Dear Ed,
Thankyou for this.
Indeed I have not pushed into the domain of as low as 0.4 or CC1/2 as
low as 0.012.
So, I do not have an answer to your query at these extremes.
But I concede I am duly corrected by your example and indeed my email did not
tabulate specifically how far one could inv
On 06/14/2013 07:00 AM, John R Helliwell wrote:
Alternatively, at poorer resolutions than that, you can monitor if the
Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as
more data are steadily added to your model refinements.
Dear John,
unfortunately the behavior of DPIfree
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Steiner,
> Roberto [roberto.stei...@kcl.ac.uk]
> Sent: Friday, June 14, 2013 12:58 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Concerns about statistics
>
> BTW there's a also an
oaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Steiner, Roberto
[roberto.stei...@kcl.ac.uk]
Sent: Friday, June 14, 2013 12:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Concer
Dear Andrea,
Checking the quality of electron density maps has been correctly mentioned
as one adds more data.
In chemical crystallography one can monitor the bond distance and angles
sigmas ie until adding more data at ever higher resolution causes them to
deteriorate in quality.
The equivalent
BTW there's a also an earlier paper (properly cited in Karplus & Diederichs
2012) showing the benefit of weak 'high-resolution' reflections.
Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. doi:
10.1107/S0907444910029938. Epub 2010 Aug 13.
Inclusion of weak high-resolution X-ray
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On 06/14/2013 11:43 AM, Dirk Kostrewa wrote:
> [...] The recommended procedure to include small resolution
> increments in refinement to decide the high resolution cutoff is
> very time-consuming.
... and very subjective: noise can look very unnoisy if
Dear Andrea,
I agree with Tim and still cut the resolution at =2. In my
experience, including higher resolution shells with poorer
signal-to-noise never changed the apparent resolution of the electron
density maps.
In addition, the high resolution limit at =2 coincides very
well with the poin
oard [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Andrea Edwards
> Sent: Thursday, June 13, 2013 17:15
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Concerns about statistics
>
> Hello group,
> I have some rather (embarrassingly) basic questions to ask. Mainly.. when
> deciding the
Tim,
my personal preference always was I/sigI=1. In my Scalepack days, I
always noticed that ~30% of the reflections in the I/sigI=1 shells had
I/sigI>2, and formed an unverified belief that there should be some
information there.
In my experience, CC1/2=0.5 would normally yield I/sigI~1, not 2.
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On 06/13/2013 06:16 PM, Ed Pozharski wrote:
> [...] With that said, I am pretty sure that in vast majority of
> cases structural conclusions derived with I/s=2 vs CC1/2=0.5 vs
> DR=0 cutoff will be essentially the same.
Hi Ed,
in my experience, CC(1
On Thu, 2013-06-13 at 08:44 -0700, Andrea Edwards wrote:
> In this case, the author should report a correlation coefficient along
> with the other standard statistics (I/sigI, Rmerg, Completeness,
> redundancy, ect.)?
Won't hurt.
> What about Rpim instead of Rmerg? and if Rpim is reported, wha
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Dear Andrea,
unless you are desperately longing for resolution, I normally cut the
resolution where I/sigI > 2.0. You should, however, make up your own
rules as to how to determine I/sigI: it must be computed in resolution
shells, and if you choose th
..and Rmerg seems to be meaningless for judging data quality?
- Original Message -
From: "Klaus Fütterer"
To: "Andrea Edwards"
Sent: Thursday, June 13, 2013 8:49:13 AM
Subject: Re: [ccp4bb] Concerns about statistics
Seems you are reviewing a paper at present. If thi
sday, June 13, 2013 8:27:33 AM
Subject: Re: [ccp4bb] Concerns about statistics
The commonly accepted answer is in
Linking crystallographic model and data quality.
Karplus PA, Diederichs K.
Science . 2012 May 25;336(6084):1030-3. doi: 10.1126/science.1218231.
On Thu, Jun 13, 2013 at 8:15 AM, Andrea Edwards wrote:
> I have some rather (embarrassingly) basic questions to ask. Mainly.. when
> deciding the resolution limit, which statistics are the most important? I
> have always been taught that the highest resolution bin should be chosen
> with I/sig no
Hello group,
I have some rather (embarrassingly) basic questions to ask. Mainly.. when
deciding the resolution limit, which statistics are the most important? I have
always been taught that the highest resolution bin should be chosen with I/sig
no less than 2.0, Rmerg no less than 40%, and %Comp
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