Re: [ccp4bb] PDB passes 100,000 structure milestone
So, a bit like Fold-it but with actual data? :-D Dr David C Briggs PhD http://about.me/david_briggs On 16 May 2014 06:19, Pavel Afonine pafon...@gmail.com wrote: What about structures that are obviously wrong based on inspection of the density, but no one has bothered to challenge yet? The TWILIGHT database helps some, if that counts, but it doesn't catch everything. How about this utopia.. Imagine PDB has two versions: one is the original data and model deposited as is, and never ever changed no matter what. Another version is a curated one obtained in a quest-like way: anyone can take an original entry, improve it and deposit (into the curated version) with his/her name tag on it. And of course anyone can take and update that improved entry and re-deposit it again with his/her name tag, etc. If desired one could keep track of all the revisions, like in svn or so. Sounds like a sport with an element of public service that might yield crowd-perfected models -:) ! Pavel
[ccp4bb] AW: [ccp4bb] PDB passes 100,000 structure milestone
I am also in favor of two versions of the pdb: one archive version with all models as originally deposited including retracted and corrected versions, which are useful for educational purposes, and a curated version with only models that meet a minimum of validation criteria, including credible ligand density. Whether crowd-perfected or original submissions that pass the validation criteria does not matter to me. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Pavel Afonine Gesendet: Freitag, 16. Mai 2014 07:19 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] PDB passes 100,000 structure milestone What about structures that are obviously wrong based on inspection of the density, but no one has bothered to challenge yet? The TWILIGHT database helps some, if that counts, but it doesn't catch everything. How about this utopia.. Imagine PDB has two versions: one is the original data and model deposited as is, and never ever changed no matter what. Another version is a curated one obtained in a quest-like way: anyone can take an original entry, improve it and deposit (into the curated version) with his/her name tag on it. And of course anyone can take and update that improved entry and re-deposit it again with his/her name tag, etc. If desired one could keep track of all the revisions, like in svn or so. Sounds like a sport with an element of public service that might yield crowd-perfected models -:) ! Pavel
Re: [ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone
2014-05-15 9:53 GMT-03:00 Colin Nave colin.n...@diamond.ac.uk: Of course exponential growth can’t go on forever – the hidden point behind my question. A nice example from another biological database is Swissprot. It had an exponential-like growth until 2009, and now it's somewhat linear: http://web.expasy.org/docs/relnotes/relstat.html I didn't looked much into that, but I guess it's because the annotators (Swissprot is human curated) simply can't keep up with everything coming from all genome projects. The other Uniprot database, automatically annotated Trembl, is still growing in a exponential-like fashion: http://www.ebi.ac.uk/uniprot/TrEMBLstats
Re: [ccp4bb] PDB passes 100,000 structure milestone
16-May-2014 Dear Patrick, Proteopedia [http://proteopedia.org] uses exactly the same style for referencing published material. Proteopedia allows for the easy insertion of Pubmed and DOI references by only requesting from the user to enter the Pubmed or DOI ids. We have extended the same software used in Wikipedia for the internal Proteopedia engine to, based on this reference ID, retrieve, format and insert the correctly formatted reference at the bottom of the page. For example, type refPMID 18673581/ref or refdoi 10.1093/nar/gku213/ref in the wikitext box and save the page. If you type the reference in this manner, the properly formatted reference will be created automatically at the bottom of the page (or wherever you place the necessary wikitext references/). See http://proteopedia.org/w/Help:Editing#Citing_Literature_References and Proteopedia pages for actual examples. best regards, Jaime Joel On 15May, 2014, at 13:48, Patrick Shaw Stewart patr...@douglas.co.ukmailto:patr...@douglas.co.uk wrote: I may be missing something here, but I don't think you have to rebut anything. You simply report that someone else has rebutted it. Along the lines of Many scientists regard this published structure as unreliable since a misconduct investigation by the University of Alabama at Birmingham has concluded that it was, more likely than not, faked [1] [1] http://www.nature.com/news/2009/091222/full/462970a.html On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.commailto:nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.ukmailto:patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat -- patr...@douglas.co.ukmailto:patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.ukhttp://www.douglas.co.uk/ Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Joel and Jaime - very nice to hear from you. I hope everything is going well in Rehovot. Proteopedia is the natural place to put comments etc. However it might look more natural if there was more info there in the first place - ie if people gave more explanation about the significance of their and other people's structures, then comments like the one I suggested could be added. I don't know how you get people to become more active at Proteopedia. Maybe your students could post occasional messages to eg the CCP4bb with comments that show how useful Proteopedia can be. Tricky though! Best wishes, Patrick On 16 May 2014 14:35, Joel Sussman joel.suss...@weizmann.ac.il wrote: 16-May-2014 Dear Patrick, *Proteopedia* [*http://proteopedia.org] http://proteopedia.org%5D* uses exactly the same style for referencing published material. *Proteopedia* allows for the easy insertion of Pubmed and DOI references by only requesting from the user to enter the Pubmed or DOI ids. We have extended the same software used in Wikipedia for the internal *Proteopedia* engine to, based on this reference ID, retrieve, format and insert the correctly formatted reference at the bottom of the page. For example, *type refPMID 18673581/ref or refdoi 10.1093/nar/gku213/ref* in the wikitext box and save the page. If you type the reference in this manner, the properly formatted reference will be created automatically at the bottom of the page (or wherever you place the necessary wikitext references/). See *http://proteopedia.org/w/Help:Editing#Citing_Literature_References http://proteopedia.org/w/Help:Editing#Citing_Literature_References* and Proteopedia pages for actual examples. best regards, Jaime Joel On 15May, 2014, at 13:48, Patrick Shaw Stewart patr...@douglas.co.uk wrote: I may be missing something here, but I don't think you have to rebut anything. You simply report that someone else has rebutted it. Along the lines of Many scientists regard this published structure as unreliable since a misconduct investigation by the University of Alabama at Birmingham has concluded that it was, more likely than not, faked [1] [1] http://www.nature.com/news/2009/091222/full/462970a.html On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] PDB passes 100,000 structure milestone
From James's figure, assuming perfect lossless compression, the information content of the PDB is 20GB or about 2X10**11 bits The information content of the universe has been estimated to be 2**305 bits or 10**92 bits (this might or might not be changing). The PDB is said to be growing exponentially. If we know the coefficients, we can work out when the PDB takes over the present universe. This would be time to retire. Can anyone do this? Thanks Colin From: James Holton [mailto:jmhol...@lbl.gov] Sent: 14 May 2014 16:19 To: ccp4bb Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone I think 249 GB is uncompressed. My local copy of the PDB only takes up 20 GB, or one Blu-Ray. I can remember a time when the whole of the PDB fit onto a single CD-ROM. The PDB booth at the ACA meeting would hand them out for free! That was impressive to me because CD-R disks were really expensive (to an undergraduate like me anyway), and I had to figure out how to do multi-session writes so I could back up my whole hard drive 2 or 3 times before I filled one up. And, of course, I had to take out my hard drive and go over to that really wealthy lab that had a CD writer to do that. Each write took about an hour, and didn't always work. Ah, those were the days. But yes, it is impressive how so much effort by so many people over so many years can be compressed into such a tiny space. Is it not a strange fate that we should suffer so much fear and doubt for so small a thing? -James Holton MAD Scientist On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote: I reckon it's two box sets of 25 discs each - am I calculating that wrong? Maybe room for a 'making of' feature ;) From: Jon Agirre jon.agi...@york.ac.ukmailto:jon.agi...@york.ac.uk To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 14:28 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 249GB? That's a whole lot of DVDs! On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.com wrote: Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) of storage' was obviously written by someone from a pre i-tunes generation http://www.wwpdb.org/news/news_2014.html#13-May-2014 ;) -M. From: mesters mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.de To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 13:41 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de/ http://www.iobcr.orghttp://www.iobcr.org/ [cid:image001.png@01CF701D.0C132EE0] [cid:image002.jpg@01CF701D.0C132EE0] -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hello, I also agree that the right order of things would be the journals taking action (i.e. retracting and commenting on why), then informing the pdb which structures are associated with a retraction - for the simple reason that very likely many readers take conclusions in made-up publications for granted even if they do not directly work with the fraudent models that are deposited, i.e. the publications do even more harm to the research community than the associated fraud structures. Because the case of Murthy came up I would like to mention that the US Office of Research Integrity (http://ori.hhs.gov/) is still reviewing the case (at least they told me so in Nov 2013), and I hope their final conclusion will result in more comprehensive action against ALL structures in question, not just 2hr0 (by the University of Birmingham and the journals). So while it may be frustratingly slow, there is actually an institution that does take care of such issues (at least in the US). Bärbel Quoting Mark Wilson mwilso...@unl.edu: Hi Nat, I agree that journals should be doing the heavy lifting here, for the reasons that you note. I also want to be clear that I believe the PDB is a crowning achievement of transparency and open access in the sciences, which is one reason that I am so concerned about this issue. I am in no way trying to impugn the hard and superb work that they have done over many decades. I still contend, however, that having models whose integrity is highly suspect lurking in the PDB with no indications of problems beyond a dodgy validation report is a non-optimal outcome. As for the meaning of integrity, I'm using this word in place of others that might be considered more legally actionable. A franker conversation would likely more clearly draw the line that we're wrestling with here. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 12:41 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, May 14, 2014 at 10:26 AM, Mark Wilson mwilso...@unl.edu wrote: Getting to Eric's point about an impasse, if the PDB will not claim the authority to safeguard the integrity of their holdings (as per their quoted statement in Bernhard's message below), then who can? I think this may in part boil down to a semantic dispute over the meaning of integrity. I interpreted it to mean integrity (and public availability) of the data as deposited by the authors, which by itself is quite a lot of work. Safeguarding the integrity of the peer-review process is supposed to be the job of the journals, some of which - unlike the PDB - are making a tidy profit from our efforts. Since they justify this profit based on the value they supposedly add as gatekeepers, I don't think it's unreasonable for us to expect them to do their job, rather than leave it to the PDB annotators, who surely have enough to deal with. I do share some of the concern about 2hr0, but I am curious where the line should be drawn. This is an extraordinary case where the researcher's institution requested retraction, but I think everyone who's been in this field for a while has a list of dodgy structures that they think should be retracted - not always with justification. -Nat -- Bärbel Blaum, Ph.D. Interfakultäres Institut für Biochemie (IFIB) Hoppe-Seyler-Strasse 4 D-72076 Tübingen Germany +49 70 71 29 73 375
Re: [ccp4bb] PDB passes 100,000 structure milestone
A logarithmic plot of cumulative entries to the PDB is approximately linear and shows a growth rate of about 15% per year. That means it doubles in size about every 5 years at current growth rate. Roger Rowlett On May 15, 2014 4:23 AM, Colin Nave colin.n...@diamond.ac.uk wrote: From James's figure, assuming perfect lossless compression, the information content of the PDB is 20GB or about 2X10**11 bits The information content of the universe has been estimated to be 2**305 bits or 10**92 bits (this might or might not be changing). The PDB is said to be growing exponentially. If we know the coefficients, we can work out when the PDB takes over the present universe. This would be time to retire. Can anyone do this? Thanks Colin From: James Holton [mailto:jmhol...@lbl.gov] Sent: 14 May 2014 16:19 To: ccp4bb Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone I think 249 GB is uncompressed. My local copy of the PDB only takes up 20 GB, or one Blu-Ray. I can remember a time when the whole of the PDB fit onto a single CD-ROM. The PDB booth at the ACA meeting would hand them out for free! That was impressive to me because CD-R disks were really expensive (to an undergraduate like me anyway), and I had to figure out how to do multi-session writes so I could back up my whole hard drive 2 or 3 times before I filled one up. And, of course, I had to take out my hard drive and go over to that really wealthy lab that had a CD writer to do that. Each write took about an hour, and didn't always work. Ah, those were the days. But yes, it is impressive how so much effort by so many people over so many years can be compressed into such a tiny space. Is it not a strange fate that we should suffer so much fear and doubt for so small a thing? -James Holton MAD Scientist On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote: I reckon it's two box sets of 25 discs each - am I calculating that wrong? Maybe room for a 'making of' feature ;) From: Jon Agirre jon.agi...@york.ac.ukmailto:jon.agi...@york.ac.uk To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 14:28 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 249GB? That's a whole lot of DVDs! On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.com mailto:martainn_oshioma...@btinternet.com wrote: Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) of storage' was obviously written by someone from a pre i-tunes generation http://www.wwpdb.org/news/news_2014.html#13-May-2014 ;) -M. From: mesters mest...@biochem.uni-luebeck.demailto: mest...@biochem.uni-luebeck.de To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 13:41 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de/ http://www.iobcr.orghttp://www.iobcr.org/ [cid:image001.png@01CF701D.0C132EE0] [cid:image002.jpg@01CF701D.0C132EE0] -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response
Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it. They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] FW: [ccp4bb] PDB passes 100,000 structure milestone
Roger Thanks for this reply. Sometime in the next millennium I guess. I did get replies from several well wishers implying that it would be a good idea if I retired as soon as possible. More usefully, Marjolein Thunnissen reminded me of the article http://www.uic.edu/labs/caz/downloads/Abad-Zapatero-PDB-rates-Acta-Cryst2012t.pdf. This gives a comprehensive analysis of growth rates. Of course exponential growth can’t go on forever – the hidden point behind my question. Regards Colin From: Roger Rowlett [mailto:rrowl...@colgate.edu] Sent: 15 May 2014 12:36 To: ccp4bb Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone A logarithmic plot of cumulative entries to the PDB is approximately linear and shows a growth rate of about 15% per year. That means it doubles in size about every 5 years at current growth rate. Roger Rowlett On May 15, 2014 4:23 AM, Colin Nave colin.n...@diamond.ac.ukmailto:colin.n...@diamond.ac.uk wrote: From James's figure, assuming perfect lossless compression, the information content of the PDB is 20GB or about 2X10**11 bits The information content of the universe has been estimated to be 2**305 bits or 10**92 bits (this might or might not be changing). The PDB is said to be growing exponentially. If we know the coefficients, we can work out when the PDB takes over the present universe. This would be time to retire. Can anyone do this? Thanks Colin From: James Holton [mailto:jmhol...@lbl.govmailto:jmhol...@lbl.gov] Sent: 14 May 2014 16:19 To: ccp4bb Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone I think 249 GB is uncompressed. My local copy of the PDB only takes up 20 GB, or one Blu-Ray. I can remember a time when the whole of the PDB fit onto a single CD-ROM. The PDB booth at the ACA meeting would hand them out for free! That was impressive to me because CD-R disks were really expensive (to an undergraduate like me anyway), and I had to figure out how to do multi-session writes so I could back up my whole hard drive 2 or 3 times before I filled one up. And, of course, I had to take out my hard drive and go over to that really wealthy lab that had a CD writer to do that. Each write took about an hour, and didn't always work. Ah, those were the days. But yes, it is impressive how so much effort by so many people over so many years can be compressed into such a tiny space. Is it not a strange fate that we should suffer so much fear and doubt for so small a thing? -James Holton MAD Scientist On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote: I reckon it's two box sets of 25 discs each - am I calculating that wrong? Maybe room for a 'making of' feature ;) From: Jon Agirre jon.agi...@york.ac.ukmailto:jon.agi...@york.ac.ukmailto:jon.agi...@york.ac.ukmailto:jon.agi...@york.ac.uk To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 14:28 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 249GB? That's a whole lot of DVDs! On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.com wrote: Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) of storage' was obviously written by someone from a pre i-tunes generation http://www.wwpdb.org/news/news_2014.html#13-May-2014 ;) -M. From: mesters mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.demailto:mest...@biochem.uni-luebeck.de To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 13:41 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065tel:%2B49-451-5004065 (secretariate 5004061) fax: +49-451-5004068tel:%2B49-451-5004068 http://www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de/ http://www.iobcr.orghttp://www.iobcr.org/ [cid:image001.png@01CF701D.0C132EE0] [cid:image002.jpg@01CF701D.0C132EE0] -- If you can look
Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, isn't the ccp4bb a very good example that spam may not be such an issue for a discussion platform on structures in the PDB? There is a great variety of opinions, some to agree with, some to disagree, but all of them interesting and contributing, and I hardly remember a message I would classify as spam. And it all works without restraints. Best, Tim On 05/15/2014 03:21 PM, Zachary Wood wrote: I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTdMOTUxlJ7aRr7hoRAinqAJ9tAzMX6DSeFO7hiyEEqFhCPV7IxQCgg0Ay Ya6HwJD/ugPU1dwGHNAJfkQ= =JABI -END PGP SIGNATURE-
Re: [ccp4bb] PDB passes 100,000 structure milestone
Adding to Tim’s comment, I would not expect a tremendous amount of spurious comments about a single PDB out of 100,000 unless there was a problem. Especially if the Pubmed Commons model was applied, and only depositors could comment. I would assume this would be very beneficial, given that we are conscientious professionals. Could actually be a great forum for authors to go a little deeper into specific approaches or problems that they had with a structure. Not all interesting details make it to the pub. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 9:39 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, isn't the ccp4bb a very good example that spam may not be such an issue for a discussion platform on structures in the PDB? There is a great variety of opinions, some to agree with, some to disagree, but all of them interesting and contributing, and I hardly remember a message I would classify as spam. And it all works without restraints. Best, Tim On 05/15/2014 03:21 PM, Zachary Wood wrote: I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG
Re: [ccp4bb] PDB passes 100,000 structure milestone
15-May-2014 Dear Martyn Proteopedia's (http://proteopedia.org) goal goes well beyond just education - it is aimed at Structural Biology and non Structural Biology Community and it would be pleased to be a forum for discussion of structures that are questionable. There are now over 2,600 registered users, who are contributing to Proteopedia, in over 50 different countries. Proteopedia has a special area for discussions related to each structure. To access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's upper border. Everyone can read the comments there, and it will open a fully editable page for every registered user to add their comments on the structure and their full name will be listed below their comments. If you would like to contribute to this, we’d be pleased to welcome your input. Best regards, Jaime Prilusky Joel Sussman On 15May, 2014, at 7:29, MARTYN SYMMONS martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edumailto:merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edumailto:z...@bmb.uga.edu mailto:z...@bmb.uga.edumailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
Dear Zachary I once suggested this sort of discussion forum to a PDB PI as a possible service that could be a ' validation fight-club ' - which suggestion was not well received ;) But as you say it is down to setting the correct professional tone. One thing that would allow a visual discussion would be the possibility to share molecular representations - similar to the way Proteopedia uses Jmol scripting to drive the graphics from the webpages. In this way commentators could share viewpoint and representations to make their points. This would make it most useful to the wider biological community. all the best Martyn From: Zachary Wood z...@bmb.uga.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 15 May 2014, 14:47 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Adding to Tim’s comment, I would not expect a tremendous amount of spurious comments about a single PDB out of 100,000 unless there was a problem. Especially if the Pubmed Commons model was applied, and only depositors could comment. I would assume this would be very beneficial, given that we are conscientious professionals. Could actually be a great forum for authors to go a little deeper into specific approaches or problems that they had with a structure. Not all interesting details make it to the pub. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 9:39 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, isn't the ccp4bb a very good example that spam may not be such an issue for a discussion platform on structures in the PDB? There is a great variety of opinions, some to agree with, some to disagree, but all of them interesting and contributing, and I hardly remember a message I would classify as spam. And it all works without restraints. Best, Tim On 05/15/2014 03:21 PM, Zachary Wood wrote: I agree with Martyn, Pubmed Commons could be a great model. I believe you have to be a published author to obtain an account. It might cut down on some of the spam/noise if the PDB adopted such a model for depositors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 7:29 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it. They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z
Re: [ccp4bb] PDB passes 100,000 structure milestone
As one of the responsible people for the pdbwiki project I feel I should comment on this one. We went out of business simply for lack of resources, it was difficult to keep things up-to-date and specially it was very difficult to combat spam. So in the end we decided to shut down the project. In any case we always thought of the project more as a proof-of-concept than anything else. We wanted to show that a community-driven feedback and annotation system is needed for the PDB. I personally think that if such a system were to be set up by the PDB, it would be a great service for anyone (including the PDB themselves since some of that feedback could eventually go back to the main database). In my opinion the system should stay as open as possible, allowing anyone to comment. The community can self-moderate it and do continuous reviewing. This kind of system is already used in many places and works extremely well. See for instance stackoverflow.com for computing-related questions, or even biostars.org for bioinformatics-related ones. Upvoting/downvoting together with user-scoring mechanisms produce stunningly good results. Just my 2 cents Jose On 15/05/14 13:29, MARTYN SYMMONS wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn *From:* Ethan A Merritt merr...@u.washington.edu *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, 14 May 2014, 19:22 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu mailto:z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
Maybe a prominent link in the summary page of e.g. PDBe 2a01 would help. So far, you need to go there and expand Links - pdb_redo - links - Proteopedia to get to the corresponding warning. http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html# http://www.cmbi.ru.nl/pdb_redo/a0/2a01/index.html http://proteopedia.org/wiki/index.php/2a01 'More information about this (or any) entry may be available in Proteopedia' Best, BR Ceterum censeo structurae Murthius delendati erunt. (Marcus Tullius Raaijmakers) From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joel Sussman Sent: Donnerstag, 15. Mai 2014 16:01 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 15-May-2014 Dear Martyn Proteopedia's (http://proteopedia.org) goal goes well beyond just education - it is aimed at Structural Biology and non Structural Biology Community and it would be pleased to be a forum for discussion of structures that are questionable. There are now over 2,600 registered users, who are contributing to Proteopedia, in over 50 different countries. Proteopedia has a special area for discussions related to each structure. To access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's upper border. Everyone can read the comments there, and it will open a fully editable page for every registered user to add their comments on the structure and their full name will be listed below their comments. If you would like to contribute to this, we'd be pleased to welcome your input. Best regards, Jaime Prilusky Joel Sussman On 15May, 2014, at 7:29, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn _ From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
Dear Jaime and Joel, Perhaps an easier solution would be to get the PDB to put an obvious link on each entry directing the user to the Proteopedia site for discussion and additional details. I would personally prefer a comments/discussion section on the PDB page, but as long as one is easily accessible I would be happy. By the way, you guys are doing a great job, and I will now go officially register on your site so that I can be user 2,601 ;-) Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 10:00 AM, Joel Sussman joel.suss...@weizmann.ac.il wrote: 15-May-2014 Dear Martyn Proteopedia's (http://proteopedia.org) goal goes well beyond just education - it is aimed at Structural Biology and non Structural Biology Community and it would be pleased to be a forum for discussion of structures that are questionable. There are now over 2,600 registered users, who are contributing to Proteopedia, in over 50 different countries. Proteopedia has a special area for discussions related to each structure. To access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's upper border. Everyone can read the comments there, and it will open a fully editable page for every registered user to add their comments on the structure and their full name will be listed below their comments. If you would like to contribute to this, we’d be pleased to welcome your input. Best regards, Jaime Prilusky Joel Sussman On 15May, 2014, at 7:29, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn From: Ethan A Merritt merr...@u.washington.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it.They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. It's immediately obvious when something is controversial. Here's the first para of the entry on statins, which are currently being debated in the UK: *Statins* (or *HMG-CoA reductase inhibitors*) are a class of drugshttp://en.wikipedia.org/wiki/Drugs used to lower cholesterol http://en.wikipedia.org/wiki/Cholesterol levels by inhibiting http://en.wikipedia.org/wiki/Enzyme_inhibitor the enzyme HMG-CoA reductase http://en.wikipedia.org/wiki/HMG-CoA_reductase, which plays a central role in the production of cholesterol in the liverhttp://en.wikipedia.org/wiki/Liver, which produces about 70 percent of total cholesterol in the body. Increased cholesterol levels have been associated with cardiovascular diseasehttp://en.wikipedia.org/wiki/Cardiovascular_disease (CVD).[1] http://en.wikipedia.org/wiki/Statins#cite_note-1 Statins have been found to prevent http://en.wikipedia.org/wiki/Preventive_medicine cardiovascular disease in those who are at high risk. The evidence is strong that statins are effective for treating CVD in the early stages of a disease (secondary prevention http://en.wikipedia.org/wiki/Secondary_prevention). The evidence is weaker that statins are effective for those with elevated cholesterol levels but without CVD (primary preventionhttp://en.wikipedia.org/wiki/Primary_prevention ).[2] http://en.wikipedia.org/wiki/Statins#cite_note-NICEquick-2[3]http://en.wikipedia.org/wiki/Statins#cite_note-Cochrane13-3 [4] http://en.wikipedia.org/wiki/Statins#cite_note-Cochrane11-4 Side effects of statins include muscle pain, increased risk of diabeteshttp://en.wikipedia.org/wiki/Diabetes and abnormalities in liver enzyme testshttp://en.wikipedia.org/wiki/Liver_function_tests .[5] http://en.wikipedia.org/wiki/Statins#cite_note-Naci2013-5 Additionally, they have rare but severe adverse effects, particularly muscle damage.[6]http://en.wikipedia.org/wiki/Statins#cite_note-Jacob2011-6 Some doctors believe that statins are over-prescribed. (Could Proteopedia adopt a style that is closer to that?) On 15 May 2014 15:35, Bernhard Rupp hofkristall...@gmail.com wrote: Maybe a prominent link in the summary page of e.g. PDBe 2a01 would help. So far, you need to go there and expand Links - pdb_redo - links - Proteopedia to get to the corresponding warning. http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html# http://www.cmbi.ru.nl/pdb_redo/a0/2a01/index.html http://proteopedia.org/wiki/index.php/2a01 ‘More information about this (or any) entry may be available in Proteopedia’ Best, BR Ceterum censeo structurae Murthius delendati erunt. (Marcus Tullius Raaijmakers) *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Joel Sussman *Sent:* Donnerstag, 15. Mai 2014 16:01 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone 15-May-2014 Dear Martyn Proteopedia's (*http://proteopedia.org http://proteopedia.org*) goal goes well beyond just education - it is aimed at Structural Biology and non Structural Biology Community and it would be pleased to be a forum for discussion of structures that are questionable. There are now over 2,600 registered users, who are contributing to Proteopedia, in over 50 different countries. *Proteopedia has a special area for discussions related to each structure*. *To access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 http://proteopedia.org/w/2x24* and *click on the 'discussion' tab* on the page's upper border. Everyone can read the comments there, and it will open a fully editable page for every registered user to add *their comments on the structure and their full name will be listed below their comments.* If you would like to contribute to this, we’d be pleased to welcome your input. Best regards, Jaime Prilusky Joel Sussman On 15May, 2014, at 7:29, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: I agree some forum for community annotation and commenting would be a good thing for users of structural data. There was an attempt to do that with the pdbwiki project which was a community resource for the bioinformatics community. Unfortunately pdbwiki has now folded (see http://pdbwiki.org/) They are now directing people to Proteopedia. However Proteopedia has a more educative focus I think - rather than capturing technical questions and input. Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum for discussing the literature, is currently under testing. Perhaps this is the sort of thing that could work for structural data? cheers Martyn -- *From:* Ethan A Merritt merr...@u.washington.edu *To:* CCP4BB
Re: [ccp4bb] PDB passes 100,000 structure milestone
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat
Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree with Nat. If you think a structure has a problem area, it is much easier to point it out to the users than to publish a rebuttal. Comments are easy. Simply state your observation. If you are wrong in your assessment, I am sure you will receive a fine education from the more learned individuals in our community. And since this pertains to the entire PDB, I do not see a lot spam/noise being produced on a single structure. I would suspect almost nothing will be said regarding the majority of the 100,000 structures. I am not aware of a ton of spam being produced on the publications in the Pubmed Commons. In fact, it saddens me that no one has said anything significant about my publications. I personally would prefer to limit the feedback to those who deposit structures (similar to how Pubmed Commons limits comments to authors). I believe that we as a community are the ones best positioned to police the database. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 1:00 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat
Re: [ccp4bb] PDB passes 100,000 structure milestone
I may be missing something here, but I don't think you have to rebut anything. You simply report that someone else has rebutted it. Along the lines of Many scientists regard this published structure as unreliable since a misconduct investigation by the University of Alabama at Birmingham has concluded that it was, more likely than not, faked [1] [1] http://www.nature.com/news/2009/091222/full/462970a.html On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] PDB passes 100,000 structure milestone
That is an extraordinary case, and it certainly took a huge amount of work. What about structures that are obviously wrong based on inspection of the density, but no one has bothered to challenge yet? The TWILIGHT database helps some, if that counts, but it doesn't catch everything. -Nat On Thu, May 15, 2014 at 10:48 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: I may be missing something here, but I don't think you have to rebut anything. You simply report that someone else has rebutted it. Along the lines of Many scientists regard this published structure as unreliable since a misconduct investigation by the University of Alabama at Birmingham has concluded that it was, more likely than not, faked [1] [1] http://www.nature.com/news/2009/091222/full/462970a.html On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] PDB passes 100,000 structure milestone
If one limits such a comment system to authors of PDB structures then you are closing the door to a lot of potentially good contributors: anyone involved in analysing protein structures. For instance that can be anyone in the fields of structural bioinformatics, molecular dynamics, computational crystallography etc. Those people can have quite a say in these discussions and are even very likely to find issues since they write tools to automatically analyse PDB structures. As I said, I'd go for a system totally open for anyone who wants to register. Modern tools to allow scoring of the feedback by the rest of the community would sort all problems out, provided there is enough participation. Jose -Original Message- From: CCP4 bulletin board on behalf of Zachary Wood Sent: Thu 5/15/2014 7:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone I agree with Nat. If you think a structure has a problem area, it is much easier to point it out to the users than to publish a rebuttal. Comments are easy. Simply state your observation. If you are wrong in your assessment, I am sure you will receive a fine education from the more learned individuals in our community. And since this pertains to the entire PDB, I do not see a lot spam/noise being produced on a single structure. I would suspect almost nothing will be said regarding the majority of the 100,000 structures. I am not aware of a ton of spam being produced on the publications in the Pubmed Commons. In fact, it saddens me that no one has said anything significant about my publications. I personally would prefer to limit the feedback to those who deposit structures (similar to how Pubmed Commons limits comments to authors). I believe that we as a community are the ones best positioned to police the database. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 15, 2014, at 1:00 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat
Re: [ccp4bb] PDB passes 100,000 structure milestone
TWILIGHT database, PDBREDO database, ... what else I forgot to name? I wonder why it should be under different brands and names, and not just be where it belongs to - the PDB?! Back in 2005 when I (and colleagues) started re-refining the entire PDB (to test phenix.refine, mostly) and seeing oddities (by now well documented in the above mentioned debases and related publications) I felt very excited about starting a databases of curated structures, but thinking a bit it appeared strange and unnatural to have a parallel version of PDB. Pavel On Thu, May 15, 2014 at 11:23 AM, Nat Echols nathaniel.ech...@gmail.comwrote: That is an extraordinary case, and it certainly took a huge amount of work. What about structures that are obviously wrong based on inspection of the density, but no one has bothered to challenge yet? The TWILIGHT database helps some, if that counts, but it doesn't catch everything. -Nat On Thu, May 15, 2014 at 10:48 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: I may be missing something here, but I don't think you have to rebut anything. You simply report that someone else has rebutted it. Along the lines of Many scientists regard this published structure as unreliable since a misconduct investigation by the University of Alabama at Birmingham has concluded that it was, more likely than not, faked [1] [1] http://www.nature.com/news/2009/091222/full/462970a.html On 15 May 2014 18:00, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: It seems to me that the Wikipedia mechanism works wonderfully well. One rule is that you can't make assertions yourself, only report pre-existing material that is attributable to a reliable published source. This rule would be a little problematic for annotating the PDB. It requires a significant amount of effort to publish a peer-reviewed article or even just a letter to the editor, and none of us are being paid to write rebuttals to dodgy structures. -Nat -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] PDB passes 100,000 structure milestone
What about structures that are obviously wrong based on inspection of the density, but no one has bothered to challenge yet? The TWILIGHT database helps some, if that counts, but it doesn't catch everything. How about this utopia.. Imagine PDB has two versions: one is the original data and model deposited as is, and never ever changed no matter what. Another version is a curated one obtained in a quest-like way: anyone can take an original entry, improve it and deposit (into the curated version) with his/her name tag on it. And of course anyone can take and update that improved entry and re-deposit it again with his/her name tag, etc. If desired one could keep track of all the revisions, like in svn or so. Sounds like a sport with an element of public service that might yield crowd-perfected models -:) ! Pavel
[ccp4bb] PDB passes 100,000 structure milestone
The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi James, I am surprised the PDB contained any data at all at that time - wouldn't people only submit their models but not the data at that time? ;-) 249GB and even the compressed 249GB data are not a 'tiny' space, as you actually point out. At 'those days' I had three operating systems installed on my 400MB disk. Rather we are used to larger disks nowadays, but most of the time that's only filled with noise. I just took an arbitrary data set covering 21GB disk space, reduced to 8.6MB hkl-data - that's only 0.04% non-noise ;-) Best, Tim On 05/14/2014 05:18 PM, James Holton wrote: I think 249 GB is uncompressed. My local copy of the PDB only takes up 20 GB, or one Blu-Ray. I can remember a time when the whole of the PDB fit onto a single CD-ROM. The PDB booth at the ACA meeting would hand them out for free! That was impressive to me because CD-R disks were really expensive (to an undergraduate like me anyway), and I had to figure out how to do multi-session writes so I could back up my whole hard drive 2 or 3 times before I filled one up. And, of course, I had to take out my hard drive and go over to that really wealthy lab that had a CD writer to do that. Each write took about an hour, and didn't always work. Ah, those were the days. But yes, it is impressive how so much effort by so many people over so many years can be compressed into such a tiny space. Is it not a strange fate that we should suffer so much fear and doubt for so small a thing? -James Holton MAD Scientist On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote: I reckon it's two box sets of 25 discs each - am I calculating that wrong? Maybe room for a 'making of' feature ;) *From:* Jon Agirre jon.agi...@york.ac.uk *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, 14 May 2014, 14:28 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone 249GB? That's a whole lot of DVDs! On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.com mailto:martainn_oshioma...@btinternet.com wrote: Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) of storage' was obviously written by someone from a pre i-tunes generation http://www.wwpdb.org/news/news_2014.html#13-May-2014 ;) -M. *From:* mesters mest...@biochem.uni-luebeck.de mailto:mest...@biochem.uni-luebeck.de *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, 14 May 2014, 13:41 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr.Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de http://www.biochem.uni-luebeck.de/ http://www.iobcr.org http://www.iobcr.org/ -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly
Re: [ccp4bb] PDB passes 100,000 structure milestone
Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or less….) valid entries only at the time of announcement. Cheers, BR Supplemental material: “The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them” *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* “With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.” http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to=CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- *Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- *Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Mark, I understand the discussion, yet as far as I understand the PDB does not claim to be the authority to decide about the integrity of an entry (or maybe better said, the PDB claims not to be this authority), and I find it very honorable that the PDB have not abused their power. I don't mean such an authority should not exist, but I think it is a good think it is not the PDB. It is a form of separation of powers. Best, Tim On 05/14/2014 06:47 PM, Mark Wilson wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- *Disclaimer * This message contains confidential information
Re: [ccp4bb] PDB passes 100,000 structure milestone
I agree with Mark. The PDB should, at the very least, attach a warning label to entries like 2HR0, where the scientific community has overwhelmingly determined that the structure is invalid. In this case, I believe the author never admitted any wrongdoing, and perhaps PDB policy prevents removal of the entry without the depositing author's consent. I note that the PDB labels some structures associated with retracted papers as obsoleted and superseded by NONE. For example, see 2qns and 2hlb. Jack On May 14, 2014, at 12:06 PM, Tim Gruene wrote: Hi Mark, I understand the discussion, yet as far as I understand the PDB does not claim to be the authority to decide about the integrity of an entry (or maybe better said, the PDB claims not to be this authority), and I find it very honorable that the PDB have not abused their power. I don't mean such an authority should not exist, but I think it is a good think it is not the PDB. It is a form of separation of powers. Best, Tim On 05/14/2014 06:47 PM, Mark Wilson wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle
Re: [ccp4bb] PDB passes 100,000 structure milestone
@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1; to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- *Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. *-- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] PDB passes 100,000 structure milestone
I think for questionable structures and those representing retracted paper, PDB should be able to ask the depositors for raw data and leave it for the community to decide if they still want to use the structure for science. If the depositors can't or would not submit the data, it should be clearly marked. Debasish -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark Wilson Sent: Wednesday, May 14, 2014 12:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone Hi Tim, Getting to Eric's point about an impasse, if the PDB will not claim the authority to safeguard the integrity of their holdings (as per their quoted statement in Bernhard's message below), then who can? I understand that there are many potential complications to the PDB claiming some plenary authority to prune out structures that they don't like for whatever reason and agree that they should not claim such authority. Furthermore, I sympathize with the difficult situation that the curators must confront in the (hopefully) very rare cases of models whose integrity is suspect. However, dealing with these in some manner surely falls squarely within a mission to safeguard the integrity and improve the quality of the PDB archive. Strict neutrality on the part of the PDB in these cases is not working well in my opinion, as evidenced by the absence of any indication of the dark history of 2HR0 on its PDB page. There are many possible ways of indicating something is seriously amiss with these entries, and I wish that the community wasn't in the position of having PDB entries that some users know are deeply suspect but that other, less informed users do not. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 12:06 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Hi Mark, I understand the discussion, yet as far as I understand the PDB does not claim to be the authority to decide about the integrity of an entry (or maybe better said, the PDB claims not to be this authority), and I find it very honorable that the PDB have not abused their power. I don't mean such an authority should not exist, but I think it is a good think it is not the PDB. It is a form of separation of powers. Best, Tim On 05/14/2014 06:47 PM, Mark Wilson wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1 tf =1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 14, 2014, at 12:47 PM, Mark Wilson mwilso...@unl.edu wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry
Re: [ccp4bb] PDB passes 100,000 structure milestone
I vote for Z's idea On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:706-583-0303 FAX: 706-542-1738 *** On May 14, 2014, at 12:47 PM, Mark Wilson mwilso...@unl.edu wrote: Hi Tim, I agree with everything you've said about the importance of validation, but aren't we really talking about something different here? Users of structural information should of course be keeping a careful eye on validation reports. On the other hand, what possible reason is there for the PDB to continue to archive and offer for public use models whose fundamental integrity (rather than quality or reliability) are highly suspect? I hope that I'm not the only one who is frustrated that the page for 2HR0 is still available and unblemished by warnings. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Eric, On 05/14/2014 06:05 PM, Eric Williams wrote: [...] We seem to be at an impasse. The PDB won't evict highly suspect structure models unless journals retract them, and the journals in question have shown no indication of desiring to retract them. Is there anything that can be done? [...] What's the appropriate course of action for conscientious consumers of PDB data? Is there a way to petition journals to issue retractions? I wonder what the gents at Retraction Watch (http://retractionwatch.com) would recommend. Eric you can teach the consumers how to help themselves - you are welcome to join my session MS-84 at the IUCr 2014 :-) because I believe that one of the New Paradigms in Crystallography is the requirement to how to correctly interpret crystallographic models, and validation is becoming more and more important as subject. Best, Tim On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1 to=hofkristall...@gmail.com wrote: which structure ended up as number 100.000? I guess that depends if we still count the Murthy corpses like 2a01 This 3-armed Swastika for example still does not come with a single warning short of a poor quality report http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So, sorry, 0 (or lessŠ.) valid entries only at the time of announcement. Cheers, BR Supplemental material: ³The PDB says it will remove the other ten structures only when editors at the journals in which they were originally published or the authors themselves retract them² *http://www.nature.com/news/2009/091222/full/462970a.html http://www.nature.com/news/2009/091222/full/462970a.html* ³With the support of the structural-biology community, the mission of the wwPDB is to safeguard the integrity and improve the quality of the PDB archive.² http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Not to be overly cynical, but http://tinyurl.com/pmupalt *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1 tf=1to=CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *mesters *Sent:* Mittwoch, 14. Mai 2014 14:42 *To:* CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to =CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr. Jeroen R. Mesters Deputy, Senior Researcher
Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson mwilso...@unl.edu wrote: Getting to Eric's point about an impasse, if the PDB will not claim the authority to safeguard the integrity of their holdings (as per their quoted statement in Bernhard's message below), then who can? I think this may in part boil down to a semantic dispute over the meaning of integrity. I interpreted it to mean integrity (and public availability) of the data as deposited by the authors, which by itself is quite a lot of work. Safeguarding the integrity of the peer-review process is supposed to be the job of the journals, some of which - unlike the PDB - are making a tidy profit from our efforts. Since they justify this profit based on the value they supposedly add as gatekeepers, I don't think it's unreasonable for us to expect them to do their job, rather than leave it to the PDB annotators, who surely have enough to deal with. I do share some of the concern about 2hr0, but I am curious where the line should be drawn. This is an extraordinary case where the researcher's institution requested retraction, but I think everyone who's been in this field for a while has a list of dodgy structures that they think should be retracted - not always with justification. -Nat
Re: [ccp4bb] PDB passes 100,000 structure milestone
As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Phil Jeffrey Princeton On 5/14/14 1:37 PM, Gloria Borgstahl wrote: I vote for Z's idea On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. Best regards, Z *** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 tel:706-583-0304 Lab: 706-583-0303 tel:706-583-0303 FAX: 706-542-1738 tel:706-542-1738 ***
Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Nat, I agree that journals should be doing the heavy lifting here, for the reasons that you note. I also want to be clear that I believe the PDB is a crowning achievement of transparency and open access in the sciences, which is one reason that I am so concerned about this issue. I am in no way trying to impugn the hard and superb work that they have done over many decades. I still contend, however, that having models whose integrity is highly suspect lurking in the PDB with no indications of problems beyond a dodgy validation report is a non-optimal outcome. As for the meaning of integrity, I'm using this word in place of others that might be considered more legally actionable. A franker conversation would likely more clearly draw the line that we're wrestling with here. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 5/14/14 12:41 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, May 14, 2014 at 10:26 AM, Mark Wilson mwilso...@unl.edu wrote: Getting to Eric's point about an impasse, if the PDB will not claim the authority to safeguard the integrity of their holdings (as per their quoted statement in Bernhard's message below), then who can? I think this may in part boil down to a semantic dispute over the meaning of integrity. I interpreted it to mean integrity (and public availability) of the data as deposited by the authors, which by itself is quite a lot of work. Safeguarding the integrity of the peer-review process is supposed to be the job of the journals, some of which - unlike the PDB - are making a tidy profit from our efforts. Since they justify this profit based on the value they supposedly add as gatekeepers, I don't think it's unreasonable for us to expect them to do their job, rather than leave it to the PDB annotators, who surely have enough to deal with. I do share some of the concern about 2hr0, but I am curious where the line should be drawn. This is an extraordinary case where the researcher's institution requested retraction, but I think everyone who's been in this field for a while has a list of dodgy structures that they think should be retracted - not always with justification. -Nat
Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: As long as it's just a Technical Comments section - an obvious concern would be the signal/noise in the comments themselves. I'm sure PDB would not relish having to moderate that lot. Alternatively PDB can overtly link to papers that discuss technical issues that reference the particular structure - wrong or fraudulent structures are often associated with refereed publications that point that out, and structures with significant errors often show up in that way too. I once did a journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish that could be associated with the relevant PDB file(s). Perhaps some combination of those two ideas? The PDB could associate with each deposited structure a crowd-sourced list of published articles citing it. They already make an effort to attach the primary citation, but so far as I know there is currently no effort to track subsequent citations. While spam comments in a free-format forum are probably inevitable, spam submission of citing papers seems less likely to be a problem. - Ethan On Wed, May 14, 2014 at 12:32 PM, Zachary Wood z...@bmb.uga.edu mailto:z...@bmb.uga.edu wrote: Hello All, Instead of placing the additional burden of policing on the good people at the PDB, perhaps the entry page for each structure could contain a comments section. Then the community could point out serious concerns for the less informed users. At least that will give users some warning in the case of particularly worrisome structures. The authors of course could still reply to defend their structure, and it may encourage some people to even correct their errors. -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] PDB passes 100,000 structure milestone
From the earliest days the PDB accepted structure factor files along with coordinate files. If you check the early newsletters you will see that, unfortunately, most authors did not deposit structure factor files. Eventually, as we all know, deposition of structure factors became mandatory. There were relatively few requests in the early years for structure factors. In fact the most common requests were from depositors who had lost their original data and had had the foresight to deposit it. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 14 May 2014, Tim Gruene wrote: Hi James, I am surprised the PDB contained any data at all at that time - wouldn't people only submit their models but not the data at that time? ;-) 249GB and even the compressed 249GB data are not a 'tiny' space, as you actually point out. At 'those days' I had three operating systems installed on my 400MB disk. Rather we are used to larger disks nowadays, but most of the time that's only filled with noise. I just took an arbitrary data set covering 21GB disk space, reduced to 8.6MB hkl-data - that's only 0.04% non-noise ;-) Best, Tim On 05/14/2014 05:18 PM, James Holton wrote: I think 249 GB is uncompressed. My local copy of the PDB only takes up 20 GB, or one Blu-Ray. I can remember a time when the whole of the PDB fit onto a single CD-ROM. The PDB booth at the ACA meeting would hand them out for free! That was impressive to me because CD-R disks were really expensive (to an undergraduate like me anyway), and I had to figure out how to do multi-session writes so I could back up my whole hard drive 2 or 3 times before I filled one up. And, of course, I had to take out my hard drive and go over to that really wealthy lab that had a CD writer to do that. Each write took about an hour, and didn't always work. Ah, those were the days. But yes, it is impressive how so much effort by so many people over so many years can be compressed into such a tiny space. Is it not a strange fate that we should suffer so much fear and doubt for so small a thing? -James Holton MAD Scientist On 5/14/2014 7:15 AM, MARTYN SYMMONS wrote: I reckon it's two box sets of 25 discs each - am I calculating that wrong? Maybe room for a 'making of' feature ;) *From:* Jon Agirre jon.agi...@york.ac.uk *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, 14 May 2014, 14:28 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone 249GB? That's a whole lot of DVDs! On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.com mailto:martainn_oshioma...@btinternet.com wrote: Although the line boasting that the PDB adds up to 'more than 249 GBbytes (sic) of storage' was obviously written by someone from a pre i-tunes generation http://www.wwpdb.org/news/news_2014.html#13-May-2014 ;) -M. *From:* mesters mest...@biochem.uni-luebeck.de mailto:mest...@biochem.uni-luebeck.de *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, 14 May 2014, 13:41 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone Amazing, great! And, which structure ended up as number 100.000? - J. - Am 14.05.14 10:42, schrieb battle: The Worldwide Protein Data Bank (wwPDB) organization is proud to announce that the Protein Data Bank archive now contains more than 100,000 entries. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached a critical milestone thanks to the efforts of structural biologists throughout the world. Read the full story at: http://www.wwpdb.org/news/news_2014.html#13-May-2014 -- Gary Battle on behalf on the wwPDB -- Dr.Jeroen R. Mesters Deputy, Senior Researcher Lecturer Institute of Biochemistry, University of L?beck Ratzeburger Allee 160, 23538 L?beck, Germany phone: +49-451-5004065 (secretariate 5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de http://www.biochem.uni-luebeck.de/ http://www.iobcr.org http://www.iobcr.org/ -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only
Re: [ccp4bb] PDB passes 100,000 structure milestone
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The policy doesn't say you can supersede someone else's entry. It says you can deposit your own version, if you have a publication. Then there will be two bogus structures instead of one. Pretty soon the PDB will start to look like one of the crappy Matrix movies. Dale Tronrud On 5/14/2014 6:47 PM, James Holton wrote: A little loophole that might make everyone happy can be found here: http://www.wwpdb.org/policy.html search for A re-refined structure based on the data from a different research group Apparently, anyone can supersede any PDB entry, even if they weren't the original depositor. All they need is a citation. Presumably, someone could re-refine 2hr0 against the data that were deposited with it. Possibly showing how to get an R-factor of 0% out of it. I'd definitely cite that paper. -James Holton MAD Scientist On 5/14/2014 11:01 AM, Nat Echols wrote: On Wed, May 14, 2014 at 10:53 AM, Mark Wilson mwilso...@unl.edu mailto:mwilso...@unl.edu wrote: As for the meaning of integrity, I'm using this word in place of others that might be considered more legally actionable. A franker conversation would likely more clearly draw the line that we're wrestling with here. The reference to integrity was Bernhard's - quoting the PDB mission statement; I just disagree with his interpretation of the meaning. As far as 2hr0 is concerned, I think we're quite safe calling it fraudulent at this point, since (ironically) Nature itself has said as much: http://www.nature.com/news/2009/091222/full/462970a.html -Nat -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlN0V1UACgkQU5C0gGfAG124eQCffE9h2fdDDi2TDLSwr9DabrZI GzoAn2QTo1/VTW8ZYSHCpcgCX+EHFv/q =Ja+6 -END PGP SIGNATURE-
