] On Behalf Of George M.
Sheldrick [gshe...@shelx.uni-ac.gwdg.de]
Sent: Sunday, March 13, 2011 12:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
Dear James,
I'm a bit puzzled by your negative R-values and unstable behavior. In
practice, whether we refine against
You do also have always to consider why you are doing this calculation -
usually to satisfy a sceptical and possibly ill-informed referee. A major
reason for doing this is to justify including an outer resolution shell of
data (see this BB passim), and for this I have come to prefer the random
Dear James,
I'm a bit puzzled by your negative R-values and unstable behavior. In
practice, whether we refine against intensity or against |F|, it is
traditional to quote an R-factor (called R1 in small molecule
crystallography) R = Sum||Fo|-|Fc|| / Sum|Fo|. Reflections that have
negative
Hi James,
May I just offer a short counter-argument to your case for not including
weak reflections in the merging residuals?
Unlike many people I rather like Rmerge, not because it tells you how good
the data are, but because it gives you a clue as to how well the unmerged
measurements agree
Although George does not mention anything about data reduction programs,
I take from his description that common small-molecule data processing
packages (SAINT, others?), have also been modernized to record all data
(no I/sigmaI 2 or 3 cutoff). I agree with him that this is a good
thing!
I should probably admit that I might be indirectly responsible for the
resurgence of this I/sigma 3 idea, but I never intended this in the
way described by the original poster's reviewer!
What I have been trying to encourage people to do is calculate R factors
using only hkls for which the
Could you please expand on your statement that small-molecule data has essentially no weak
spots.? The small molecule data sets I've worked with have had large numbers of unobserved
reflections where I used 2 sigma(I) cutoffs (maybe 15-30% of the reflections). Would you consider those
weak
Yes, I would classify anything with I/sigmaI 3 as weak. And yes, of
course it is possible to get weak spots from small molecule crystals.
After all, there is no spot so strong that it cannot be defeated by a
sufficient amount of background! I just meant that, relatively
speaking, the
Since small molecules are being discussed maybe I should comment. A widely
used small molecule program that I don't need to advertise here refines
against all measured intensities unless the user has imposed a resolution
cutoff. It prints R values for all data and for I2sig(I) [F4sig(F)].
The
Dear Colleagues,
Agreed! There is a wider point though which is that the 3D structure and data
can form a potential for further analysis and thus the data and the structure
can ideally be more than the current paper's contents. Obviously artificially
high I/ sig I cut offs are both
that version. The reason may be that a
licensed, non-expiring version was used - make sure you always rather
use the latest version available!
Original Message
Subject: [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]
Date: Thu, 3 Mar 2011 10:45:03 -0700
From: Maia Cherney ch...@ualberta.ca
Dear Roberto,
Overnight I recall an additional point:-
In chemical crystallography, where standard uncertainties are
routinely avaliable for the molecular model from the full matrix
inversion in the model refinement, it is of course possible to keep
extending your resolution until your bond
Dear all,
just to say that I really appreciate and thank the many people who spent time
responding to my issue. I have read with much interest (and sometimes with fun)
all comments and suggestions, very interesting and useful.
Thanks a lot,
Bye,
Roberto.
Roberto Battistutta
Associate Professor
This is very closely related to the way in which I would like to think about
this: if you consider adding another thin shell of data, are you adding any
significant information? Unfortunately as Garib Murshudov has pointed out, we
don't have any reliable way of estimating the information
hi
Recently on a paper I submitted, it was the editor of the journal who wanted
exactly the same thing. I never argued with the editor about this (should have
maybe), but it could be one cause of the epidemic that Bart Hazes saw
best regards
Marjolein
On Mar 3, 2011, at 12:29 PM,
Subject: [Fwd: Re: [ccp4bb] I/sigmaI of 3.0 rule]
Date: Thu, 3 Mar 2011 10:45:03 -0700
From: Maia Cherney ch...@ualberta.ca
Original Message
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
Date: Thu, 03 Mar 2011 10:43:23 -0700
From: Maia Cherney ch...@ualberta.ca
Am 04.03.2011 11:11, schrieb Kay Diederichs:
There is nothing wrong with R_meas of 147.1% since, as others have said,
R_meas is not limited to 59% (or similar) as a refinement R-factor is.
Rather, R_meas is computed from a formula that has a denominator which
in the asymptotic limit (noise)
Dear Phil,
I completely agree with you, your words seem to me the best
philosophical outcome of the discussion and indicate the right
perspective to tackle this topic. In particular you write In the end, the
important question as ever is does the experimental data support the
conclusions drawn
No - and I dont think it is accepted practice now either..
I often use I/SigI 1.5 for refinement..
Look at your Rfactor plots from REFMAC - if they look reasonable at
higher resolution use the data
Eleanor
On 03/03/2011 11:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer
Roberto,
The reviewer's request is complete nonsense. The problem is how to best and
politely respond so as not to prevent the paper from being accepted. Best would
be to have educated editors who could simply tell you to ignore that request.
Since this issue comes up quite often still, I
Dear Roberto,
As indicated by others in reply to you the current best practice in
protein crystallography is not a rigid application of such a cut off
criterion. This is because there is such a diverse range of crystal
qualities. However in chemical crystallography where the data quality
from such
On Thu, 2011-03-03 at 12:29 +0100, Roberto Battistutta wrote:
Does anyone know the origin or the theoretical basis of this I/sigmaI
3.0 rule for an appropriate resolution?
There is none. Did editor ask you to follow this suggestion? I
wonder if there is anyone among the subscribers of this bb
There seem to be quite a few rule followers out there regarding resolution
cutoffs. One that I have encountered several times is reviewers objecting to
high Rsym values (say 60-80% in the last shell), which may be even worse than
using some fixed value of I/sigI.
On 3/3/11 9:55 AM, Ed
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I have
processed (so far) there is a break in the curve and the curve shoots
up. To near vertical. This inflexion point is where I decide to place
the high
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) I/sigmaI and not I/sigmaI.
A review of similar articles in the same journal will show what is typical
for the journal. I think you will find that the I/sigmaI cutoff varies.
This information can be used
My preferred criterion is the half-dataset correlation coefficient output by
Scala (an idea stolen from the EM guys): I tend to cut my data where this falls
to not less than 0.5.
The good thing about this is that it is independent of the vagaries of
I/sigma (or rather of the SD estimation) and
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
There seems to be an epidemic of papers with I/Sigma 3 (sometime much
larger). In fact such cases have become so frequent that I fear some people
start to believe that this is the proper procedure. I don't know where that
has come from as the I
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I
have
processed (so far) there is a break in the curve and the curve shoots
up. To near
On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote:
I don't know what has caused this wave of high I/Sigma threshold use
but
here are some ideas
It may also be related to what I feel is recent revival of the
significance of the R-values in general. Lower resolution cutoffs in
this context
Does the position of this inflection point depend on the redundancy? Maybe it
does not; for high-redundancy data one would simply get a much higher
corresponding Rsym.
On 3/3/11 11:13 AM, Ed Pozharski epozh...@umaryland.edu wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
On Thu, 2011-03-03 at 09:34 -0600, Jim Pflugrath wrote:
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) I/sigmaI and not I/sigmaI.
A review of similar articles in the same journal will show what is
typical
for the journal. I think you will find
: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Thursday, March 03, 2011 8:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote:
I don't know what has caused this wave of high I/Sigma
Hi,
I don't think XDS generates an Rpim value, does it? The XDS CORRECT
strep provides the old fashioned Rsym (R-FACTOR) plus R-meas and Rmrgd-F.
The curves look all the same though
Fred.
Ed Pozharski wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I
Discussions of I/sigma(I) or less-than cutoffs have been going on for at least
35 years. For example, see Acta Cryst. (1975) B31, 1507-1509. I was taught by
my elders (mainly Lyle Jensen) that less-than cutoffs came into use when
diffractometers replaced film methods for small molecule work,
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Thursday, March 03, 2011 8:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote:
I don't know
a license.
-
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bart
Hazes
Sent: Thursday, March 03, 2011 7:08 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
There seems
I take the point about a tendency in those days to apply sigma cutoffs to get
lower R values, which were erroneously expected to indicate better structures.
I wonder how many of us remember this paper by Arnberg et al (1979) Acta Cryst
A35, 497-499, where it is shown for (small molecule)
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
determined regularized problem! Just
as easy as running a gel!
Best BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ed Pozharski
Sent: Thursday, March 03, 2011 8:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
We should compile this discussion and send it as compulsive reading to journal
editors...;-)
Bert
On 3/3/11 12:07 PM, Simon Phillips s.e.v.phill...@leeds.ac.uk wrote:
I take the point about a tendency in those days to apply sigma cutoffs to get
lower R values, which were erroneously
When will we finally jettison Rsym/Rcryst/Rmerge?
1. Perhaps software developers should either not even calculate the
number, or hide it somewhere obscure, and of course replacing it with
a better R flavor?
2. Maybe reviewers should insist on other R's (Rpim etc) instead of Rmerge?
JPK
PS is
?) and reprocess the data. Maybe one of our data
collection specialist should comment on that.
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Maia
Cherney
Sent: Thursday, March 03, 2011 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I
Original Message
Subject:Re: [ccp4bb] I/sigmaI of 3.0 rule
Date: Thu, 03 Mar 2011 10:43:23 -0700
From: Maia Cherney ch...@ualberta.ca
To: Oganesyan, Vaheh oganesy...@medimmune.com
References: 2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it
4d6faed8.7040
just to clarify that, at least in my case, my impression is that the editor was
fair, I was referring only to the comment of one reviewer.
Roberto
Roberto Battistutta
Associate Professor
Department of Chemistry
University of Padua
via Marzolo 1, 35131 Padova - ITALY
tel. +39.049.8275265/67
To: CCP4BB@JISCMAIL.AC.UK
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,
Relatively recent statistics on I/sigmaI and Rmerge in PDB deposits are
presented in two following publications:
1.Benefits of structural genomics for drug discovery research.
Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W.
Infect Disord Drug Targets. 2009 Nov;9(5):459-74.
03, 2011 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
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
data collection specialist should comment on that.
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Maia Cherney
Sent: Thursday, March 03, 2011 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
I have
specialist should comment on that.
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Of Maia Cherney
Sent: Thursday, March 03, 2011 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule
I have to resend my statistics
03, 2011 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
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
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
not sure whether this option has been mentioned before ...
i think what we really would like to do is decide by the quality of the
density. i see that this is difficult.
so, short of that ... how about the figure of merit in refinement ?
wouldn't the fom reflect how useful our data really are ?
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