Dear Robbie 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.
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. Depositors' coordinate files nowadays are the output of reputable, documented programs. 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). Structural genomic groups could also take a lead here by making their final refined coordinates and restraint files available alongside the PDB data. 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!... 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 <[email protected]> To: [email protected] 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:[email protected]] On Behalf Of > Garib N Murshudov > Sent: Friday, April 12, 2013 21:39 > To: [email protected] > 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; [email protected] > http://bmb.bsd.uchicago.edu/Faculty_and_Research/ > > http://www.rsc.org/shop/books/2008/9780854042722.asp > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of > Michel Fodje [[email protected]] > Sent: Friday, April 12, 2013 2:17 PM > To: [email protected] > 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:[email protected]] > On Behalf Of > > > Michel Fodje > > > Sent: April-12-13 1:14 PM > > > To: [email protected] > > > 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: [email protected] > Web http://www.mrc-lmb.cam.ac.uk <http://www.mrc-lmb.cam.ac.uk/> > > > > > >
