As I said, those omissions of promised deposition are probably just bookkeeping errors, but nevertheless, a promise is a promise. The other ones I agree are probably unrecoverable. I know I lost an early SF set completely and was really pleased when the PDB actively solicited SFs, because now I could actually FIND our SFs again!
And this is also a good opportunity to bring up again the preservation of images. More later. BR From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Robbie Joosten Sent: Sunday, January 09, 2011 11:45 PM To: [email protected] Subject: Re: [ccp4bb] deposited SF (or not)? Hi Bernhard, 1) I'm sure the PDB has this sorted out now. Perhaps someone atone of the sites can give some details. 2) Backfilling all 10k missing reflection files will be nearly impossible, but the subset of 'promised' reflection files should be recovered. I guess the first step is getting a list of IDs. That would involve some serious text mining. The next step is getting in touch with the depositors (and hoping they are still alive). If that fails, a public posting of all the depositors who didn't stick to previous promises may be a more drastic option. Ideally, depositors who didn't deposit their reflections yet, but have them lying around, should deposit them now. Perhaps the PDB should keep a list of all depositions of 'old' data. Naming and praising is better than naming and shaming. Cheers, Robbie > Date: Sun, 9 Jan 2011 16:15:09 -0800 > From: [email protected] > Subject: Re: [ccp4bb] deposited SF (or not)? > To: [email protected] > > Yes, exactly. 2002 papers, the question is how to > 1) assure consistent deposition verification > 2) how to fix omissions in earlier entries > > Best, BR > > PS: How did the EO confirm deposition - just ask you or the PDB, or some > more automated mechanism? > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > Sent: Sunday, January 09, 2011 3:35 PM > To: [email protected] > Cc: [email protected] > Subject: Re: [ccp4bb] deposited SF (or not)? > > Hi, Bernhard, > > I recently published a paper in JBC that was published online only after > the Editorial Office confirmed release of PDB coordinates and structure > factors. Maybe those structures you mention are older and their internal > checking procedures were not yet fully developed ? > > Cheers, > > Pedro. > > > Dear All, > > > > during a random search for a model structure I found a situation where the > > journal article clearly states that coordinates and SFs were deposited for > > a > > series of structures. EDS and SF files were absent and I confirmed with > > PDB > > that no SFs were ever deposited. > > > > I have no feeling for how frequent this is nor do I suggest anything more > > than book-keeping errors. Nevertheless I wonder if there is a way to > > crosscheck this in an automatic fashion (maybe PDB has some tools to do > > that?) or whose responsibility it is to ensure consistency here. JBC > > editors > > have not responded so far. > > > > Best, BR > > ----------------------------------------------------------------- > > Bernhard Rupp > > 001 (925) 209-7429 > > +43 (676) 571-0536 > > [email protected] > > [email protected] > > http://www.ruppweb.org/ > > ----------------------------------------------------------------- > > No animals were hurt or killed during the production of this email. > > ----------------------------------------------------------------- > >
