Hi Douglas,
Using two Table Is is a good way to show the difference between the two
cut-offs, but I assume you will only discuss one of the models in your
paper. IMO you only need to deposit the high res model, so there should be
no problems with resolution conflicts in the PDB file. The annotators will
probably help you if there is a problem with Rmerge > 1.00.
As for the title of your paper: nobody forces you to put a resolution in it
if it causes to much of a stir.
Cheers,
Robbie
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Boaz Shaanan
Sent: Friday, December 07, 2012 12:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refining against weak data and Table I stats
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/
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