Adding an RSS feed means installing and configuring an RSS server. Aren't there rules against cruel and inhumane punishment? There are many free newsfeed disseminators. Twitter is the most famous. There are others, maybe better, so I'm not being a twittervangelist here. My point is this: free and easy is better than difficult. James
Re: [ccp4bb] very informative - Trends in Data Fabrication
James makes an important point. I've come to regret my joke as showing poor manners. I hesitate to add to more email that no one cares about, but I do think it is important to contribute the idea that the positive tone of this forum needs to be protected. I apologize, and suggest my comments should have been offered directly and off-line in order to be constructive and not off-putting to others who would want to contribute or ask questions. Kendall On Apr 3, 2012, at 10:01 PM, James Stroud xtald...@gmail.commailto:xtald...@gmail.com wrote: On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote: I would also consider looking into adding an RSS feed to your site so that those people interested in your articles can be informed without spamming the boards. Why continue to punish him? Adding an RSS feed means installing and configuring an RSS server. Aren't there rules against cruel and inhumane punishment? There are many free newsfeed disseminators. Twitter is the most famous. There are others, maybe better, so I'm not being a twittervangelist here. My point is this: free and easy is better than difficult. James
Re: [ccp4bb] modelling a flexible peptide
As already suggested you should use NCS averaging, but I would go the Parrot way http://www.ccp4.ac.uk/html/parrot.html or DM using a mask for your monomer of the hexamer and first ignoring the peptide. Do you have a ring or a dimer of trimers ? If however your two peptides follow NCS as well you might define a separate NCS operator for two-fold averaging of the peptide. The improved map can then be exposed to Buccaneer (http://www.ysbl.york.ac.uk/~cowtan/buccaneer/buccaneer.html) for extension of your current model and possible automatic fitting of your two peptide chains. Jürgen On Apr 3, 2012, at 9:37 PM, intekhab alam wrote: Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL .. 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 uninformative
Ok Kevin, thank you for your response. You got it, and that is good, and I am sure we'll hear from you again and that is good too. But let me explain the Orcus (however, keep in mind, I am only a single contributor and almost always do not represent the majority of CCP4BB users' opinions. So that alone should be some comfort). The title of Orcus means that you have earned yourself a nickname. Nicknames are a brutal invention, common in Western civilization, almost always addressing some personal idiosyncrasy, in general politically incorrect, but nevertheless they stick*). So let me explain: St. Orcus is the patron saint of trolls, hobgoblins and troglodytes, and the defender of off-topic posters and otherwise chastised contributors (just like the Hofkristallrat sitting in his Hofkristallamt is the defender of structures collected from real data. That is for example why I do not get invited to modelers' conferences. Everything has its price). So you are now in the unique position to evaluate the orcness of a contribution - perhaps first by making sure that your own contributions are not orcish - and exercise your right to identify any contributions you consider orcward. Experiencing a new culture can be a confusing and upsetting experience. If I may offer some comforting example relating to your blogs, and coming from a different planet myself, I once considered it a shocking calamity that protein-ligand structures are published that do not contain a ligand. I have mellowed a lot since and prevented a few cardiac events and assassination attempts by accepting the editorial indifference towards such orcward orcness. Maybe you'll get there too, and maybe you'll become a Hofkristallamtsapprentice. But let me tell you, if you are serious about correcting poor science, you've got to be ready to take a lot more flak to get there than being beatified on the BB. Oh, and by the way, no academic career. Wingardium Leviosa! Over and out, B *) Like Kim Jong-il probably means something like Gold Upright Sun. Just to demonstrate how poor those things translate into reality.. PS: Orcward ligand orcs, the Amt is watching! PPS: it is still ok to ride a trolley. From: Kevin Jin [mailto:kevin...@gmail.com] Sent: Tuesday, April 03, 2012 5:23 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Thanks of your education. I got it. By the way, what does Orcus mean here? Regards, Kevin On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote:
Re: [ccp4bb] very informative - Trends in Data Fabrication
The sad situation is that more and more scientists are becoming desperate (for funding or tenure or both) and are told 'publish or perish'; they become obsessed with impact factors, sensationalise the data in the process (be it complete fabrication or 'massaging' the results) and rush to publish to be the 'first' to do so. This was recently highlighted in the following article: http://www.nature.com/nature/journal/v483/n7391/full/483531a.html I personally think that whole review process should be open and transparent where the coordinates are available for everyone to see (after deposition and with authors' consent) along with the names and comments of the reviewers. If sloppy mistakes are made (deliberately or otherwise), they will be picked up by the wider scientific community if not the reviewers. Regards Ravi On 02/04/2012 19:00, Maria Sola i Vilarrubias wrote: Dear Phoebe, I cannot imagine myself delivering maps and coordinates (after years of work... I insist: after years of work) to a reviewer that could be, for whatever chance, my best competitor (even if I suggested to the editor not to include him/her as a reviewer... but decisions from editors are of all kind). I simply prefer not imagine this after two publications fuelled by clear, direct and strong competition. That was stressful enough, already. If I have to add to this stress the thought that my coordinates can go to the wrong hands, then I think I would just give up or, alternatively, send the work to a lower impact, fast-publishing journal and make my life easier while sending my scientific future to the low-impact bin, killing future opportunities. Competition is there. I see that data to be deposited is strictly confidential. I support the PDB to make the quality check work at the level you mention, but not a reviewer: People are nice but the world is big and competition is crazy... at least enough to make fraud or copy other's work. The latter is less difficult; by copying (simply copy and paste to my computer this nice structure that I was looking for!), there is no need to invent anything. About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. Maria On 2 April 2012 18:43, Phoebe Rice pr...@uchicago.edu mailto:pr...@uchicago.edu wrote: Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 tel:773%20834%201723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com mailto:hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 http://www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2 and Louise Jones form the IUCr office has kindly made the article open access. http://journals.iucr.org/f/issues/2012/04/00/issconts.html BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) Sent: Sunday, April 01, 2012 06:06 To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication Hofkristallrat auA*er 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 A* 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
Re: [ccp4bb] very informative - Trends in Data Fabrication
If journals would require that not only coordinates, but also structure factors would be made publicly available immediately AFTER publication, any sloppy author will be caught within days by the Rups, redo people and Bricognes. Anyone who would then still submit and publish questionable data has choosen the wrong metier and, as has been mentioned before, should probably look for a job in the financial sector. my 2 cents, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ravi Nookala Sent: Tuesday, April 03, 2012 9:31 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication The sad situation is that more and more scientists are becoming desperate (for funding or tenure or both) and are told 'publish or perish'; they become obsessed with impact factors, sensationalise the data in the process (be it complete fabrication or 'massaging' the results) and rush to publish to be the 'first' to do so. This was recently highlighted in the following article: http://www.nature.com/nature/journal/v483/n7391/full/483531a.html I personally think that whole review process should be open and transparent where the coordinates are available for everyone to see (after deposition and with authors' consent) along with the names and comments of the reviewers. If sloppy mistakes are made (deliberately or otherwise), they will be picked up by the wider scientific community if not the reviewers. Regards Ravi On 02/04/2012 19:00, Maria Sola i Vilarrubias wrote: Dear Phoebe, I cannot imagine myself delivering maps and coordinates (after years of work... I insist: after years of work) to a reviewer that could be, for whatever chance, my best competitor (even if I suggested to the editor not to include him/her as a reviewer... but decisions from editors are of all kind). I simply prefer not imagine this after two publications fuelled by clear, direct and strong competition. That was stressful enough, already. If I have to add to this stress the thought that my coordinates can go to the wrong hands, then I think I would just give up or, alternatively, send the work to a lower impact, fast-publishing journal and make my life easier while sending my scientific future to the low-impact bin, killing future opportunities. Competition is there. I see that data to be deposited is strictly confidential. I support the PDB to make the quality check work at the level you mention, but not a reviewer: People are nice but the world is big and competition is crazy... at least enough to make fraud or copy other's work. The latter is less difficult; by copying (simply copy and paste to my computer this nice structure that I was looking for!), there is no need to invent anything. About a wrongly fit compound, the reviewer can ask images about the model in a map calculated at a specific sigma and in different orientations. Maria On 2 April 2012 18:43, Phoebe Rice pr...@uchicago.edu wrote: Can we leverage this to push journals to routinely allow reviewers access coordinates and maps? Outright fraud is outrageous, but I'm actually more worried about ligands fit to marginal density and other issues of under-supervised model building. = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 tel:773%20834%201723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 2 Apr 2012 08:41:02 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com) Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication To: CCP4BB@JISCMAIL.AC.UK Robbie has restored the PDB_REDO of 3k78 It is at www.cmbi.ru.nl/pdb_redo/others/3k78.tar.bz2
[ccp4bb] Substitution to glycerol during crystallogenesis
Dear all, My question is related to a sample preparation. I’m working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby
Re: [ccp4bb] very informative - Trends in Data Fabrication
I think that to review a paper containing a structure derived from crystallographic data should indeed involve the referee having access to coordinates and to the electron density. Without this access it is not possible to judge the quality and very often even the soundness of statements in the paper. I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. Unfortunately however, there is another serious issue. After a very troubling experience with a paper I reviewed, I discussed this issue with journal editors. What they said was that they already have a hell of time to find people who agree to referee, by raising the task level (asking refs to look at coords and density) they feared that no one would agree. Actually, perhaps many have noticed the large number of 5 liner referee reports saying really not much about a full length research article. People simply don't have the time to put the effort in. So I am not sure how realistic is to ask even more, for something that at some level, is pro bono work. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
[ccp4bb] ccp4i project display
Dear colleagues, likely some of you have experienced that with 100s of ccp4i projects, the menu (limited to 25 lines?) exceeds the horizontal limitations of the computer display. Are there any suggestions how to handle this many projects? Added difficulty: I expect that were I to eliminate selected old projects from the list, I would have to return to said old project the following day. Thank you in advance, Wolfram Tempel
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hi I was thinking about the last statement in the Acta editorial - It is important to note, however, that in neither of these cases was a single frame of data collected. Not one.. This brought me back to the images.. To date there is no global acceptance that original diffractiom images must be deposited (though I personally think there should be). Many of the arguments around this issue relate to the time and space required to house such data. However (and apologies if this has already been raised and I have missed it), if our sole intent is to ascertain that there's no trouble at t'mill then deposition of a modest wedge of data and / or a 0 and 90, while not ideal, may be sufficient to provide a decent additional check and balance, particularly if such images, headers etc were automatically analysed as part of the already excellent validation tools in development. I'm sure there are a number of clever ways (that could be unadvertised or kept confidential to the pdb) that could be used to check off sufficient variables within such data such that it should (?) be very difficult to falsify images without triggering alarm bells. Of course this would probably then drive those that are truly bonkers to attempt to fabricate realistically noisy false diffraction images, however I would hope that such a scheme might make things just a little more difficult for those with fraudulent intent, particularly if no one (apart from the developers) knows precisely how and what the checking software checks! While it seems sad that it's come to this cell biologists and biochemists have had to deal with more and more sophisticated versions of the photoshopped western for years. Accordingly, most high profile journals run figures through commercial software that does a reasonable job of detection of such issues. J Sent from my iPhone On 03/04/2012, at 11:10 PM, Dyda d...@ulti.niddk.nih.gov wrote: I think that to review a paper containing a structure derived from crystallographic data should indeed involve the referee having access to coordinates and to the electron density. Without this access it is not possible to judge the quality and very often even the soundness of statements in the paper. I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. Unfortunately however, there is another serious issue. After a very troubling experience with a paper I reviewed, I discussed this issue with journal editors. What they said was that they already have a hell of time to find people who agree to referee, by raising the task level (asking refs to look at coords and density) they feared that no one would agree. Actually, perhaps many have noticed the large number of 5 liner referee reports saying really not much about a full length research article. People simply don't have the time to put the effort in. So I am not sure how realistic is to ask even more, for something that at some level, is pro bono work. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] very informative - Trends in Data Fabrication
Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them - that's how I found out about the identity of the reviewer - as it couldn't be changed by the journal. I agree though that it shouldn't happen and I hope it only happens in very few cases. Jürgen On Apr 3, 2012, at 9:10 AM, Dyda wrote: I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. .. 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
The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I have witnessed authors being hesitant to complain about possible violations and journals not always taking complaints seriously enough. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 16:45, Bosch, Juergen wrote: Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them - that's how I found out about the identity of the reviewer - as it couldn't be changed by the journal. I agree though that it shouldn't happen and I hope it only happens in very few cases. Jürgen On Apr 3, 2012, at 9:10 AM, Dyda wrote: I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. .. 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/
[ccp4bb] zinc fingre
Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals.It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only).Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well?I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks,Rajesh
Re: [ccp4bb] zinc fingre
Read a book. If you can't find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh
Re: [ccp4bb] zinc fingre
Thanks.. I will. Date: Tue, 3 Apr 2012 15:17:34 + From: debas...@uab.edu Subject: Re: [ccp4bb] zinc fingre To: CCP4BB@JISCMAIL.AC.UK Read a book. If you can’t find a book then ask the all knowing Google. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh
Re: [ccp4bb] zinc finger
There are review articles on various motifs. I think that I remember that you can also find motifs via sequence or structure classes on places like SWISSPROT/EXPASY. A quick search of PUBMED did not produce a single-source paper listing the various motifs...and there are several. Biochemistry texts will list a few motifs but will be far from exhaustive. Adding Zinc acetate to your fermentation and being careful not to use EDTA/EGTA in the prep may give you a more definitive answer. Similarly, DTT and TCEP can be good chelators of metals, so I would avoid those. Your initial comment indicated that you had no diffraction yet. Does that mean you have crystals??? If so, what percent of your produced protein is the putative zinc finger region? If it is high, and you already have crystals, then you may be searching for a problem that does not exist. -- James Kiefer, Ph.D. Structural Biology Genentech, Inc. 1 DNA Way, Mailstop 27 South San Francisco, CA 94080-4990
Re: [ccp4bb] Substitution to glycerol during crystallogenesis
Dear Toby, I don't think there is a basic problem using glycerol in crystallization. Glycerol will affect the vapour pressure (if it is not present in the well/precipitant solution) and 10 % glycerol is ~ 1.3 molar concentration. During equilibration the drops may increase in volume, decreasing the protein concentration. Thus, when using glycerol I think it is generally beneficial to start with a high protein concentration. Perhaps, you can concentrate your protein sample further. I have on several occasions observed immediate precipitation upon mixing protein solution (containing glycerol) and precipitant solution; drops then cleared up after a short period of time (and crystals eventually formed). In this case, the crystallization experiment starts in the supersaturated zone, and moves towards an undersaturated concentration, traversing the (metastable) zone where nucleation and crystallization can happen (rather than the other way around, which seems the more traditional approach with crystallization by vapour diffusion). Enrico Stura published a recent article, describing an effect of glycerol on crystallization. Vera,L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11 :2755–2762. You could replace glycerol with ethylenglycol or a small molecular weight PEG (e.g. 400), which may also have a stabilizing effect on your complex. Regards, Florian On Apr 3, 2012, at 7:49 AM, Toby Longwood wrote: Dear all, My question is related to a sample preparation. I’m working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby
Re: [ccp4bb] an ambiguous result of molecular replacement
When this happens there is usually a serious problem with the data. Have you checked the truncate output for a non-cryst translation vector? It would look as though you have something which is generating a pseudo translation along x of ~ 0.2 Look at the hklview pictures of your data and see if the 0kl 1kl 2kl etc show something funny ? Do the plots indicate twinning? In that case you may have lower symmetry.. Hard to say without seeing data but I think your problem probably pre-dates the MR search! Eleanor On Mar 30 2012, Zhiyi Wei wrote: Dear all, I got a weird solution from Phaser. The background is that, space group C2221, resolution ~4A, in complex with a peptide, and having a apo form structure as the search model. Phaser gave two rotation function peaks with Z 7. But when searching translation function peaks, Phaser gave many high Z score peaks listed below rather than a single solution. These peaks share same fraction YZ but with different X. Most of them pasted the packing validation. The when searching the second copy, each solutions have a single translation peak that showed very high Z score ( 20). I check some of these solutions in Coot, and found that the two copies of each solution has the same relative orientation and each solution shifts several angerstroms in X axis. I also tried C222 and did not get better result than C2221. Any comments or suggestion? Thanks a lot! Best, Zhiyi # (#) Frac X Frac Y Frac Z LLG Z-score Split #Groupraw/top 1 1 0.155 0.436 0.287 +219.80 11.17 0 1 272.58/272.58 2 2 0.350 0.436 0.287 +211.92 10.53 24 1 267.42/267.42 3 3 0.542 0.436 0.287 +211.31 10.48 44 1 266.05/266.05 4 5 0.579 0.436 0.287 +209.66 10.34 40 2 260.14/260.14 5 12 0.267 0.436 0.287 +209.11 10.30 14 2 256.53/256.53 6 4 0.224 0.435 0.288 +208.41 10.24 8 2 261.39/261.39 7 11 0.485 0.436 0.287 +208.28 10.23 40 2 256.95/257.13 8 7 0.191 0.435 0.287 +205.18 9.97 4 2 258.95/258.95 9 15 0.400 0.436 0.287 +201.90 9.70 30 2 254.20/254.20 10 9 0.297 0.437 0.287 +201.79 9.69 17 1 257.75/257.75 11 16 0.449 0.436 0.287 +198.77 9.45 36 1 252.80/252.80 12 17 0.129 0.437 0.287 +195.66 9.19 3 1 252.41/252.41 13 20 0.377 0.436 0.287 +194.95 9.13 27 1 246.37/246.37 14 21 0.422 0.436 0.287 +190.72 8.78 33 1 245.42/245.42 15 19 0.521 0.437 0.287 +190.22 8.74 45 1 246.46/246.46 -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] zinc fingre
Hi Rajesh, First of all you did the right thing to ask people here about our doubts. There is nothing wrong in asking questions. The board is for asking questions realted to crystallography (all aspects). Padayatti On Tue, Apr 3, 2012 at 11:07 AM, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only). Is there a way if I could check using bioinformatic tools if my protein has Zinc finger or zinc finger-like motif? If so, is it possible assume it would bind some sort of DNA and could I check that as well? I appreciate any suggestions to this BROAD question and some references would be helpful. I thought its OK to ask for help here though its nothing to do with CCP4, but eventually I want to get there. I appreciate your time. Thanks, Rajesh -- Pius S Padayatti,PhD, Phone: 216-658-4528
Re: [ccp4bb] Substitution to glycerol during crystallogenesis
We use ethylene glycol and glycerol mainly to reduce nucleation (or showering of crystals). However, we also found that these two additives may not be interchangeable, that is effects of these reagents were markedly different on crystallization behavior of a particular protein. Debasish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Tuesday, April 03, 2012 11:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Substitution to glycerol during crystallogenesis Dear Toby, I don't think there is a basic problem using glycerol in crystallization. Glycerol will affect the vapour pressure (if it is not present in the well/precipitant solution) and 10 % glycerol is ~ 1.3 molar concentration. During equilibration the drops may increase in volume, decreasing the protein concentration. Thus, when using glycerol I think it is generally beneficial to start with a high protein concentration. Perhaps, you can concentrate your protein sample further. I have on several occasions observed immediate precipitation upon mixing protein solution (containing glycerol) and precipitant solution; drops then cleared up after a short period of time (and crystals eventually formed). In this case, the crystallization experiment starts in the supersaturated zone, and moves towards an undersaturated concentration, traversing the (metastable) zone where nucleation and crystallization can happen (rather than the other way around, which seems the more traditional approach with crystallization by vapour diffusion). Enrico Stura published a recent article, describing an effect of glycerol on crystallization. Vera,L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11 :2755-2762. You could replace glycerol with ethylenglycol or a small molecular weight PEG (e.g. 400), which may also have a stabilizing effect on your complex. Regards, Florian On Apr 3, 2012, at 7:49 AM, Toby Longwood wrote: Dear all, My question is related to a sample preparation. I'm working with a complex that can be stabilized with glycerol (at least 10%) during purification. The use of detergents does not help. After purification, the sample is homogeneous (EM) and can be concentrated (3-4mg.mL-1) . I already set up many drops, changing several conditions (pH, salt...) but nothing conclusive appeared. I know that crystallogenesis in presence of glycerol works (Sousa, Acta Cryst (1995), ...) however, because of the aspect of the drops (precipitates that seem close to the nucleation phase), I suspect that the glycerol can be one of the limiting factors of the protocol. Has anybody else been already confronted to the same problem? Does someone know if there is an alternate additive to glycerol? Thanks in advance for suggestions/help With best wishes Toby
[ccp4bb] 2nd Annual CLS Mx Data Collection School
This is a final reminder that the Canadian Macromolecular Crystallography Facility (CMCF) is accepting applications for an intensive 5-day hands-on synchrotron data collection school at the Canadian Light Source (CLS) in Saskatoon. The School will take place June 5 - 9, 2012. Participants will attend a series of lectures and be actively engaged in macromolecular crystallography (Mx) data collection at CMCF beamlines. Completing the school will be an essential step to making use of the crystallography beamlines remotely and will better equip participants to effectively collect diffraction data on-site. Additionally, this year’s special topic will be an in-depth look at using COOT during structure solution and modeling with invited speaker Dr. Trevor Moraes (University of Toronto). Participants should have a basic grounding in crystallography prior to attending the course. Application deadline is April 13, 2012. Please visit the CMCF website for more information and application form, at http://cmcf.lightsource.ca/school
Re: [ccp4bb] very informative - Trends in Data Fabrication
Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more results for the reviewer to be able to submit its own paper (with new ideas) in time, or copy a structure from the figures, or ask for experiments that only the reviewer can do so he/she is included in the paper, or submit as fast as possible in another journal with an extremely short delay of acceptance (e.g. 10 days, without revision?, talking to the editorial board?) things like this. Well, it is not question of making a full list, here!. The whole problem comes from publishing first, from competition. The hope with fraud with X-ray data is that it seems to be detectable, thanks to valuable people that develop methods to detect it. But it is very difficult to demonstrate that your work, ideas or results have been copied. How do you defend from this? And how after giving to them the valuable PDB? Finally, how many crystallographers are in the world? 5000? The concept of ethics can change from one place to another and, more than this, there is the fact that the reviewer is anonymous. I try to respond to my reviewers the best I can and I really trust their criteria, sometimes a bit too much, indeed. I think they all have done a very nice job. But some of the stories from above happened to me or close to me and I feel really insecure with the idea of sending a manuscript, the X-ray data and the PDB, altogether, to a reviewer shielded by anonymity. It's too risky: with an easy molecular replacement someone can solve a difficult structure and publish it first. And then the only thing left to the bad reviewer is to change the author's list! (and for the true author what is left is to feel like an idiot). In my humble opinion, we must be strict but not kill ourselves. Trust authors as we trust reviewers. Otherwise, the whole effort might be useless. Maria Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es On 3 April 2012 16:58, Mark J van Raaij mjvanra...@cnb.csic.es wrote: The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I have witnessed authors being hesitant to complain about possible violations and journals not always taking complaints seriously enough. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 16:45, Bosch, Juergen wrote: Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them - that's how I found out about the identity of the reviewer - as it couldn't be changed by the journal. I agree though that it shouldn't happen and I hope it only happens in very few cases. Jürgen On Apr 3, 2012, at 9:10 AM, Dyda wrote: I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. .. 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
I don't agree, if we know a referee is dishonest we should try and ruin his whole career, not just prevent him from scooping us in this one case. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 19:13, Maria Sola i Vilarrubias wrote: Mark, I know some stories (which of course I'll not post here) from the Crystallography field and from other fields where reviewers profit from the fact that suddenly they have new, interpreted data which fits very well with their own results. Stories like to block a manuscript or ask for more results for the reviewer to be able to submit its own paper (with new ideas) in time, or copy a structure from the figures, or ask for experiments that only the reviewer can do so he/she is included in the paper, or submit as fast as possible in another journal with an extremely short delay of acceptance (e.g. 10 days, without revision?, talking to the editorial board?) things like this. Well, it is not question of making a full list, here!. The whole problem comes from publishing first, from competition. The hope with fraud with X-ray data is that it seems to be detectable, thanks to valuable people that develop methods to detect it. But it is very difficult to demonstrate that your work, ideas or results have been copied. How do you defend from this? And how after giving to them the valuable PDB? Finally, how many crystallographers are in the world? 5000? The concept of ethics can change from one place to another and, more than this, there is the fact that the reviewer is anonymous. I try to respond to my reviewers the best I can and I really trust their criteria, sometimes a bit too much, indeed. I think they all have done a very nice job. But some of the stories from above happened to me or close to me and I feel really insecure with the idea of sending a manuscript, the X-ray data and the PDB, altogether, to a reviewer shielded by anonymity. It's too risky: with an easy molecular replacement someone can solve a difficult structure and publish it first. And then the only thing left to the bad reviewer is to change the author's list! (and for the true author what is left is to feel like an idiot). In my humble opinion, we must be strict but not kill ourselves. Trust authors as we trust reviewers. Otherwise, the whole effort might be useless. Maria Dep. Structural Biology IBMB-CSIC Baldiri Reixach 10-12 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.s...@ibmb.csic.es On 3 April 2012 16:58, Mark J van Raaij mjvanra...@cnb.csic.es wrote: The remedy for the fact that some reviewers act unethically is not withholding coordinates and structure factors, but a more active role for the authors to denounce these possible violations and more effective investigations by the journals whose reviewers are suspected by the authors of committing these violations. I have witnessed authors being hesitant to complain about possible violations and journals not always taking complaints seriously enough. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Apr 2012, at 16:45, Bosch, Juergen wrote: Hi Fred, I'll go public on this one. This happened to me. I will not reveal who reviewed my paper and which paper it was only that your naive assumption might not always be correct. I have learned my lesson and exclude people with overlapping interests (even though they actually might be the best critical reviewers for your work). Unfortunately you don't really have control if the journal still decides to pick those excluded reviewers. As a suggestion to people out there, make sure to not encrypt your comments as pdf and PW protect them - that's how I found out about the identity of the reviewer - as it couldn't be changed by the journal. I agree though that it shouldn't happen and I hope it only happens in very few cases. Jürgen On Apr 3, 2012, at 9:10 AM, Dyda wrote: I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health
