wishes,
The STARANISO developers.
-
Date: Tue, 16 Oct 2018 16:52:40 +0800
From: Zhang Foggy
Subject: Re: [ccp4bb] R-merge is too high !!
To: CCP4BB@JISCMAIL.AC.UK
Dear All,
Sorry for the late reply. I was out of town in last two weeks.
Again, thanks for your kindly comments, and
Dear All,
Sorry for the late reply. I was out of town in last two weeks.
Again, thanks for your kindly comments, and here are the summary for the
additional comments and my responses:
1. Summary:
The high value of the R-merge might be due to the wrong orientation matrix
(beam center), anisotrop
I once had a problem that seemed to manifest itself similarly to what you
describe. It turned out to be a misindexing of the diffraction origin
by +/- 1 due to a slightly incorrect beam center. You can use the pointless
"centre" option to do a search for the correct center. There's an example
of th
I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for
cutting the data. Rmerge is old approach as it is data redundancy dependent.
Thank you
Rajesh
---x
With regards
Rajesh K. Harijan, Ph.D.
Schramm Laboratory
Albert Einstein College of Medicine
1300 Morris Park Ave., Bro
The fact that chi^2 is approximately 1.0 in all shells says that the deviations
are about what is expected from the error model. The fact that Rpim is much
lower than Rmeas means that you have rather high redundancy. This would seem to
be a case of collecting low dose per image and making up fo
1) Double check space group (run POINTLESS with unmerged data).
2) Process only as much data as needed for full completenes and see what you
get (Rpim is OK, so the means of your structure factors are good, which also is
consistent with your low refinement R factors and the maps).
Best,
Ditlev
It is well known that Rmerge is a terrible criterion for determining a
resolution cutoff, see eg
P.A.Karplus,K.Diederichs,Science336,1030(2012)
As the intensities get weaker at high resolution, Rmerge tends to infinity,
with no sensible cutoff. CC(1/2) is generally considered the best criterion
frames to see what kind
of Rmerges come out then.
Good luck!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zhang
Foggy
Gesendet: Freitag, 28. September 2018 10:10
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] R-merge is too high !!
Dear All,
Sorry for
Dear All,
Sorry for the off-topic.
I recently collected a set of data. The diffraction spots are extremely
sharp. However, When I used HKL3000 to scale it, I get a final resolution
at 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell:
1.59). Then I solve the structure with f
