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 <bshaa...@exchange.bgu.ac.il>
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: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Douglas
Theobald [dtheob...@brandeis.edu]
Sent: Friday, December 07, 2012 1:05 AM
To: CCP4BB@JISCMAIL.AC.UK
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
dtheob...@brandeis.edu
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: che...@lmb.uni-muenchen.de
--
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: che...@lmb.uni-muenchen.de
