I was confused because it seemed like CC1/2 wasn't very informative at
lower resolution since (in my datasets) they were all 99.9-100. So if
i've understood this correctly (and i'm honestly not sure that i have)
could CC1/2 be useful to show the quality of low resolution data, given
more precision?
On 07/12/2012 18:14, Zbyszek Otwinowski wrote:
> The difference between one and the correlation coefficient is a square
> function of differences between the datapoints. So rather large 6%
> relative error with 8-fold data multiplicity (redundancy) can lead to
> CC1/2 values about 99.9%.
> It is just the nature of correlation coefficients.
>
> Zbyszek Otwinowski
>
>
>
>> Related to this, I've always wondered what CC1/2 values mean for low
>> resolution. Not being mathematically inclined, I'm sure this is a naive
>> question, but i'll ask anyway - what does CC1/2=100 (or 99.9) mean?
>> Does it mean the data is as good as it gets?
>>
>> Alan
>>
>>
>>
>> On 07/12/2012 17:15, Douglas Theobald wrote:
>>> Hi Boaz,
>>>
>>> I read the K&K paper as primarily a justification for including
>>> extremely weak data in refinement (and of course introducing a new
>>> single statistic that can judge data *and* model quality comparably).
>>> Using CC1/2 to gauge resolution seems like a good option, but I never
>>> got from the paper exactly how to do that. The resolution bin where
>>> CC1/2=0.5 seems natural, but in my (limited) experience that gives
>>> almost the same answer as I/sigI=2 (see also K&K fig 3).
>>>
>>>
>>>
>>> On Dec 7, 2012, at 6:21 AM, Boaz Shaanan <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm sure Kay will have something to say about this but I think the
>>>> idea of the K & K paper was to introduce new (more objective) standards
>>>> for deciding on the resolution, so I don't see why another table is
>>>> needed.
>>>>
>>>> Cheers,
>>>>
>>>>
>>>>
>>>>
>>>> Boaz
>>>>
>>>>
>>>> Boaz Shaanan, Ph.D.
>>>> Dept. of Life Sciences
>>>> Ben-Gurion University of the Negev
>>>> Beer-Sheva 84105
>>>> Israel
>>>>
>>>> E-mail: [log in to unmask]
>>>> Phone: 972-8-647-2220 Skype: boaz.shaanan
>>>> Fax: 972-8-647-2992 or 972-8-646-1710
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ________________________________________
>>>> From: CCP4 bulletin board [[log in to unmask]] on behalf of Douglas
>>>> Theobald [[log in to unmask]]
>>>> Sent: Friday, December 07, 2012 1:05 AM
>>>> To: [log in to unmask]
>>>> Subject: [ccp4bb] refining against weak data and Table I stats
>>>>
>>>> Hello all,
>>>>
>>>> I've followed with interest the discussions here about how we should be
>>>> refining against weak data, e.g. data with I/sigI << 2 (perhaps using
>>>> all bins that have a "significant" CC1/2 per Karplus and Diederichs
>>>> 2012). This all makes statistical sense to me, but now I am wondering
>>>> how I should report data and model stats in Table I.
>>>>
>>>> Here's what I've come up with: report two Table I's. For comparability
>>>> to legacy structure stats, report a "classic" Table I, where I call the
>>>> resolution whatever bin I/sigI=2. Use that as my "high res" bin, with
>>>> high res bin stats reported in parentheses after global stats. Then
>>>> have another Table (maybe Table I* in supplementary material?) where I
>>>> report stats for the whole dataset, including the weak data I used in
>>>> refinement. In both tables report CC1/2 and Rmeas.
>>>>
>>>> This way, I don't redefine the (mostly) conventional usage of
>>>> "resolution", my Table I can be compared to precedent, I report stats
>>>> for all the data and for the model against all data, and I take
>>>> advantage of the information in the weak data during refinement.
>>>>
>>>> Thoughts?
>>>>
>>>> Douglas
>>>>
>>>>
>>>> ^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
>>>> Douglas L. Theobald
>>>> Assistant Professor
>>>> Department of Biochemistry
>>>> Brandeis University
>>>> Waltham, MA 02454-9110
>>>>
>>>> [log in to unmask]
>>>> http://theobald.brandeis.edu/
>>>>
>>>> ^\
>>>> /` /^. / /\
>>>> / / /`/ / . /`
>>>> / / ' '
>>>> '
>>>>
>>>
>>>
>>
>> --
>> Alan Cheung
>> Gene Center
>> Ludwig-Maximilians-University
>> Feodor-Lynen-Str. 25
>> 81377 Munich
>> Germany
>> Phone: +49-89-2180-76845
>> Fax: +49-89-2180-76999
>> E-mail: [log in to unmask]
>>
>
>
--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [log in to unmask]
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