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 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 > <[email protected]> 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 Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
