In the meantime we could follow Phoebe Rice's example and put
the resolution at I/sigma=2 in REMARK 2 "resolution of structure"
but put the actual bleeding-edge resolution we used in the
reduction and refinement statistics (At least if the PDB
will allow us to have different values in these three places)
And cite the REM 2 value in the article.
eab
PS - I believe optical resolution actually gives significantly
more optimistic numbers for resolution than extending from
I/sigma=2 to 0.5. The "resolution" we are used to is the d-spacing
of the Fourier components, which is theoretically larger than the
microscopist's definition of resolution (how close objects can
be and still give separate maxima with a minimum between).
Miller, Mitchell D. wrote:
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
On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Rice<[email protected]> 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!
Dale Tronrud wrote:
On 05/31/12 12:07, Jacob Keller wrote:
Alas, how many lines like the following from a recent Science paper
(PMID: 22605777), probably reviewer-incited, could have been avoided!
"Here, we present three high-resolution crystal structures of the
Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or
YfiA that were refined by using data extending to 3.0 Å (I/sI = 1),
3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The
resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å,
respectively."
I don't see how you can avoid something like this. With the new,
higher, resolution limits for data (which are good things) people will
tend to assume that a "2.6 A resolution model" will have roughly the
same quality as a "2.6 A resolution model" from five years ago when
the old criteria were used. K&K show that the weak high resolution
data contain useful information but certainly not as much information
as the data with stronger intensity.
The resolution limit of the data set has been such an important
indicator of the quality of the resulting model (rightly or wrongly)
that it often is included in the title of the paper itself. Despite
the fact that we now want to include more, weak, data than before
we need to continue to have a quality indicator that readers can
use to assess the models they are reading about. While cumbersome,
one solution is to state what the resolution limit would have been
had the old criteria been used, as was done in the paper you quote.
This simply gives the reader a measure they can compare to their
previous experiences.
Now would be a good time to break with tradition and institute
a new measure of quality of diffraction data sets. I believe several
have been proposed over the years, but have simply not caught on.
SFCHECK produces an "optical resolution". Could this be used in
the title of papers? I don't believe it is sensitive to the cutoff
resolution and it produces values that are consistent with what the
readers are used to. With this solution people could include whatever
noisy data they want and not be guilty of overstating the quality of
their model.
Dale Tronrud
JPK
On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry<[email protected]> wrote:
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL (I) : 1.21700
I noticed structure 3RKO reported Rmerge in the last shell greater
than 1, suggesting the police who were defending R-merge were fighting
a losing battle. And this provides a lot of ammunition to those
they are fighting.
Jacob Keller wrote:
Dear Crystallographers,
in case you have not heard, it would appear that the Rmerge statistic
has died as of the publication of PMID: 22628654. Ding Dong...?
JPK
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [email protected]
*******************************************
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [email protected]
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