[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
[ccp4bb] CCP4-6.4.0 Update 015
Dear CCP4 users, An update for the CCP4-6.4.0 series has just been released, consisting of the following changes: * BLEND: New program for optimum selection of multi-crystal datasets for merging * Documentation: Help for BLEND * CCP4i: BLEND interface and allow view of PNG files * Examples: BLEND example script * iMosflm: Correct link to iMosflm web pages Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team
[ccp4bb] Ph.D. position available in Germany
Dear all, a Ph.D. position in pharmaceutical and protein science is immediately available in a pharmaceutical setting in collaboration with an academic chair of interest. The selected candidate will work with biomolecules of therapeutic relevance in a highly modern environment at the interface of research and development covering the area of protein stability. The research group aims to mechanistically understand protein aggregation/particle formation during biopharmaceutical drug development and manufacture using a multidisciplinary approach. The Ph.D. candidate will assist in a project that involves protein-protein interactions (PPI) using the development of new PPI methods along with complementary methods for the evaluation of physicochemical properties of biomolecules. Applicants should have a strong background in at least one of the following field: protein science, biophysics, biochemistry, pharmacy or related field and should provide a strong interest in the physical understanding of biophysical approaches/methods. Previous experience with proteins, and/or protein chemistry/science as well as biophysical techniques to characterize protein interactions would be a great advantage. Good English language skills (oral and written) are essential and writing scientific research papers would be advantageous. The Ph.D. position is fully funded for a period of 3 - 4 years. The candidates should be highly motivated, goal-driven, and dedicated individuals who can think critically and work both independently and collaboratively. It is also important that the candidates are creative in problem solving and have a strong desire to seek answers to questions related to the project. Preferred start is at the earliest possible date. Review of applications will begin immediately and continue until the positions are filled. Interested students please send applications and informal inquiries including a short letter of motivation detailing research interests and expertise, CV and contact information of two/three references as a single pdf file. For more information, contact Michaela Blech (michaela.bl...@boehringer-ingelheim.com). We are looking forward to receiving your applications, preferably before May 29th. Michaela Blech, Ph.D.
[ccp4bb] Release of BLEND in Update 15
Dear all, Following on from the CCP4BB posting about the release of update 15 we would like to highlight a few points about BLEND and encourage you to try it out should you have multi crystal data that needs analysing: 1) the software needs the R package to be installed on your system. This is free (GNU) and easy to install: http://www.r-project.org/ Dependency from R will be soon eliminated and users will be informed through the update mechanism. 2) This is very new software, dealing with a more and more prominent class of data collection from multiple crystals. BLEND has worked well on many data sets to date but less well on others. Like many programs for crystallography, improvements for this software are very much dependent on users feedback. We know how precious your time is, but strongly encourage you to send us critical issues, comments and requests. Ultimately these will help guide BLEND's development. 3) We are always available to assist with your data processing while using BLEND. You can send requests for help via the CCP4 BB or, if you prefer, directly to the program authors: James Foadi: james.fo...@diamond.ac.ukmailto:james.fo...@diamond.ac.uk or j.fo...@imperial.ac.ukmailto:j.fo...@imperial.ac.uk Gwyndaf Evans: gwyndaf.ev...@diamond.ac.ukmailto:gwyndaf.ev...@diamond.ac.uk We hope BLEND can help you with the analysis of your multiple data sets. Best wishes, Gwyndaf Evans and James Foadi -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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 or
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 and is
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 on
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=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
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 they
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
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
[ccp4bb] correct pdb encoding for split-personality solvent HETATM?
On the subject of not (willfully) contaminating the pdb database, any suggestions on the following are appreciated. I am refining the solvent structure of some RNAs. Inspection of difference and anomalous difference maps suggests that some closely-spaced positions are alternately taken by distinct entities with partial occupancy. One pattern suggests partial occupancy by a Ca++ ion with a nearby site partially occupied by water (confirmed by an anomalous peak only for the former). I am refining this with shelxl and expressing this in the ins file is straightforward (and I'd like to express much gratitude for the multi-core version of shelxl!). However it's not clear to me how to say this in PDBese : choosing the HETATM residue name as either HOH or CA and assigning alternate positions with HOH and CA in the atom name field seems to make trouble for pdb reader software, eg mmdb. thanks, Alastair Fyfe
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] correct pdb encoding for split-personality solvent HETATM?
thanks Tim. I have been using different AltLoc values (A,B) and different Atom name values (HOH,CA) but the problem seems to be which value to set for the Residue name field. Assigning different residues numbers would seem to lose the distinction between partial and alternate occupancy. The ins file seems to have no problem with the pattern RESI CA PART 1 CA .. PART 2 O .. PART 0 On 05/14/2014 11:01 AM, Tim Gruene wrote: Dear Alastair, I think that refinement programs usually interpret chain ids A, B, ... the way shelxl uses PART 1, 2, ... and a blank chain ID corresponds to PART 0. You may have to assign different residue numbers to CA and HOH, but I think this is also the case for shelxl. Does this resolve your problem? Best, Tim On 05/14/2014 07:48 PM, Alastair Fyfe wrote: On the subject of not (willfully) contaminating the pdb database, any suggestions on the following are appreciated. I am refining the solvent structure of some RNAs. Inspection of difference and anomalous difference maps suggests that some closely-spaced positions are alternately taken by distinct entities with partial occupancy. One pattern suggests partial occupancy by a Ca++ ion with a nearby site partially occupied by water (confirmed by an anomalous peak only for the former). I am refining this with shelxl and expressing this in the ins file is straightforward (and I'd like to express much gratitude for the multi-core version of shelxl!). However it's not clear to me how to say this in PDBese : choosing the HETATM residue name as either HOH or CA and assigning alternate positions with HOH and CA in the atom name field seems to make trouble for pdb reader software, eg mmdb. thanks, Alastair Fyfe
Re: [ccp4bb] correct pdb encoding for split-personality solvent HETATM?
Dear Alastair, As you point out, SHELXL allows atom names, RESIdue numbers and PARTs (=Altlocs) to be used in any combination. The only rule is that no two non-hydrogen atoms may have the same settings for all three. Other refinement programs may be more restrictive. Best wishes, George On 05/14/2014 08:26 PM, Alastair Fyfe wrote: thanks Tim. I have been using different AltLoc values (A,B) and different Atom name values (HOH,CA) but the problem seems to be which value to set for the Residue name field. Assigning different residues numbers would seem to lose the distinction between partial and alternate occupancy. The ins file seems to have no problem with the pattern RESI CA PART 1 CA .. PART 2 O .. PART 0 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] puzzle of reference zone in HKL2000
Thank you! There is no exact definition of the reference zone in the HKL2000 manual. Given a reciprocal lattice observed from one direction, there may be several RotXYZs to reach it. It might be that the reference zone is a sampling parallelogram from the real space used to determine the orientation difference with its counterpart(s) in reciprocal space that has been established by reverse projecting of spots from the CCD to the Ewald sphere. Thanks a lot! Best wishes, Shiqiang Lin On Tue, May 13, 2014 at 5:14 PM, Felix Frolow mbfro...@post.tau.ac.ilwrote: these are symmetry alternative choices of the cell axes they sure are the same as there are 14 Bravais lattices I guess it is not space group related. they were introduced to maintain a precision of calculationI guess, so to choose and alternative orientation were trigonometric parameters are in the region were small change in angle does not bring large change in the trigonometric function (or vice versa) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 13, 2014, at 23:19 , 林世强 linshiqiang1...@gmail.com wrote: Hi everybody! I met with a problem when I was reading the HKL2000 online manual. It's the reference zone setup in the Step 11: What is the reference zone? How is this useful? (page 38, figure 38). Does anybody know the definition of reference zone, and why the reference zone setup window seems always contain the same 10 options, h0l, hk0, l0h, kh0, ..., 0-kl? Thanks. Best regards, Shiqiang Lin
[ccp4bb] Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography
The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS Macromolecular Crystallography Group operates two high performance undulator beamlines as well as a state-of-the-art bending magnet beamline for protein crystallography. The group is involved in several aspects of protein crystallography including the development of advanced beamline instrumentation and crystallographic methods, as well as structural biology projects in collaboration with the Biomolecular Research Group at PSI and external partners. In collaboration with Prof. Kay Diederichs at University of Konstanz, we are looking for a Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography Your tasks == * Serial crystallography with bright micro-focused X-ray beams from both synchrotron and free electron laser sources has brought new opportunities in micro- and nanocrystallography. At the same time, obtaining best diffraction data from hundreds and thousands of crystals presents unprecedented challenges. New statistics based method of multi-crystal merging and analysis need to be developed and validated. * Develop multi-crystal data analysis, processing and merging methods for serial micro- and nanocrystallography at synchrotron radiation (SR) and X-ray free electron laser (XFEL) sources * Actively participate in serial crystallography experiments at both SR and XFEL sources * Implement an automated data merging pipeline at the SLS protein crystallography beamlines Your profile You hold a PhD degree in (bio-)chemistry or physics and have several years of experience in protein crystallography. Working knowledge for data processing programs is a must. Experience in computer programming would be a significant advantage. If you are a good team player with good communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please contact Prof. Kay Diederichs, phone +49 7531 88 40 49 or Dr Meitian Wang, phone +41 56 310 41 75. Please submit your application online (including list of publications and addresses of referees) for the position as a Postdoctoral Fellow (index no. 6112-00) to: Paul Scherrer Institute, Human Resources Management, Miriam Zehnder, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0789-1 smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] error in NCONT?... or misinterpretation?
Hello, I'm evaluating changes in crystal packing between different forms of my protein. I use NCONT to calculate the number of atoms within a distance of 10 A from each CA atom of the protein chain. My protein is also a crystallographic dimer, then I want to list contacts between the two monomers in the ASU too. When I run the calculation for chain A, using the option all interchain contacts in NCONT GUI, I obtain the desired output: contacts between A and symmetry related A or B chains, plus contacts between A and B in the same ASU. The problem appears when I repeat the calculation for chain B: contacts between symmetry related molecules are listed, but the contacts between chain A and B in the ASU are replaced by the intramolecular ones. I copy below the header of log files generated by NCONT. I can obtain the desired output by calculating all the contacts (using the +/- two unit cells in NCONT), and removing the intramolecular ones later but...What is the explanation for the different behavior when I run the same calculation using the A or B chains? Thanks log for chain B: Input cards Data line--- source B/1-104/CA Data line--- target B, A/1-104/[C, O, N, S] Data line--- mindist 0.0 Data line--- maxdist 10.0 Data line--- cells INTER Data line--- symm P21 log for chain A: Data line--- source A/1-104/CA Data line--- target B, A/1-104/[C, O, N, S] Data line--- mindist 0.0 Data line--- maxdist 10.0 Data line--- cells INTER Data line--- symm P21
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 for the
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-
