higher redundancy lowers Rpim because it increases precision. However,
it need not increase accuracy if the observations are not drawn from the
"true distribution". If pathologic behaviour of Rfactor statistics is
due to radiation damage, as I believe is often the case, we are
combining observations that are no longer equivalent. If you used long
exposures per image and collected just enough data for a complete data
set you are out of luck. If you used shorter exposures and opted for a
high-redundancy set then you have the option to toss out the last N
images to get rid of the most damaged data, or you can try to compensate
for the damage with zerodose, or whatever the name was of the program, I
think from Wolfgang Kabsch.
Rejecting data is never desirable but I think it may be better than
merging non-equivalent data that can't be properly modeled by a single
structure.
Bart
On 11-03-03 12:34 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
I don't like Rmeas either.
Given the Angst caused by actually useful redundancy, would it not be more
reasonable then to report Rpim which decreases with redundancy? Maybe Rpim
in an additional column would help to reduce the Angst?
BR
Maia
Tim Gruene wrote:
Hello Maia,
Rmerge is obsolete, so the reviewers had a good point to make you
publish Rmeas instead. Rmeas should replace Rmerge in my opinion.
The data statistics you sent show a mulltiplicity of about 20! Did you
check your data for radiation damage? That might explain why your
Rmeas is so utterly high while your I/sigI is still above 2 (You
should not cut your data but include
more!)
What do the statistics look like if you process just about enough
frames so that you get a reasonable mulltiplicity, 3-4, say?
Cheers, Tim
On Thu, Mar 03, 2011 at 10:57:37AM -0700, Maia Cherney wrote:
I see, there is no consensus about my data. Some people say 2.4A,
other say all. Well, I chose 2.3 A. My rule was to be a little bit
below Rmerg 100%. At 2.3A Rmerg was 98.7% Actually, I have published
my paper in JMB. Yes, reviewers did not like that and even made me
give Rrim and Rpim etc.
Maia
Bernhard Rupp (Hofkristallrat a.D.) wrote:
First of all I would ask a XDS expert for that because I don't know
exactly what stats the XDS program reports (shame on me, ok) nor
what the quality of your error model is, or what you want to use the
data for (I guess refinement - see Eleanor's response for that, and use
all data).
There is one point I'd like to make re cutoff: If one gets greedy
and collects too much noise in high resolution shells (like way
below<I/sigI> =
0.8 or so) the scaling/integration may suffer from an overabundance
of nonsense data, and here I believe it makes sense to select a
higher cutoff (like what exactly?) and reprocess the data. Maybe one
of our data collection specialist should comment on that.
BR
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf
Of Maia Cherney
Sent: Thursday, March 03, 2011 9:13 AM
To: [email protected]
Subject: Re: [ccp4bb] I/sigmaI of>3.0 rule
I have to resend my statistics.
Maia Cherney wrote:
Dear Bernhard
I am wondering where I should cut my data off. Here is the
statistics from XDS processing.
Maia
On 11-03-03 04:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer comment that indicate the "need to refine the
structures
at an appropriate resolution (I/sigmaI of>3.0), and re-submit the
revised coordinate files to the PDB for validation.". In the
manuscript I present some crystal structures determined by
molecular replacement using the same protein in a different space
group as search model. Does anyone know the origin or the
theoretical basis of this "I/sigmaI>3.0" rule for an appropriate
resolution?
Thanks,
Bye,
Roberto.
Roberto Battistutta
Associate Professor
Department of Chemistry
University of Padua
via Marzolo 1, 35131 Padova - ITALY tel. +39.049.8275265/67 fax.
+39.049.8275239 [email protected]
www.chimica.unipd.it/roberto.battistutta/
VIMM (Venetian Institute of Molecular Medicine) via Orus 2,
35129 Padova - ITALY tel. +39.049.7923236 fax
+39.049.7923250 www.vimm.it
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