Hi Martyn, > I think the question is where the error was made - seeing the uploaded file > would clear this up. But it seems unlikely to me that the depositor saw a huge > R factor discrepancy at the end of refinement and just blithely uploaded it. > So scenario 3 :- > PDB : we cannot reproduce your R factor with our programs > Depositor : that's your problem mate - it was fine when it left me...up to > you to sort it... > Which seems a sort of reasonable attitude to me. Not quite, the depositor has to give, i.e. type, the space group (example depositions: https://www.ebi.ac.uk/pdbe-xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFNAVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me why, because it is clearly a source of error.
> Checking back to see the space group misparsed and re-running the water > moving-rem500 - and validation scripts would have cleared this problem with > no action needed from the depositor. I totally agree that the annotator could have intercepted the problem. But the responsibility lies with the depositor. Hooray for bureaucracy! Cheers, Robbie > > Cheers > Martyn > > > > ------------------------------ > On Sat, Apr 13, 2013 23:03 BST Robbie Joosten wrote: > > >Hi Martyn, > > > >> A shame then that these 'helpful' annotators did not make use of > >> Pavel's basic sanity on the space group (*mentioned below) and check > >> back to the one listed in the uploaded PDB file. > >As far as I know, EDS is run on all new depositions at PDBe. I don't > >know whether they already did that when this model was deposited. Even > >if they did, this may not solve the problem because the PDB does not > refuse models. > >Possible scenarios (there may be more): > > > >1) Pretty bad case > >- Annotator: We cannot reproduce your R-factors in EDS. Could you check > >the annotated coordinate and reflection files? > >- Depositor: Not interested (the paper is almost accepted anyway). > >Approve model as-is. > > > >2) Worst case > >- Annotator: ... (doesn't notice the problem) > >- Depositor: ... (doesn't notice the problem) > > > >> I often wonder why the PDB does not make the deposited coordinate > >> file publicly available so that these sorts of issues can be checked > >> and > >tracked. > >Good point, I wonder about that as well. Also about whether depositors > >would like that? > > > >> The whole PDB data (excluding the EMDB that was recently merged into > >> it) amounts to about a laptop hard drive's worth of data - so surely > >> space > >can be > >> made for the deposited coordinates? (and restraint files which will > >> be > >very > >> useful for other workers including pdb-redo). > >Yes, having access to certain restraint files (particularly for LINKs) > >would be very nice. That said, a proper repository of > >consensus-restraints for hetero compounds and LINKs would be more > >reliable than potentially different restraints for each PDB entry. > > > > > Having the depositors' uploaded data would help me understand other > >> puzzling features of structures such as the current 4GRV.pdb which > >> seems > >to > >> have a list of TLS groups but contains not a single ANISOU line!... > >I'm not a big fan of using ANISOU records for TLS contributions anyway > >;-) But, more seriously, PDB entries should adhere to the PDB standard. > > > >Cheers, > >Robbie > > > > > >> > >> > >> Cheers > >> Martyn > >> > >> *In this particular case attempting to calculate R-factor using data > >> and > >model > >> files and making sure that the R you get is not twice as large as > >published one > >> would entirely suffice -:) > >> > >> Pavel > >> > >> ________________________________ > >> > >> From: Robbie Joosten <robbie_joos...@hotmail.com> > >> To: CCP4BB@JISCMAIL.AC.UK > >> Sent: Friday, 12 April 2013, 22:57 > >> Subject: Re: [ccp4bb] Puzzling Structure > >> > >> > >> Waters are moved during annotation using the perceived space group's > >> symmetry operation. So if the authors give the wrong space group, > >> then the annotation pipeline understandably messes things up. If the > >> originally uploaded PDB file was kept by PDBe, then the problem can > >> be recovered quite easily by the annotators. Perhaps the topic > >> starter, Michel Fodje, can > >send > >> a bug report to PDBe. In my experience, the annotators are very > >> helpful resolving these matters. > >> > >> <potential flame> > >> Hoping that the depositors solve the problem by themselves, is > >> probably in > >> vain: There are many crystallographers who do not read the CCP4BB > >> (which > >is > >> a shame, really); they didn't notice the enormous amount of water > >> related bumps in their final model (which is in the validation report > >> you get > >after > >> deposition and in REMARK 500 of the PDB file you have to approve); > >> they also didn't notice the huge number of symmetry-related bumps; > >> the R-factors in the PDB file are different from (and better than) > >> the ones in Table 1. > >Also > >> notice that the paper was submitted on April 21st 2009 and the model > >> was deposited on June 29th 2009. Paper accepted on July 8th 2009. But > >> I'm sure the referees had a chance to properly assess the quality of > >> the structure model ;-) </ potential flame> > >> > >> Cheers, > >> Robbie > >> > >> P.S. It's pretty awesome that the problem was solved in less than 20 > >minutes > >> by the CCP4BB (that is, by Phoebe Rice) > >> > >> > >> > -----Original Message----- > >> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf > >> > Of Garib N Murshudov > >> > Sent: Friday, April 12, 2013 21:39 > >> > To: CCP4BB@JISCMAIL.AC.UK > >> > Subject: Re: [ccp4bb] Puzzling Structure > >> > > >> > It is typo: > >> > R factor for p212121 - 0.4 > >> > for p21212 - around 0.18 > >> > > >> > Although water seem to have been moved around using p212121 > >> > > >> > > >> > > >> > > >> > On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote: > >> > > >> > > >> > Looks like a typo to me: if you change the CRYST space group > >> > record from P212121 to P21212, as the paper says it is, the packing > >> > problem > >goes > >> > away. > >> > > >> > ++++++++++++++++++++++++++++++++++++++++++ > >> > > >> > Phoebe A. Rice > >> > Dept. of Biochemistry & Molecular Biology > >> > The University of Chicago > >> > > >> > 773 834 1723; pr...@uchicago.edu > >> > http://bmb.bsd.uchicago.edu/Faculty_and_Research/ > >> > > >> > http://www.rsc.org/shop/books/2008/9780854042722.asp > >> > > >> > ________________________________________ > >> > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of > >> > Michel Fodje [michel.fo...@lightsource.ca] > >> > Sent: Friday, April 12, 2013 2:17 PM > >> > To: CCP4BB@JISCMAIL.AC.UK > >> > Subject: Re: [ccp4bb] Puzzling Structure > >> > > >> > By the way, you will need to show symmetry atoms to see the > >> > problem. > >> > > >> > > >> > > >> > -----Original Message----- > >> > > >> > > >> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On > >> > Behalf Of > >> > > >> > > >> > Michel Fodje > >> > > >> > > >> > Sent: April-12-13 1:14 PM > >> > > >> > > >> > To: CCP4BB@JISCMAIL.AC.UK > >> > > >> > > >> > Subject: [ccp4bb] Puzzling Structure > >> > > >> > > >> > > >> > Has anyone else noticed a problem with the structure of > >> > the N-terminal > >> > > >> > > >> > capsid domain of HIV-2 PDB 2wlv. > >> > > >> > > >> > > >> > Load it up to in coot and navigate to residue B118. > >> > > >> > > >> > > >> > > >> > > >> > /Michel. > >> > > >> > > >> > Dr Garib N Murshudov > >> > Group Leader, MRC Laboratory of Molecular Biology Francis Crick > >> > Avenue Cambridge Biomedical Campus Cambridge > >> > CB2 0QH UK > >> > Email: ga...@mrc-lmb.cam.ac.uk > >> > Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc- > lmb.cam.ac.uk/> > >> <http://www.mrc-lmb.cam.ac.uk/> > >> > > >> > > >> > > >> > > >> > > >> > > >> > >>
