Exactly why I deposit the structure factors Thank you PDB!!
On Wed, May 14, 2014 at 7:35 PM, Frances C. Bernstein < f...@bernstein-plus-sons.com> wrote: > 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 > *** * > * *** 1-631-286-1339 FAX: 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_oshiomains@ >>>> 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 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 Jon Agirre >>>> York Structural Biology Laboratory / Department of Chemistry >>>> University of York, Heslington, YO10 5DD, York, England >>>> http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/ >>>> +44 (0) 1904 32 8253 >>>> >>>> >>>> >>> >> -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> >>
