Re: [ccp4bb] delete subject
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0053374 On Fri, Mar 29, 2013 at 4:09 AM, Eric Bennett er...@pobox.com wrote: Scott, I'm not sure I understand your last paragraph. Once researchers have had their data pass peer review (which I interpret as meaning a journal has accepted it), how often do you think it happens that it does not immediately get published? Just depositing data in the PDB, or posting it on a public web site, is not meet[ing] the veracity of peer review. There is something to be said for giving credit to the first people who have subjected their data to peer review and had the data pass that step, otherwise people will be tempted to just post data of dubious quality to stake a public claim before the quality of the data has been independently checked. In a case where this initial public non-peer-reviewed posting is of unacceptable data quality, that would dilute credit granted to another person who later obtained good data. An unfortunate number of problematic structures still sneak through peer review. Relaxing quality review standards that must be passed before a scientist gets to claim credit for a discovery is a step backwards IMO. Cheers, Eric On Mar 28, 2013, at 5:06 PM, Scott Pegan wrote: Hey everyone, Both Mark and Fred make some good points. I totally agree with Nat (beat me to the send button). Although in an ideal world with all the advancements in crowd sourcing and electronic media, one might think that posting data on a bulletin board might be considered marking one's turf and protect the scientist place in that pathway towards discoveries. Regrettably, the current reality doesn't' support this case. As structural biologists, we are still in the mode of first to publish gets the bulk of the glory and potentially future funding on the topic. For instance, when I was in graduate school, the lab I was in had KcsA crystals at the same time as a couple of competing groups. Several groups including the one I belong to had initial diffraction data. One group was able to solve KcsA, the first K channel trans-membrane protein structure, first. That group was led by Roderick Mackinnon, now a Noble Laureate partly because of this work. Now imagine if one of Mackinnon's student would have put up the web their initial diffraction data and another group would have used it to assist in their interpretation of their own data and either solved the structure before Mackinnon, or at least published it prior. Even if they acknowledged Mackinnion for the assistance of his data (as they should), Mackinnion and the other scientists in his lab would likely not have received the broad acclaim that they received and justly deserved. Also, ask Rosalind Franklin how data sharing worked out for her. Times haven't changed that much since ~10 years ago. Actually, as many have mentioned, things have potentially gotten worse. Worse in the respect that the scientific impact of structure is increasingly largely tide to the biochemical/biological studies that accompany the structure. In other words, the discoveries based on the insights the structure provides. Understandably, this increasing emphasis on follow up experiments to get into high impact journals in many cases increases the time between solving the structure and publishing it. During this gap, the group who solved the structure first is vulnerable to being scoped. Once scoped unless the interpretation of the structure and the conclusion of the follow up experiments are largely and justifiably divergent from the initial publications, there is usually a significant difficulty getting the article published in a top tier journal. Many might argue that they deposited it first, but I haven't seen anyone win that argument either. Because follow up articles will cite the publication describing the structure, not the PDB entry. Naturally, many could and should argue that this isn't they way it should be. We could rapidly move science ahead in many cases if research groups were entirely transparent and made available their discovers as soon as they could meet the veracity of peer-review. However, this is not the current reality or model we operate in. So, until this changes, one might be cautious about tipping your competition off whether they be another structural biology group looking to publish their already solved structure, or biology group that could use insights gathered by your structure information for a publication that might limit your own ability to publish. Fortunately, for Tom his structure sounds like it is only important to a pretty specific scientific question that many folks might not be working on exactly. Scott -- ** Toufic El Arnaout Trinity Biomedical Science Institute (TCD) 152-160 Pearse Street, Dublin 2
Re: [ccp4bb] delete subject
There's a second side to that. Reviewers who can't get enough data and request even more when you submit a decent paper with 18 pages of supplement for example. Jürgen On Mar 29, 2013, at 7:32 AM, Toufic El Arnaout wrote: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0053374 On Fri, Mar 29, 2013 at 4:09 AM, Eric Bennett er...@pobox.commailto:er...@pobox.com wrote: Scott, I'm not sure I understand your last paragraph. Once researchers have had their data pass peer review (which I interpret as meaning a journal has accepted it), how often do you think it happens that it does not immediately get published? Just depositing data in the PDB, or posting it on a public web site, is not meet[ing] the veracity of peer review. There is something to be said for giving credit to the first people who have subjected their data to peer review and had the data pass that step, otherwise people will be tempted to just post data of dubious quality to stake a public claim before the quality of the data has been independently checked. In a case where this initial public non-peer-reviewed posting is of unacceptable data quality, that would dilute credit granted to another person who later obtained good data. An unfortunate number of problematic structures still sneak through peer review. Relaxing quality review standards that must be passed before a scientist gets to claim credit for a discovery is a step backwards IMO. Cheers, Eric On Mar 28, 2013, at 5:06 PM, Scott Pegan wrote: Hey everyone, Both Mark and Fred make some good points. I totally agree with Nat (beat me to the send button). Although in an ideal world with all the advancements in crowd sourcing and electronic media, one might think that posting data on a bulletin board might be considered marking one's turf and protect the scientist place in that pathway towards discoveries. Regrettably, the current reality doesn't' support this case. As structural biologists, we are still in the mode of first to publish gets the bulk of the glory and potentially future funding on the topic. For instance, when I was in graduate school, the lab I was in had KcsA crystals at the same time as a couple of competing groups. Several groups including the one I belong to had initial diffraction data. One group was able to solve KcsA, the first K channel trans-membrane protein structure, first. That group was led by Roderick Mackinnon, now a Noble Laureate partly because of this work. Now imagine if one of Mackinnon's student would have put up the web their initial diffraction data and another group would have used it to assist in their interpretation of their own data and either solved the structure before Mackinnon, or at least published it prior. Even if they acknowledged Mackinnion for the assistance of his data (as they should), Mackinnion and the other scientists in his lab would likely not have received the broad acclaim that they received and justly deserved. Also, ask Rosalind Franklin how data sharing worked out for her. Times haven't changed that much since ~10 years ago. Actually, as many have mentioned, things have potentially gotten worse. Worse in the respect that the scientific impact of structure is increasingly largely tide to the biochemical/biological studies that accompany the structure. In other words, the discoveries based on the insights the structure provides. Understandably, this increasing emphasis on follow up experiments to get into high impact journals in many cases increases the time between solving the structure and publishing it. During this gap, the group who solved the structure first is vulnerable to being scoped. Once scoped unless the interpretation of the structure and the conclusion of the follow up experiments are largely and justifiably divergent from the initial publications, there is usually a significant difficulty getting the article published in a top tier journal. Many might argue that they deposited it first, but I haven't seen anyone win that argument either. Because follow up articles will cite the publication describing the structure, not the PDB entry. Naturally, many could and should argue that this isn't they way it should be. We could rapidly move science ahead in many cases if research groups were entirely transparent and made available their discovers as soon as they could meet the veracity of peer-review. However, this is not the current reality or model we operate in. So, until this changes, one might be cautious about tipping your competition off whether they be another structural biology group looking to publish their already solved structure, or biology group that could use insights gathered by your structure information for a publication that might limit your own ability to publish. Fortunately, for Tom his structure sounds like it is only important to a pretty specific scientific question that many folks might
Re: [ccp4bb] delete subject
Hello, I stayed away from this thread until now - the major reason being that I was fitting snugly under my quilt. However I feel compelled to react now: placing your data in a public repository (thereby proving that you did the work) also means that a colleague, friend or whatever can and will publish your work for you. Once your work has been published you cannot publish it again, you did the work and the colleague, friend or whatever has in fact appropriated your work. In the world of dreams I was living in until a few moments ago (it was night time), this is perhaps the way we should act. In the real world we live in, even your colleague upstairs will publish your work if he / she has a chance to do it because by doing so he / she will improve his / her career while ensuring that yours doesn't take off. Fred. On 28/03/13 01:34, mjvdwo...@netscape.net wrote: Earlier today, I thought this and did not write it. It is a slightly different theme on your suggestion: I hear there are now (but have not seen examplesof) journals (web sites) where you do exactly what Tom did: you put your data there, which proves that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because making data public is the reason why you got the data in the first place. And nobody can claim to have done the work, because everybody knows that someone else was first - the web site is proof. Theresults are not peer-reviewed of course (even though, in the case of CCP4, things are inherently peer-reviewed to some extent, that is what he asked us to do). And I hear that there are now journals that will accept references to such web sites. Freely sharing unpublished data on a public forum might well be the future, even if in our corner of science this is not yet commonplace. The pivotal point to Tom is that he can learn from the suggestions that have been made. I hope he will. I actually hope that he will follow up on the suggestions (privately maybe). Unlike some, I do not feel that it was bad to find a big file in my inbox, this is what move to is for. I think my reaction was ouch, he did not want to do what he just did and it cannot be undone. But maybethis is not true. There is definitely value in sharing preliminary data, especially for junior people. To have such a function as part of CCP4 might be a very good suggestion, but I agree with you that perhaps it should not land in its full glory in everyone's mailbox. Mark -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] delete subject
Dear all, Let me start by apologizing for finally making this email longer than I intended - I did not have the time to make it shorter. I must say I am humbled by the amount of positive energy and constructive thinking that Bill has. That must explain also how he manages to keep up a fantastic resource for the community, what is a largely thankless task with little academic reward, but still so helpful. His response did get me thinking, as his opinions often do. In principle, in an era of information sharing, why don't we indeed solve structures with the collective brain of world crystallographers? We could share data, and educate people, and also get better structures at the end of the day. As indeed many people are in a small institution somewhat off the beaten path - I work in a cancer research institute after all and I am the weirdo here - and as indeed I see my knowledge getting obsoleted in a steady pace, this idea sounds great! However, its a bit like 'true' socialism - a grant idea, that we may find it will not work too well in practice, at least not under the constraints of human nature. I will keep advocating the greatness of ccp4bb. Its a fantastic resource, which is made truly amazing by the many questions that are being asked, and keep educating everybody. But, at the same time, I will keep advocating the usefulness of the typical constructions we have in science, whereupon people work in teams. These teams are there to share experience and help each other with overlapping expertise. Why such a basic question (and others in the past) need to come out of the 'team'? Is there no competence within the team to address it, or is there no correct communication? In either case, should we as scientists encourage such teams with low-level competence? May I remind you that Tom is in Lueven/Belgium, a large and outstanding University, with at least two very competent (and friendly) crystallographers in campus. Does the fact he has to post the ccp4bb with a basic question testify for a complete failure of his supervisor to either help him or get other people on site to help him? Should such supervisors be left to guide students? I have nothing against sharing data. I am the fool that submits data at the same time as I submit my paper, a practice that is followed by surprisingly a few people, as most people wait a few weeks until the paper is accepted to submit their structure (some data mining shows that 1/3 of the PDB entries associated with papers even in journals like Acta D are only deposited to the PDB at least a week after the paper submission date!.. no think what this % is in other journals). And the mild consequence of this is that somebody picks the structure up, panics to be scooped, submits his/her story, and scoops you while your paper is being rejected for reasons that are not connected to the structure (I am not implying foul play here, but suggesting a consequence of basic openness). Are we finally, at the end, with this open and sharing spirit, encouraging people to think that crystallography is too trivial? It has once been said in this bb, that 'solving a structure is trivial in the same way that climbing mountain Everest is trivial: it has been down before, its being done now, and it will be done again, by many well-trained and determined people'. Many people have read and trained for this task. If you do not read a couple of books and train before attempting the climb, and you send an email asking the everestbb 'does anybody know how to open this oxygen valve?' you are asking for trouble though … and the people that let you attempt the climb without that knowledge, are also in the wrong. The end result of this open and sharing spirit, which downgrades the importance of competence in major methodologies like X-ray crystallography, was summarized recently is some text I recently got by email from Brussels: ... advanced methods for X-ray crystallography and Electron Microscopy is a very narrow field that will limit the employability of the graduates There are the wise words of the referees of a joined grant (with 10 other people from Europe) advocating to educate students to get an in-depth PhD-level training in crystallography and in EM. Maybe that explains my grumpiness. Or, as the crystallographer previously known as DVD mailed me in private welcome to the club of grumpy old men. Maybe I am just being grumpy. Or I am justifiably worried. A. PS For the record I admire Tom's spirit and courage - he is the kind of guy I would hire for a PhD (not that he will ever want to work with me any more). I am less impressed by the team and his supervisors, as it stands, and without knowing all the details of what might be behind this. On Mar 28, 2013, at 1:04, William G. Scott wrote: Dear Tom et al: Although arriving too late to participate in the snark-fest, it occurred to me that maybe this is almost exactly how we
Re: [ccp4bb] delete subject
I fully agree that questions should keep coming. In addition it might be worth pointing out that CCP4 (and others) organise great crystallographic schools which are ideal for this sort of problem. Most of the schools ask you to bring your own data (!) and you can sit down with developers and experts who will help at length with practical and theoretical questions. Roberto From my iPhone On 28 Mar 2013, at 04:47, Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:frank.vonde...@sgc.ox.ac.uk wrote: mistake? I beg to differ, violently: a student had an honest question and did exactly what the ccp4bb exists for: posted his question there. Moreover, when asking he showed he had thought about it, and provided complete background -- that's what we all want, right? * I disagree with Tassos: the email was not rude, on not one of the counts he listed. (I concede he may have had a bad day... I had one on Monday :-) * I disagree (slightly) with Tim: the teasing was not malicious. * And I share Mark's dream... Students: please don't stop asking your questions here!!! phx. On 27/03/2013 22:47, VAN RAAIJ , MARK JOHAN wrote: Dear Tom, don't feel too bad about it - everyone can make a mistake. Some of the replies give crystallographic tips that may be useful to other beginning and not-so-beginning crystallographers. Although I agree the attachments to the first mail would perhaps better be deleted from the records. Greetings, Mark Quoting Tom Van den Bergh mailto:tom.vandenbe...@student.kuleuven.betom.vandenbe...@student.kuleuven.bemailto:tom.vandenbe...@student.kuleuven.be: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
Re: [ccp4bb] delete subject
All, I personally would feel awkward at depositing my hard fought data before the associated paper is accepted. However, a recent paper from our institution (I was not part of that study) originated from precisely the model that has been suggested in this thread: http://www.nejm.org/doi/full/10.1056/NEJMoa1107643 Given the success of various 'open source' endeavours in recent years, I'm slowly coming around to a view that with smart procedures in place, an 'open data' approach could indeed help to solve structures that would otherwise remain unsolved, unpublished and unused. Klaus On 28 Mar 2013, at 08:46, Anastassis Perrakis wrote: Dear all, Let me start by apologizing for finally making this email longer than I intended - I did not have the time to make it shorter. I must say I am humbled by the amount of positive energy and constructive thinking that Bill has. That must explain also how he manages to keep up a fantastic resource for the community, what is a largely thankless task with little academic reward, but still so helpful. His response did get me thinking, as his opinions often do. In principle, in an era of information sharing, why don't we indeed solve structures with the collective brain of world crystallographers? We could share data, and educate people, and also get better structures at the end of the day. As indeed many people are in a small institution somewhat off the beaten path - I work in a cancer research institute after all and I am the weirdo here - and as indeed I see my knowledge getting obsoleted in a steady pace, this idea sounds great! However, its a bit like 'true' socialism - a grant idea, that we may find it will not work too well in practice, at least not under the constraints of human nature. I will keep advocating the greatness of ccp4bb. Its a fantastic resource, which is made truly amazing by the many questions that are being asked, and keep educating everybody. But, at the same time, I will keep advocating the usefulness of the typical constructions we have in science, whereupon people work in teams. These teams are there to share experience and help each other with overlapping expertise. Why such a basic question (and others in the past) need to come out of the 'team'? Is there no competence within the team to address it, or is there no correct communication? In either case, should we as scientists encourage such teams with low-level competence? May I remind you that Tom is in Lueven/Belgium, a large and outstanding University, with at least two very competent (and friendly) crystallographers in campus. Does the fact he has to post the ccp4bb with a basic question testify for a complete failure of his supervisor to either help him or get other people on site to help him? Should such supervisors be left to guide students? I have nothing against sharing data. I am the fool that submits data at the same time as I submit my paper, a practice that is followed by surprisingly a few people, as most people wait a few weeks until the paper is accepted to submit their structure (some data mining shows that 1/3 of the PDB entries associated with papers even in journals like Acta D are only deposited to the PDB at least a week after the paper submission date!.. no think what this % is in other journals). And the mild consequence of this is that somebody picks the structure up, panics to be scooped, submits his/her story, and scoops you while your paper is being rejected for reasons that are not connected to the structure (I am not implying foul play here, but suggesting a consequence of basic openness). Are we finally, at the end, with this open and sharing spirit, encouraging people to think that crystallography is too trivial? It has once been said in this bb, that 'solving a structure is trivial in the same way that climbing mountain Everest is trivial: it has been down before, its being done now, and it will be done again, by many well-trained and determined people'. Many people have read and trained for this task. If you do not read a couple of books and train before attempting the climb, and you send an email asking the everestbb 'does anybody know how to open this oxygen valve?' you are asking for trouble though … and the people that let you attempt the climb without that knowledge, are also in the wrong. The end result of this open and sharing spirit, which downgrades the importance of competence in major methodologies like X-ray crystallography, was summarized recently is some text I recently got by email from Brussels: ... advanced methods for X-ray crystallography and Electron Microscopy is a very narrow field that will limit the employability of the graduates There are the wise words of the referees of a joined grant (with 10 other people from Europe) advocating to educate students to get an in-depth PhD-level
Re: [ccp4bb] delete subject
Dear ccp4 members, Thanks for all the help. I am now rebuilding my structure now based on all your advice (which was my intention all along). I am glad to see there are still scientists who dont only care about making and publishing their own data, but are always ready to help less experienced students with their experiments. Its also my personal believe that this approach can be a great help in scientific research as some people have already said and i am happy to see that i am not the only one who has this opinion. I think this is a good time to end the discussion. Kind regards, Tom Van: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] namens Steiner, Roberto [roberto.stei...@kcl.ac.uk] Verzonden: donderdag 28 maart 2013 10:08 To: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] delete subject I fully agree that questions should keep coming. In addition it might be worth pointing out that CCP4 (and others) organise great crystallographic schools which are ideal for this sort of problem. Most of the schools ask you to bring your own data (!) and you can sit down with developers and experts who will help at length with practical and theoretical questions. Roberto From my iPhone On 28 Mar 2013, at 04:47, Frank von Delft frank.vonde...@sgc.ox.ac.ukmailto:frank.vonde...@sgc.ox.ac.uk wrote: mistake? I beg to differ, violently: a student had an honest question and did exactly what the ccp4bb exists for: posted his question there. Moreover, when asking he showed he had thought about it, and provided complete background -- that's what we all want, right? * I disagree with Tassos: the email was not rude, on not one of the counts he listed. (I concede he may have had a bad day... I had one on Monday :-) * I disagree (slightly) with Tim: the teasing was not malicious. * And I share Mark's dream... Students: please don't stop asking your questions here!!! phx. On 27/03/2013 22:47, VAN RAAIJ , MARK JOHAN wrote: Dear Tom, don't feel too bad about it - everyone can make a mistake. Some of the replies give crystallographic tips that may be useful to other beginning and not-so-beginning crystallographers. Although I agree the attachments to the first mail would perhaps better be deleted from the records. Greetings, Mark Quoting Tom Van den Bergh mailto:tom.vandenbe...@student.kuleuven.betom.vandenbe...@student.kuleuven.bemailto:tom.vandenbe...@student.kuleuven.be: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
Re: [ccp4bb] delete subject
I am agree with Tassos. For me it is a quite stranger to think about hide the data to nobody see until the paper be published. In my opinion, a lot of data become obsolete (or even forgotten) because that one more experiment you need to publish a great paper (it some times takes years...). For me science has become an aggressive capitalist market where the paper is its currency, mainly in life sciences. But, due to the human nature, this sharing-data ideal world is far to become true and we need to try play this game to keep alive and try to change it for better. On the other hand, in my opinion, crystallography research are near of this ideal world in comparison with other areas (pharmacy, molecular and functional biology, ...) some proofs are the ccp4bb, workshops where you can get help to process your data, etc. So, please, do not stop to posting your questions and commentaries, they are very important to students like me. Cheers, *Andrey Fabricio Ziem Nascimento* PhD Student in Biochemistry/UNICAMP Biophysics and Structural Biology Group Brazilian Biosciences National Laboratory (LNBio) – CNPEM 2013/3/28 Klaus Fütterer k.futte...@bham.ac.uk All, I personally would feel awkward at depositing my hard fought data before the associated paper is accepted. However, a recent paper from our institution (I was not part of that study) originated from precisely the model that has been suggested in this thread: http://www.nejm.org/doi/full/10.1056/NEJMoa1107643 Given the success of various 'open source' endeavours in recent years, I'm slowly coming around to a view that with smart procedures in place, an 'open data' approach could indeed help to solve structures that would otherwise remain unsolved, unpublished and unused. Klaus On 28 Mar 2013, at 08:46, Anastassis Perrakis wrote: Dear all, Let me start by apologizing for finally making this email longer than I intended - I did not have the time to make it shorter. I must say I am humbled by the amount of positive energy and constructive thinking that Bill has. That must explain also how he manages to keep up a fantastic resource for the community, what is a largely thankless task with little academic reward, but still so helpful. His response did get me thinking, as his opinions often do. In principle, in an era of information sharing, why don't we indeed solve structures with the collective brain of world crystallographers? We could share data, and educate people, and also get better structures at the end of the day. As indeed many people are in a small institution somewhat off the beaten path - I work in a cancer research institute after all and I am the weirdo here - and as indeed I see my knowledge getting obsoleted in a steady pace, this idea sounds great! However, its a bit like 'true' socialism - a grant idea, that we may find it will not work too well in practice, at least not under the constraints of human nature. I will keep advocating the greatness of ccp4bb. Its a fantastic resource, which is made truly amazing by the many questions that are being asked, and keep educating everybody. But, at the same time, I will keep advocating the usefulness of the typical constructions we have in science, whereupon people work in teams. These teams are there to share experience and help each other with overlapping expertise. Why such a basic question (and others in the past) need to come out of the 'team'? Is there no competence within the team to address it, or is there no correct communication? In either case, should we as scientists encourage such teams with low-level competence? May I remind you that Tom is in Lueven/Belgium, a large and outstanding University, with at least two very competent (and friendly) crystallographers in campus. Does the fact he has to post the ccp4bb with a basic question testify for a complete failure of his supervisor to either help him or get other people on site to help him? Should such supervisors be left to guide students? I have nothing against sharing data. I am the fool that submits data at the same time as I submit my paper, a practice that is followed by surprisingly a few people, as most people wait a few weeks until the paper is accepted to submit their structure (some data mining shows that 1/3 of the PDB entries associated with papers even in journals like Acta D are only deposited to the PDB at least a week after the paper submission date!.. no think what this % is in other journals). And the mild consequence of this is that somebody picks the structure up, panics to be scooped, submits his/her story, and scoops you while your paper is being rejected for reasons that are not connected to the structure (I am not implying foul play here, but suggesting a consequence of basic openness). Are we finally, at the end, with this open and sharing spirit, encouraging people to think that crystallography is too trivial? It has once been said in
Re: [ccp4bb] delete subject
Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.eduwrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] delete subject
By coincidence this just landed in my Inbox: http://membercentral.aaas.org/multimedia/webinars/how-recruit-citizen-scientists-discovery So maybe after all Tom is way ahead of the rest of us in his structure-solving strategy - though I agree with others that his tactics need to be honed somewhat! Cheers -- Ian On 28 March 2013 14:43, Raji Edayathumangalam r...@brandeis.edu wrote: Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.eduwrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] delete subject
That last paragraph is great: Adam is the author of the book Surviving Your Stupid, Stupid Decision to Go to Grad School (Broadway Books, 2010) -- Bill On Mar 28, 2013, at 9:09 AM, Ian Tickle ianj...@gmail.com wrote: By coincidence this just landed in my Inbox: http://membercentral.aaas.org/multimedia/webinars/how-recruit-citizen-scientists-discovery So maybe after all Tom is way ahead of the rest of us in his structure-solving strategy - though I agree with others that his tactics need to be honed somewhat! Cheers -- Ian On 28 March 2013 14:43, Raji Edayathumangalam r...@brandeis.edu wrote: Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.edu wrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] delete subject
Hi all, This has indeed been a highly informative and educational thread from many view points, and it highlights the opportunities and challenges that scientists face today by having access to tools like the CCP4BB . I just wanted to touch on something that was briefly alluded to at the early stages of this saga, and it has to do with data confidentiality and to some degree understanding the various policies that your institution adheres to. I raise this issue for the benefit of students like Tom, who may not have been exposed to the various implications that this brings. In my view, understanding your institution's (or your lab's) data sharing policies is extremely important prior to taking such action. In some institutions and specially in industry, sharing data without prior approval would be grounds for dismissal or even worst (lawsuits come to mind). So as we all learn from Tom's experience in this thread, I think we should all use good judgment when seeking help and deciding when to share data to an open forum. My 2 cents. Francisco From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji Edayathumangalam [r...@brandeis.edu] Sent: Thursday, March 28, 2013 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] delete subject Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.edumailto:epozh...@umaryland.edu wrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] delete subject
No. :-) When you are a reviewer for structural papers in journals (I do this work sometimes), and when you see an article that has (in this example) Tom's structure in it, but he and/or his mentor is not an author, then you call the editor and tell them you may have a problem. I realize that the case may not be closed with that statement because the manuscript could indeed be totally legitimate and genuine, but it would be a signal in my mind to watch for. A friend could not just run with the data and publish. A competing group could take advantage and get ahead in their project inexpensively (provided that the posted data are what you think they are). But that is sort of the point of publishing result (I must remember to leave my idealism at home tomorrow). Our old approach is to keep a lid on all your data until the paper is published. Although it is hard to imagine, there could be a mechanism by which you make all your data public, immediately when you get it and this public record shows who owns it. The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries. The disadvantage to the method is that you will sometimes post experiments that are just completely wrong (you did not measure what you said you measured) and this might make you look dumb (not really, this happens all the time; a favorite saying is 'we all make mistakes, we just make sure they don't leave the room'). And furthermore, you would finally have a journal of unpublishable data, where all the experiments that we should not have done for one reason or another reside and can act as a warning what not to do in the future. It is possible that I am socialist. In the US that is not a good thing, but I don't worry about it. Furthermore, teaching/learning is a concern. More and more places no longer have the resources or the patience to teach or learn crystallography. I once heard a friend say something along these lines: people who did not learn crystallography are now teaching the next generation. As proof for that, he explained that experiments are done at synchrotrons that clearly show that not the beamline is broken, but the operator does not understand the concepts and therefore the data collected are not useful. In my world I see crystallography as a tool, and no longer as a goal all by itself (it was a goal when I was a graduate student). I am frequently concerned that protein crystallography will go the way of small molecule crystallography: a few places provide this service and as an experimentalist you don't much worry about how they do it. Of course, until it becomes super-easy to produce high-quality protein and crystals, this won't happen. Mark With apologies to Tom, I don't have a stop-button, Raji is right about that. -Original Message- From: vellieux frederic.velli...@ibs.fr To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Mar 28, 2013 1:54 am Subject: Re: [ccp4bb] delete subject Hello, I stayed away from this thread until now - the major reason being that I was fitting snugly under my quilt. However I feel compelled to react now: placing your data in a public repository (thereby proving that you did the work) also means that a colleague, friend or whatever can and will publish your work for you. Once your work has been published you cannot publish it again, you did the work and the colleague, friend or whatever has in fact appropriated your work. In the world of dreams I was living in until a few moments ago (it was night time), this is perhaps the way we should act. In the real world we live in, even your colleague upstairs will publish your work if he / she has a chance to do it because by doing so he / she will improve his / her career while ensuring that yours doesn't take off. Fred. On 28/03/13 01:34, mjvdwo...@netscape.net wrote: Earlier today, I thought this and didnot write it. It is a slightly different theme on your suggestion: I hear there are now (but have not seen examples of) journals (web sites) where you do exactlywhat Tom did: you put your data there, which proves that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because makingdata public is the reason why you got the datain the first place. And nobody can claim to havedone the work, because everybody knows thatsomeone else was first - the web site
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On Thu, Mar 28, 2013 at 11:28 AM, mjvdwo...@netscape.net wrote: Although it is hard to imagine, there could be a mechanism by which you make all your data public, immediately when you get it and this public record shows who owns it. http://deposit.rcsb.org (or international equivalent) The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries. The disadvantage to the method is that you will sometimes post experiments that are just completely wrong There is a further problem: since as Frank pointed out, structures are increasingly less valuable without accompanying non-crystallographic experiments, there is a risk of other groups taking advantage of the availability of data and performing the experiments that *you* had hoped to do. Or, similarly, a group who already has compelling biochemical data lacking a structural explanation would immediately have everything they needed to publish. Either way, you would be deprived of what might have been a thorough and genuinely novel publication. Since most employment and funding decisions in the academic world are made on the basis of original and high-profile research and not simply number of structures deposited in the PDB, this puts the crystallographer at a distinct disadvantage. This isn't purely hypothetical - a grad school classmate who worked on genome sequences complained about the same problem (in her case, the problem was bioinformatics groups analyzing the data - freely available on the NCBI site, as mandated by the funding agencies - before the sequencing was even complete). Of course the same argument has been used in the past against immediate release of PDB entries upon publication - and the community (quite appropriately, IMHO) rejected it as nonsense. I actually like the idea of releasing data ASAP without waiting to publish, but it has a lot of practical difficulties. -Nat
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On 28/03/2013 18:50, Nat Echols wrote: http://deposit.rcsb.org (or international equivalent) The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries. The disadvantage to the method is that you will sometimes post experiments that are just completely wrong There is a further problem: since as Frank pointed out, structures are increasingly less valuable without accompanying non-crystallographic experiments, there is a risk of other groups taking advantage of the availability of data and performing the experiments that *you* had hoped to do. Or, similarly, a group who already has compelling biochemical data lacking a structural explanation would immediately have everything they needed to publish. Either way, you would be deprived of what might have been a thorough and genuinely novel publication. Since most employment and funding decisions in the academic world are made on the basis of original and high-profile research and not simply number of structures deposited in the PDB, this puts the crystallographer at a distinct disadvantage. If someone has already done the other experiments, the absolutely best outcome for society is for the two to get together and write the paper as co-authors -- instead of precious funding money being wasted with a second fool doing exactly the same experiments in a silly rat-race. Lovely, so that leaves us with the trivial question of making people acknowledge other people's data when they publish. I suppose we can ask Watson for pointers (not Crick, he's not around anymore).
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, this happens all the time; a favorite saying is 'we all make mistakes, we just make sure they don't leave the room'). And furthermore, you would finally have a journal of unpublishable data, where all the experiments that we should not have done for one reason or another reside and can act as a warning what not to do in the future. It is possible that I am socialist. In the US that is not a good thing, but I don't worry about it. Furthermore, teaching/learning is a concern. More and more places no longer have the resources or the patience to teach or learn crystallography. I once heard a friend say something along these lines: people who did not learn crystallography are now teaching the next generation. As proof for that, he explained that experiments are done at synchrotrons that clearly show that not the beamline is broken, but the operator does not understand the concepts and therefore the data collected are not useful. In my world I see crystallography as a tool, and no longer as a goal all by itself (it was a goal when I was a graduate student). I am frequently concerned that protein crystallography will go the way of small molecule crystallography: a few places provide this service and as an experimentalist you don't much worry about how they do it. Of course, until it becomes super-easy to produce high-quality protein and crystals, this won't happen. Mark With apologies to Tom, I don't have a stop-button, Raji is right about that. -Original Message- From: vellieux frederic.velli...@ibs.fr To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Mar 28, 2013 1:54 am Subject: Re: [ccp4bb] delete subject Hello, I stayed away from this thread until now - the major reason being that I was fitting snugly under my quilt. However I feel compelled to react now: placing your data in a public repository (thereby proving that you did the work) also means that a colleague, friend or whatever can and will publish your work for you. Once your work has been published you cannot publish it again, you did the work and the colleague, friend or whatever has in fact appropriated your work. In the world of dreams I was living in until a few moments ago (it was night time), this is perhaps the way we should act. In the real world we live in, even your colleague upstairs will publish your work if he / she has a chance to do it because by doing so he / she will improve his / her career while ensuring that yours doesn't take off. Fred. On 28/03/13 01:34, mjvdwo...@netscape.net wrote: Earlier today, I thought this and did not write it. It is a slightly different theme on your suggestion: I hear there are now (but have not seen examples of) journals (web sites) where you do exactly what Tom did: you put your data there, which proves that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because making data public is the reason why you got the data in the first place. And nobody can claim to have done the work, because everybody knows that someone else was first - the web site is proof. The results are not peer-reviewed of course (even though, in the case of CCP4, things are inherently peer-reviewed to some extent, that is what he asked us to do). And I hear that there are now journals that will accept references to such web sites. Freely sharing unpublished data on a public forum might well be the future, even if in our corner of science this is not yet commonplace. The pivotal point to Tom is that he can learn from the suggestions that have been made. I hope he will. I actually hope that he will follow up on the suggestions (privately maybe). Unlike some, I do not feel that it was bad to find a big file in my inbox, this is what move to is for. I think my reaction was ouch, he did not want to do what he just did and it cannot be undone. But maybe this is not true. There is definitely value in sharing preliminary data, especially for junior people. To have such a function as part of CCP4 might be a very good suggestion, but I agree with you that perhaps it should not land in its full glory in everyone's mailbox. Mark -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494 -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] delete subject
structure sounds like it is only important to a pretty specific scientific question that many folks might not be working on exactly. Scott On Thu, Mar 28, 2013 at 12:28 PM, mjvdwo...@netscape.net wrote: No. :-) When you are a reviewer for structural papers in journals (I do this work sometimes), and when you see an article that has (in this example) Tom's structure in it, but he and/or his mentor is not an author, then you call the editor and tell them you may have a problem. I realize that the case may not be closed with that statement because the manuscript could indeed be totally legitimate and genuine, but it would be a signal in my mind to watch for. A friend could not just run with the data and publish. A competing group could take advantage and get ahead in their project inexpensively (provided that the posted data are what you think they are). But that is sort of the point of publishing result (I must remember to leave my idealism at home tomorrow). Our old approach is to keep a lid on all your data until the paper is published. Although it is hard to imagine, there could be a mechanism by which you make all your data public, immediately when you get it and this public record shows who owns it. The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries. The disadvantage to the method is that you will sometimes post experiments that are just completely wrong (you did not measure what you said you measured) and this might make you look dumb (not really, this happens all the time; a favorite saying is 'we all make mistakes, we just make sure they don't leave the room'). And furthermore, you would finally have a journal of unpublishable data, where all the experiments that we should not have done for one reason or another reside and can act as a warning what not to do in the future. It is possible that I am socialist. In the US that is not a good thing, but I don't worry about it. Furthermore, teaching/learning is a concern. More and more places no longer have the resources or the patience to teach or learn crystallography. I once heard a friend say something along these lines: people who did not learn crystallography are now teaching the next generation. As proof for that, he explained that experiments are done at synchrotrons that clearly show that not the beamline is broken, but the operator does not understand the concepts and therefore the data collected are not useful. In my world I see crystallography as a tool, and no longer as a goal all by itself (it was a goal when I was a graduate student). I am frequently concerned that protein crystallography will go the way of small molecule crystallography: a few places provide this service and as an experimentalist you don't much worry about how they do it. Of course, until it becomes super-easy to produce high-quality protein and crystals, this won't happen. Mark With apologies to Tom, I don't have a stop-button, Raji is right about that. -Original Message- From: vellieux frederic.velli...@ibs.fr To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Mar 28, 2013 1:54 am Subject: Re: [ccp4bb] delete subject Hello, I stayed away from this thread until now - the major reason being that I was fitting snugly under my quilt. However I feel compelled to react now: placing your data in a public repository (thereby proving that you did the work) also means that a colleague, friend or whatever can and will publish your work for you. Once your work has been published you cannot publish it again, you did the work and the colleague, friend or whatever has in fact appropriated your work. In the world of dreams I was living in until a few moments ago (it was night time), this is perhaps the way we should act. In the real world we live in, even your colleague upstairs will publish your work if he / she has a chance to do it because by doing so he / she will improve his / her career while ensuring that yours doesn't take off. Fred. On 28/03/13 01:34, mjvdwo...@netscape.net wrote: Earlier today, I thought this and did not write it. It is a slightly different theme on your suggestion: I hear there are now (but have not seen examples of) journals (web sites) where you do exactly what Tom did: you put your data there, which proves that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because making data public is the reason why you got the data in the first place. And nobody can claim to have done the work, because everybody knows that someone else was first - the web site is proof. The results are not peer-reviewed of course (even though, in the case of CCP4, things are inherently peer-reviewed to some extent, that is what he asked us to do). And I hear
Re: [ccp4bb] delete subject
Scott, I'm not sure I understand your last paragraph. Once researchers have had their data pass peer review (which I interpret as meaning a journal has accepted it), how often do you think it happens that it does not immediately get published? Just depositing data in the PDB, or posting it on a public web site, is not meet[ing] the veracity of peer review. There is something to be said for giving credit to the first people who have subjected their data to peer review and had the data pass that step, otherwise people will be tempted to just post data of dubious quality to stake a public claim before the quality of the data has been independently checked. In a case where this initial public non-peer-reviewed posting is of unacceptable data quality, that would dilute credit granted to another person who later obtained good data. An unfortunate number of problematic structures still sneak through peer review. Relaxing quality review standards that must be passed before a scientist gets to claim credit for a discovery is a step backwards IMO. Cheers, Eric On Mar 28, 2013, at 5:06 PM, Scott Pegan wrote: Hey everyone, Both Mark and Fred make some good points. I totally agree with Nat (beat me to the send button). Although in an ideal world with all the advancements in crowd sourcing and electronic media, one might think that posting data on a bulletin board might be considered marking one's turf and protect the scientist place in that pathway towards discoveries. Regrettably, the current reality doesn't' support this case. As structural biologists, we are still in the mode of first to publish gets the bulk of the glory and potentially future funding on the topic. For instance, when I was in graduate school, the lab I was in had KcsA crystals at the same time as a couple of competing groups. Several groups including the one I belong to had initial diffraction data. One group was able to solve KcsA, the first K channel trans-membrane protein structure, first. That group was led by Roderick Mackinnon, now a Noble Laureate partly because of this work. Now imagine if one of Mackinnon's student would have put up the web their initial diffraction data and another group would have used it to assist in their interpretation of their own data and either solved the structure before Mackinnon, or at least published it prior. Even if they acknowledged Mackinnion for the assistance of his data (as they should), Mackinnion and the other scientists in his lab would likely not have received the broad acclaim that they received and justly deserved. Also, ask Rosalind Franklin how data sharing worked out for her. Times haven't changed that much since ~10 years ago. Actually, as many have mentioned, things have potentially gotten worse. Worse in the respect that the scientific impact of structure is increasingly largely tide to the biochemical/biological studies that accompany the structure. In other words, the discoveries based on the insights the structure provides. Understandably, this increasing emphasis on follow up experiments to get into high impact journals in many cases increases the time between solving the structure and publishing it. During this gap, the group who solved the structure first is vulnerable to being scoped. Once scoped unless the interpretation of the structure and the conclusion of the follow up experiments are largely and justifiably divergent from the initial publications, there is usually a significant difficulty getting the article published in a top tier journal. Many might argue that they deposited it first, but I haven't seen anyone win that argument either. Because follow up articles will cite the publication describing the structure, not the PDB entry. Naturally, many could and should argue that this isn't they way it should be. We could rapidly move science ahead in many cases if research groups were entirely transparent and made available their discovers as soon as they could meet the veracity of peer-review. However, this is not the current reality or model we operate in. So, until this changes, one might be cautious about tipping your competition off whether they be another structural biology group looking to publish their already solved structure, or biology group that could use insights gathered by your structure information for a publication that might limit your own ability to publish. Fortunately, for Tom his structure sounds like it is only important to a pretty specific scientific question that many folks might not be working on exactly. Scott
[ccp4bb] delete subject
Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
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Dear Tom, don't feel too bad about it - everyone can make a mistake. Some of the replies give crystallographic tips that may be useful to other beginning and not-so-beginning crystallographers. Although I agree the attachments to the first mail would perhaps better be deleted from the records. Greetings, Mark Quoting Tom Van den Bergh tom.vandenbe...@student.kuleuven.be: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
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Dear Tom et al: Although arriving too late to participate in the snark-fest, it occurred to me that maybe this is almost exactly how we should solve structures and educate graduate students (or others). Instead of attachments, the relevant files could be shared via dropbox. Those of generous spirit could help solve, refine, correct, critique or otherwise improve structures before formal peer review. (If everyone knows the source of the data, it is far less likely to be ripped off, not more.) It might cut down on the number of mistakes (or worse) that appear in the PDB and journals, new mentorships and collaborations might be established, in exceptional cases co-authorship, or more generally, an acknowledgement could be offered. For students like mine who are comparatively isolated in a small institution somewhat off the beaten path, it would be a real asset and advantage to them not to have to rely only upon my limited abilities and increasingly obsolete knowledge. We should all be able to learn from one anther without fear of reproach. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Mar 27, 2013, at 3:36 PM, Tom Van den Bergh tom.vandenbe...@student.kuleuven.be wrote: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
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Dear Tom, I'm sure the files can be easily removed from the server, if that is what you wish / want to happen. A quick email to the administrators at c...@ccp4.ac.ukmailto:c...@ccp4.ac.uk should do the trick. Reading around all the all leg-pulling / other comments aside - from your post you've got actually got a really good number of useful suggestions and comments that should help you along the path to solve and refine your structure yourself. Best of luck with your data. With regards, Tony. Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings,
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Earlier today, I thought this and did not write it. It is a slightly different theme on your suggestion: I hear there are now (but have not seen examples of) journals (web sites) where you do exactly what Tom did: you put your data there, which proves that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because making data public is the reason why you got the data in the first place. And nobody can claim to have done the work, because everybody knows that someone else was first - the web site is proof. The results are not peer-reviewed of course (even though, in the case of CCP4, things are inherently peer-reviewed to some extent, that is what he asked us to do). And I hear that there are now journals that will accept references to such web sites. Freely sharing unpublished data on a public forum might well be the future, even if in our corner of science this is not yet commonplace. The pivotal point to Tom is that he can learn from the suggestions that have been made. I hope he will. I actually hope that he will follow up on the suggestions (privately maybe). Unlike some, I do not feel that it was bad to find a big file in my inbox, this is what move to is for. I think my reaction was ouch, he did not want to do what he just did and it cannot be undone. But maybe this is not true. There is definitely value in sharing preliminary data, especially for junior people. To have such a function as part of CCP4 might be a very good suggestion, but I agree with you that perhaps it should not land in its full glory in everyone's mailbox. Mark -Original Message- From: William G. Scott wgsc...@ucsc.edu To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Wed, Mar 27, 2013 6:09 pm Subject: Re: [ccp4bb] delete subject Dear Tom et al: Although arriving too late to participate in the snark-fest, it occurred to me that maybe this is almost exactly how we should solve structures and educate graduate students (or others). Instead of attachments, the relevant files could be shared via dropbox. Those of generous spirit could help solve, refine, correct, critique or otherwise improve structures before formal peer review. (If everyone knows the source of the data, it is far less likely to be ripped off, not more.) It might cut down on the number of mistakes (or worse) that appear in the PDB and journals, new mentorships and collaborations might be established, in exceptional cases co-authorship, or more generally, an acknowledgement could be offered. For students like mine who are comparatively isolated in a small institution somewhat off the beaten path, it would be a real asset and advantage to them not to have to rely only upon my limited abilities and increasingly obsolete knowledge. We should all be able to learn from one anther without fear of reproach. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Mar 27, 2013, at 3:36 PM, Tom Van den Bergh tom.vandenbe...@student.kuleuven.be wrote: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
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mistake? I beg to differ, violently: a student had an honest question and did exactly what the ccp4bb exists for: posted his question there. Moreover, when asking he showed he had thought about it, and provided complete background -- that's what we all want, right? * I disagree with Tassos: the email was not rude, on not one of the counts he listed. (I concede he may have had a bad day... I had one on Monday :-) * I disagree (slightly) with Tim: the teasing was not malicious. * And I share Mark's dream... Students: please don't stop asking your questions here!!! phx. On 27/03/2013 22:47, VAN RAAIJ , MARK JOHAN wrote: Dear Tom, don't feel too bad about it - everyone can make a mistake. Some of the replies give crystallographic tips that may be useful to other beginning and not-so-beginning crystallographers. Although I agree the attachments to the first mail would perhaps better be deleted from the records. Greetings, Mark Quoting Tom Van den Bergh tom.vandenbe...@student.kuleuven.be: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
