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
half
shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of George M.
> Sheldrick [gshe...@shelx.uni-ac.gwdg.de]
> Sent: Sunday, March 13, 2011 12:11 AM
> To: CCP4B
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 measu
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 wit
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! An
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 I>2sig(I) [F>4sig(F)].
The
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
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
"we
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 s
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 cut offs are both unfortunate for the
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
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) appr
- Original Message
> Subject: [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]
> Date: Thu, 3 Mar 2011 10:45:03 -0700
> From: Maia Cherney
>
>
>
> Original Message --------
> Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule
> Date: Thu, 03 Mar 2011 10:43:23
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, Roberto
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 content
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
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 distanc
ce 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
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 ?
half
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.
Maia Cherney wrote:
Dear Bernhard
I am wondering where I should cut my data off. Here is the
statistics from XDS processing.
lieve 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
On Thu, 2011-03-03 at 17:20 +0100, Vellieux Frederic wrote:
> The curves look all the same though
Right. Actually, my suggestion was a little dumb - Rpim and Rmeas only
differ by a constant factor, so they will behave the same way
resolution-wise.
--
"I'd jump in myself, if I weren't so good
>>> 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: Thursda
K] 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.
Maia Cherney wrote:
Dear Bernhard
I am wondering where I should cut my data off. Here is the
statistics fro
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.
> >
> >Maia Cherney wro
t; >
> >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
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.
...@ualberta.ca]
Sent: Thursday, March 03, 2011 9:58 AM
To: hofkristall...@gmail.com
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule
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 Rm
3 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
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
fax.
Original Message
Subject:Re: [ccp4bb] I/sigmaI of >3.0 rule
Date: Thu, 03 Mar 2011 10:43:23 -0700
From: Maia Cherney
To: Oganesyan, Vaheh
References: <2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it>
<4d6faed8.7040...@ualberta.ca>
<021
t exactly?) 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: [ccp4
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 th
We should compile this discussion and send it as compulsive reading to journal
editors...;-)
Bert
On 3/3/11 12:07 PM, "Simon Phillips" wrote:
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 str
o: 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 threshold use
>> but here are some ideas
>>
>
> It may also be rela
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
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) struc
nse.
-
-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 to be an epidemic of papers with I/Sig
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 ru
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,
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 deci
---
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 what has caused this w
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) and not /.
>
> A review of similar articles in the same journal will show what is
> typical
> for the journal. I think you will find that the c
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" wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
> For myself, I decid
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 cont
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 ver
without 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 r
alf Of
> Roberto Battistutta
> Sent: Thursday, March 03, 2011 5:30 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] I/sigmaI of >3.0 rule
>
> Dear all,
> I got a reviewer comment that indicate the "need to refine the structures at
> an appropriate resolution (I/si
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Roberto Battistutta
Sent: Thursday, March 03, 2011 5:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] I/sigmaI of >3.0 rule
Dear all,
I got a reviewer comment that indicate the "need to refine the structures at
an appropriate re
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 res
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/Sigma ~ 2 criterion has been
established long ag
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 Pozha
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 t
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
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 think
Ciao Roberto B.
You might want to cite:
Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. Epub 2010 Aug
13.
Inclusion of weak high-resolution X-ray data for improvement of a group II
intron structure.
Wang J.
Department of Molecular Biophysics and Biochemistry, Yale University,
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 com
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 usi
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