This HKL2000 (scalepack) feature is actually extremely sensible: an
Rmerge that high is mathematically meaningless, it quite literally tells
you nothing at all about he signal in your data.
So I second James's advice: just put "n/a" in your table 1.
If the reviewer complains, point them to Karplus & Diederichs, Science,
2012, and Evans and Murshudov, ActaD, 2013, and tell them to join us in
the 21st century.
On 14/08/2013 16:41, Jeffrey, Philip D. wrote:
Hello Yafang,
The answer lies in the fact that you used HKL2000. Scalepack has a
long standing "feature" where it reports Rmerge > 100% as zero. Quite
why they do that is a mystery, but your Rmerge in the outermost shell
is NOT zero - the Rmerge for the lower resolution shells will show up
as non-zero if Rmerge < 100%.
That feature is overdue for a fix.
Alternatively export your scaled data with NO MERGE ORIGINAL INDEX and
import into CCP4 via Pointless and have Scala or Aimless report the
correct statistics. Reprocessing the data using XDS or Mosflm will
ultimately lead you to scaling the data with a program that doesn't
have that bug. If you do this, report Rmeas rather than Rmerge, the
former being a better measure.
Phil Jeffrey
Princeton
------------------------------------------------------------------------
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Yafang Chen [yafangche...@gmail.com]
*Sent:* Wednesday, August 14, 2013 11:32 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Rmerge of the last shell is zero
Dear All,
Here are some more details about the question I asked earlier about
"Rmerge is 0 in the last shell". I processed the data using HKL2000.
The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8
(2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last
shell, I preferred not to cut back the resolution any more. But I
don't know how to explain Rmerge in the last shell being 0. Besides, I
am wondering if this data is publishable (with Rmerge being 0 in the
last shell). Thank you so much for your help!
Best,
Yafang
On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen <yafangche...@gmail.com
<mailto:yafangche...@gmail.com>> wrote:
Dear All,
I recently processed a dataset, in which I/sigmaI of the last
shell is 2.3, while Rmerge of the last shell is 0. Does anyone
know why the Rmerge is 0? The completeness is 100 (100). Thank you
so much for your help in advance!
Best,
Yafang
--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907
--
Yafang Chen
Graduate Research Assistant
Mesecar Lab
Department of Biological Sciences
Purdue University
Hockmeyer Hall of Structural Biology
240 S. Martin Jischke Drive
West Lafayette, IN 47907
