Good idea, but how to get it to catch on without publishing in Science?
JPK
On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud <[log in to unmask]> 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]
>> *******************************************
>>
>>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
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