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 >
