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<[log in to unmask]>   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<[log in to unmask]>  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: [log in to unmask]
>>>> *******************************************
>>>>
>>>
>>
>>
>>
>> --
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: [log in to unmask]
>> *******************************************
>>
>>
>