> Let's say you collect data (or rather indices) to 1.4 Ang but the real
> resolution is 2.8 Ang and you use all the data in refinement with no
> resolution cut-off, so there are 8 times as many data. Then your 15
> mins becomes 2 hours - is that still acceptable? It's unlikely that
> you'll see
Hi, as we reported in our paper in Table 1 (actually Supplementary Table 1), at
the end of Scaling 2, completeness in the outer shell after aniso truncation
was 54%. Whilst 96% completeness and I/sigma 0.8 is of course before aniso
truncation. I/sigma after truncation would be higher, but it is
Let's say you collect data (or rather indices) to 1.4 Ang but the real
resolution is 2.8 Ang and you use all the data in refinement with no
resolution cut-off, so there are 8 times as many data. Then your 15
mins becomes 2 hours - is that still acceptable? It's unlikely that
you'll see any differ
I don't think any data should be discarded, and I think that although
we are not there yet, refinement should work directly with the images,
iterating back and forth through all the various levels of data
processing. As I think was pointed out by Wang, even an intensity of 0
provides information pl
http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html
http://scripts.iucr.org/cgi-bin/paper?S0021889800018227
Just collect 360 sweep instead of 180 on a non-decaying crystal and see
Rmerge go up due to increase in multiplicity (and enough with redundancy
term - the extra data is not really
As the K & D paper points out, as the signal/noise declines at higher
resolution, Rmerge goes up to infinity, so there is no sensible way to set a
limiting value to determine "resolution".
That is not to say that Rmerge has no use: as you say it's a reasonably good
metric to plot against image
Please excuse my ignorance, but I cannot understand why Rmerge is unreliable
for estimation of the resolution?
I mean, from a theoretical point of view, <1/sigma> is indeed a better
criterion, but it is not obvious from a practical point of view.
<1/sigma> depends on a method for sigma estimatio
On 1 June 2012 03:22, Edward A. Berry wrote:
> Leo will probably answer better than I can, but I would say I/SigI counts
> only
> the present reflection, so eliminating noise by anisotropic truncation
> should
> improve it, raising the average I/SigI in the last shell.
We always include unmeasure
tions?
Zhijie
--
From: "Edward A. Berry"
Sent: Thursday, May 31, 2012 2:59 PM
To:
Subject: Re: [ccp4bb] Death of Rmerge
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL (I) : 1.21700
I noticed structure 3RKO reported
n? Does it mean that 96% completeness in the spherical shell
of 3.16-3.0A was achieved, by including a great number of I=0 reflections?
Zhijie
--
From: "Edward A. Berry"
Sent: Thursday, May 31, 2012 2:59 PM
To:
Subject: Re: [ccp
In the meantime we could follow Phoebe Rice's example and put
the resolution at I/sigma=2 in REMARK 2 "resolution of structure"
but put the actual bleeding-edge resolution we used in the
reduction and refinement statistics (At least if the PDB
will allow us to have different values in these three
> There are things you can expect to learn from a
> 2Å structure that you are unlikely to learn from a 5Å structure, even
> if equal care has been given to both experiments, so it makes sense
> for the title to give the potential reader an idea which of the two
> cases is presented. But for this p
On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote:
>The resolution limit of the data set has been such an important
> indicator of the quality of the resulting model (rightly or wrongly)
> that it often is included in the title of the paper itself. Despite
> the fact that we now want to
Good idea, but how to get it to catch on without publishing in Science?
JPK
On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud wrote:
>
> On 05/31/12 12:07, Jacob Keller wrote:
>> Alas, how many lines like the following from a recent Science paper
>> (PMID: 22605777), probably reviewer-incited, could
On 05/31/12 12:07, Jacob Keller wrote:
> Alas, how many lines like the following from a recent Science paper
> (PMID: 22605777), probably reviewer-incited, could have been avoided!
>
> "Here, we present three high-resolution crystal structures of the
> Thermus thermophilus (Tth) 70S ribosome in com
Alas, how many lines like the following from a recent Science paper
(PMID: 22605777), probably reviewer-incited, could have been avoided!
"Here, we present three high-resolution crystal structures of the
Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or
YfiA that were refined by
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL(I) : 1.21700
I noticed structure 3RKO reported Rmerge in the last shell greater
than 1, suggesting the police who were defending R-merge were fighting
a losing battle. And this provides a lot of ammunition to those
2 2:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Death of Rmerge
It wasn't doing well lately. So, it was expected.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Thursday, May 31
It wasn't doing well lately. So, it was expected.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Thursday, May 31, 2012 2:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Death of R
Meant to include the following link in the previous message:
http://www.youtube.com/watch?v=9Jn8K8EA7-Q
JPK
On Thu, May 31, 2012 at 1:20 PM, Jacob Keller
wrote:
> Dear Crystallographers,
>
> in case you have not heard, it would appear that the Rmerge statistic
> has died as of the publication
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