What freaked me out is that REMARK 2 seems to have changed over time: I have a version of 1ihf.pdb (deposited around 1995) that was apparently downloaded in 1998, where remark 2 says 2.5, and a version downloaded yesterday where remark 2 says 2.2. The whole thing actually started because the newer file has some odd LINK records as well, which I've written to PDB about (my fault, sort of: I apparently modeled 2 close but alternate positions of the same Cd++ ion as two different ions with low occupancy. PDB has now put a LINK between them, which makes no chemical sense).
===================================== 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 ---- Original message ---- >Date: Wed, 25 Apr 2012 11:08:52 -0400 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of "Edward A. >Berry" <ber...@upstate.edu>) >Subject: Re: [ccp4bb] "resolution" on PDB web page >To: CCP4BB@JISCMAIL.AC.UK > >My apologies, I guess there is a separate entry for resolution, >and in my depositions it gets filled from the remark 200 records >from CNS xtal_pdb_submission and I never thought to change it. >I guess now the PDB is enforcing the requirement that it >should be "the highest resolution used" and hence the same >as remark 200 and hence redundant. > >I guess if you want to qualify the resolution on line 3 of >remark 2 you need to ask the annotator to do it for you. >(We have some structures that really should be qualified.) > >Miller, Mitchell D. wrote: >> I too believe that the value is set from the >> high resolution limit form data collection or refinement. >> All three numbers (high resolution limit in remark 2, remark 3 >> and Remark 200) are supposed to be consistent and are >> defined as the highest resolution reflection used. >> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html >> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html >> >> Looking at the PDB specification, it shows that there is an option >> to add a free text comment to the remark 2 resolution -- >> "Additional explanatory text may be included starting with the third line of >> the REMARK 2 record. For example, depositors may wish to qualify the >> resolution value provided due to unusual experimental conditions." >> http://www.wwpdb.org/documentation/format33/remarks1.html >> >> We have not done this, but we have in a number of cases >> qualified the resolution by using a lower resolution in the >> title of the entry and further detailing this "nominal" >> resolution in the remark 3 other refinement remarks. E.g. see >> http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0 >> http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk >> >> Regards, >> Mitch >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward >> A. Berry >> Sent: Wednesday, April 25, 2012 6:55 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] "resolution" on PDB web page >> >> We also use the US portal. Can't speak to the solvent content as we never >> had a value much over 70%. >> >> As for the resolution range, I never saw any place to enter this >> user-defined resolution of the structure. >> As far as i know it comes from the record: >> REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 >> which should be the high resolution used in refinement. >> >> I suppose in an "additional remark" you could give the >> optical resolution or the resolution of 90% complete at I/sig=2. >> Or the title could be "The 2.2A resolution structure of protein x", >> never mind that there were a few reflections used at 1.7A. >> eab >> >> Mark J van Raaij 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 >>> >>
