Our policy is to request the pdb to update the stated resolution limit
after the deposition's gone through.
That said, I suspect it did not happen for many of our structures, because:
1) it's not part of the deposition mechanism, i.e. easy to forget.
2) the various programs (especially integration & scaling) don't
really make it obvious that anisotropic limits can be done and are a
good idea.
The real problem is that we crystallographers have not come up with
conventions to distinguish between "effective resolution" and "where are
there still spots with signal" - instead we just conflate them into a
single number.
phx.
On 25/04/2012 15:33, 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
