We indeed used the US portal for deposition which may be "the difference". Nevertheless the recent reported resolution values etc. are projected also to the PDBe portal.
Jan On Wed, Apr 25, 2012 at 10:10 AM, Mark J van Raaij <mjvanra...@cnb.csic.es>wrote: > Phoebe, Jan, PDB, > is this something particular to the US portal of the PDB, or general? > We always use the European portal pdbe and have not had such "problems". > Mark > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > > > On 25 Apr 2012, at 09:41, Jan Dohnalek wrote: > > > There have been other manipulations with user-input values. We could not > input solvent content 83% for 3cg8 (the real value!!!) as "being out of the > allowed range". > > The resulting value in the PDB is "NULL" not showing the actually > interesting feature of the structure. > > > > I also noticed that the reported resolution values are nonsensically > advertised with three decimal positions after the point which is not the > way we would put it, is it? > > > > Either fight it or live with it ... > > > > Jan Dohnalek > > > > > > > > > > On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice <pr...@uchicago.edu> > wrote: > > I just noticed that the PDB has changed the stated resolution for one of > my old structures! It was refined against a very anisotropic data set that > extended to 2.2 in the best direction only. When depositing I called the > resolution 2.5 as a rough average of resolution in all 3 directions, but > now PDB is advertising it as 2.2, which is misleading. > > > > I'm afraid I may not have paid enough attention to the fine print on > this issue - is the PDB now automatically advertising the "resolution" of a > structure as that of the outermost flyspeck used in refinement, regardless > of more cautious assertions by the authors? If so, I object! > > > > ===================================== > > Phoebe A. Rice > > Dept. of Biochemistry & Molecular Biology > > The University of Chicago > > phone 773 834 1723 > > > http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 > > http://www.rsc.org/shop/books/2008/9780854042722.asp > > > > > > > > -- > > Jan Dohnalek, Ph.D > > Institute of Macromolecular Chemistry > > Academy of Sciences of the Czech Republic > > Heyrovskeho nam. 2 > > 16206 Praha 6 > > Czech Republic > > > > Tel: +420 296 809 340 > > Fax: +420 296 809 410 > > -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
