Hi, All CCP4BB Users,
I have quite some data sets(~15) collected at different beam intensities,
the individual dataset can diffract to ~3.8 A @I/dI=2. If I combine them,
with AIMLESS in CCP4, the resolution can be extended to ~3A@I/dI=2. But,
the Rmerge or Rpim is way high, in 10s or even 100s.
Dear Charles,
I would ignore (high resolution) R-values for justifying the rsolution
cut-off. If you are talkig about 100s %, I have published data with
Rmeas 500% in the highest resolution shell.
You are quite save cutting the resolution where I/sigI = 2.0, by todays
knowledge this is actually
David, Thanks for providing your data. my CC1/2 is often about 0.6, 0.7
since I cut at I/sigmaI =2.
Tim, you are right. I am conservative on this since I am still a new comer
in this field.
Charles
On Thu, Sep 4, 2014 at 2:36 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear Charles,
I
).
That is the confusion at least on my side.
BR
-Original Message-
From: Manfred S. Weiss [mailto:manfred.we...@helmholtz-berlin.de]
Sent: Thursday, April 17, 2014 8:46 AM
To: b...@hofkristallamt.org
Cc: Bernhard Rupp; CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn
an unresolved mess see the papers/threads on cc1/2, cc*
etc...
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto
Battistutta
Sent: Wednesday, April 16, 2014 5:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge, Rmeas, I/sigma
Hi Roberto,
for my taste the answers so far have not mentioned (or I did not understand
them) that there is a distinction between indicators of the precision of merged
data, and those for the precision of unmerged data.
It is not possible to directly compare (or equate) indicators of one
[There is] a distinction between indicators of the precision of merged data,
and those for the precision of unmerged data.
Let's take a step back - definitions matter:
(i) We have multiple observations of the same, already integrated h: the
'unmerged' data - most important data set which
On Fri, 18 Apr 2014 12:33:30 +0200, Bernhard Rupp hofkristall...@gmail.com
wrote:
[There is] a distinction between indicators of the precision of merged data,
and those for the precision of unmerged data.
Let's take a step back - definitions matter:
(i) We have multiple observations of the
(i) We have multiple observations of the same, already integrated h: the
'unmerged' data - most important data set which SHOULD BE deposited and
rarely is.
yes, fully agree.
Perfect.
I don't quite understand the difference between (ii) and (iii). As soon as
you take the weighted average,
Roberto Battistutta wrote:
Hi,
in the Rupp book the following relation is reported (on pag 415):
Rmerge ≈ 0.8/I/σ(I)
referring to a relation of the linear merging R-value with the signal-to-noise
ratio.
in a 2006 CCP4bb, Manfred Weiss reported:
Rrim (or Rmeas) = 0.8*sd(i)/I
Bernhard Rupp
Hi Ed,
your example seems to be designed to show that the average of reciprocal values
is not the same as the reciprocal of an average value? If that is what you are
alluding to, then please not that the (relatively narrow) Wilson distribution
of intensities has the effect of making the
an unresolved mess see the papers/threads on cc1/2, cc*
etc...
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto
Battistutta
Sent: Wednesday, April 16, 2014 5:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge, Rmeas, I/sigma
).
That is the confusion at least on my side.
BR
-Original Message-
From: Manfred S. Weiss [mailto:manfred.we...@helmholtz-berlin.de]
Sent: Thursday, April 17, 2014 8:46 AM
To: b...@hofkristallamt.org
Cc: Bernhard Rupp; CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn
Hi,
in the Rupp book the following relation is reported (on pag 415):
Rmerge ≈ 0.8/I/σ(I)
referring to a relation of the linear merging R-value with the signal-to-noise
ratio.
in a 2006 CCP4bb, Manfred Weiss reported:
Rrim (or Rmeas) = 0.8*sd(i)/I
so,
First question: is it Rmerge or Rmeas
...
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto
Battistutta
Sent: Wednesday, April 16, 2014 5:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
Hi,
in the Rupp book the following relation
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob
[kell...@janelia.hhmi.org]
Sent: Wednesday, February 12, 2014 10:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge of Images
Dear Crystallographers,
Where can I find the definition of the R
Dear Crystallographers,
Where can I find the definition of the R vs batch reported in scaling?
Specifically I am wondering whether it is cumulative (each new frame versus all
previous ones pooled together) or something else, and also how this metric can
have any meaning on early frames when
Dear All,
The purpose of statistics in the output of Scalepack is to help the
experimenter to assess the data. The question is, what is the purpose of
R-merge statistics and its usefulness when its value exceeds 100%?
When Scalepack was originally written 20 years ago, I made a decision to
Great! and (oops) now I realize what I meant to say was compare cc* with
cc-work and cc-free.
eab
Nat Echols wrote:
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
If you refine once in phenix you can use phenix.cc_star to calculate
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
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
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Yafang,
a mathematically simple answer would be you collected no symmetry
equivalent reflections, although experimentally this is probably
difficult to achieve, unless your space group is P1. If you could tell
the name of the software you used,
multiplicity = 1.0?
On 14 Aug 2013, at 15:59, Yafang Chen 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
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
]
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
: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen
[yafangche...@gmail.com]
Sent: 14 August 2013 16:32
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
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang
Chen [yafangche...@gmail.com]
Sent: 14 August 2013 16:32
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
:* 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
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
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.eduwrote:
If you refine once in phenix you can use phenix.cc_star to calculate cc*
and compare with R and R-free; from the output mtz file and your unmerged
.sca file.
FYI, this should also work with structures refined in
James,
Graeme is right. While I does indeed (approximately) follow a
Gaussian, |I-I| cannot. The absolute value operator keeps it
positive (reflects the negative across the origin), and hence it is a
half Gaussian. Its mean cannot be zero unless the variance is zero.
For standard
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