t; -Original Message-
> From: CCP4 bulletin board On Behalf Of Kay
> Diederichs
> Sent: Tuesday, March 10, 2020 2:48 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [3dem] Which resolution?
>
> I'd say that it depends on your state of knowledge, and on their
hat we can ensure such a mistake does not occur in the future.
-Original Message-
From: CCP4 bulletin board On Behalf Of Kay Diederichs
Sent: Tuesday, March 10, 2020 2:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [3dem] Which resolution?
I'd say that it depends on your state of
wishes,
Gergely
-Original Message-
From: CCP4 bulletin board On Behalf Of Bohdan Schneider
Sent: March 12, 2020 11:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [3dem] Which resolution?
Hello,
B-factors actually do have a physical meaning which is at least to some extent
reflected by
Hello,
B-factors actually do have a physical meaning which is at least to some
extent reflected by the crystal structures as refined. This can be
demonstrated at higher resolution structures: when we created three
tiers of structures, better than 1.9 Å, 1.9-2.4 Å, and 2.4-3.0 Å,
structures in
resting discussions
Colin
From: CCP4 bulletin board On Behalf Of Randy Read
Sent: 09 March 2020 12:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [3dem] Which resolution?
Hi Alexis,
A brief summary of the relevant points in the paper that Pavel mentioned
(https://journals.iuc
If this is the case, why can't we use model B factors to validate our
structure? I know some people are skeptical about this approach because B
factors are refinable parameters.
Rangana
It is not clear to me exactly what you are asking.
B factors _should_ be validated, precisely because they
;>> contrasts can occur and, if you want to see features with only a
>>> small contrast above the surroundings then I think the half bit
>>> threshold would be inappropriate.
>>>
>>> It would be good to see a clear message from the MX and EM
>>> com
chnique/problem dependent.
We might then progress from the bronze age to the iron age.
Regards
Colin
*From:*CCP4 bulletin board *On Behalf Of
*Alexis Rohou
*Sent:* 21 February 2020 16:35
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] [3dem] Which resolution?
Hi all,
For those bewild
Well, in the example I made the individual atomic B factors, the Wilson
B, and "true B-factor" were all the same thing. Keeps it simple.
But to be clear, yes: the B factors at the end of refinement are not the
"true B-factors", they are our best estimation of them. Given that no
protein mode
roundings
> then I think the half bit threshold would be inappropriate.
>
>
>
> It would be good to see a clear message from the MX and EM communities as to
> why an information content threshold of ½ a bit is generally appropriate for
> these techniques and an acknowl
AC.UK>
On Behalf Of colin.n...@diamond.ac.uk<mailto:colin.n...@diamond.ac.uk>
Sent: 17 February 2020 11:26
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
Dear all.
Would it help to separate out the issue of t
n age.
>
>
>
> Regards
>
> Colin
>
>
>
>
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Alexis
> Rohou
> *Sent:* 21 February 2020 16:35
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [3dem] Which resolution?
>
>
>
> Hi all,
&
Just a note: James Holton said "true B-factor" not "true B-factors".
I believe he was talking about the overall B not the individual B's.
Dale Tronrud
On 3/8/2020 3:25 PM, Rangana Warshamanage wrote:
> Sorry for not being clear enough.
> If B-factors at the end of refinement are the "true B-f
Sorry for not being clear enough.
If B-factors at the end of refinement are the "true B-factors" then they
represent a true property of data. They should be good enough to assess the
model quality directly. This is what I meant by B factor validation.
However, how far are the final B-factors simila
On Sunday, 8 March 2020 01:08:32 PDT Rangana Warshamanage wrote:
> "The best estimate we have of the "true" B factor is the model B factors
> we get at the end of refinement, once everything is converged, after we
> have done all the building we can. It is this "true B factor" that is a
> property
we can use model B factors to validate structures - see
Analysis and validation of macromolecular B values
R. C. Masmaliyeva and G. N. Murshudov
Acta Cryst. (2019). D75, 505-518
https://doi.org/10.1107/S2059798319004807
HTH
Kay
On Sun, 8 Mar 2020 09:08:32 +, Rangana Warshamanage
wrote:
"The best estimate we have of the "true" B factor is the model B factors
we get at the end of refinement, once everything is converged, after we
have done all the building we can. It is this "true B factor" that is a
property of the data, not the model, "
If this is the case, why can't we use mod
James answer seems right, and make abject sense. -and makes sense by experience
too..
Bob
Robert Stroud
str...@msg.ucsf.edu
> On Mar 7, 2020, at 12:01 PM, James Holton wrote:
>
> Yes, that's right. Model B factors are fit to the data. That Boverall gets
> added to all atomic B factors in
James,
> On 7 Mar 2020, at 21:01, James Holton wrote:
>
> Yes, that's right. Model B factors are fit to the data. That Boverall gets
> added to all atomic B factors in the model before the structure is written
> out, yes?
Almost true. It depends how the programs are written. In MAIN this is
Yes, that's right. Model B factors are fit to the data. That Boverall
gets added to all atomic B factors in the model before the structure is
written out, yes?
The best estimate we have of the "true" B factor is the model B factors
we get at the end of refinement, once everything is converge
James,
The case you’ve chosen is not a good illustration of the relationship between
atomic B and resolution. The problem is that during scaling of Fcalc to Fobs
also B-factor difference between the two sets of numbers is minimized. In the
simplest form with two constants Koverall and Bovera
ess in the 3.0 A bin. Now we are saying we have a
> >>> 3.0 A data set when we can prove statistically that a few
> >>> non-background counts fell into the sum of all spot areas at 3.0 A.
> >>> These are not the same thing.
> >>>
> >>> Don't get
tion.
The question, if referring to an information threshold for nominal
resolution, could be “Is there significant information in the data at
the required contrast and resolution?”. Then “Can one obtain this
information at a dose below any radiation damage limit”
Keep posting!
Regards
Colin
*From
gt;> Then do it again well above the absorption edge. The second one gives
>> much greater Bijvoet differences despite the fact that the nominal
>> resolution is the same. I doubt whether anyone doing this would be
>> misled by this as they would examine the statistics for the
endent.
We might then progress from the bronze age to the iron age.
Regards
Colin
*From:*CCP4 bulletin board
<mailto:CCP4BB@JISCMAIL.AC.UK> *On Behalf Of *Alexis Rohou
*Sent:* 21 February 2020 16:35
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*S
threshold is
technique/problem dependent.
We might then progress from the bronze age to the iron age.
Regards
Colin
From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>
On Behalf Of Alexis Rohou
Sent: 21 February 2020 16:35
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK&
To: CCP4BB@JISCMAIL.AC.UK
Cc: Nave, Colin (DLSLtd,RAL,LSCI)
Subject: Re: [ccp4bb] [3dem] Which resolution?
In my opinion the threshold should be zero bits. Yes, this is where CC1/2 = 0
(or FSC = 0). If there is correlation then there is information, and why throw
out information if there is
threshold is technique/problem dependent.
We might then progress from the bronze age to the iron age.
Regards
Colin
*From:*CCP4 bulletin board *On Behalf Of
*Alexis Rohou
*Sent:* 21 February 2020 16:35
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] [3dem] Which resolution?
Hi all
absolutely.
jon
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Gerard Bricogne
Gesendet: Sonntag, 23. Februar 2020 20:42
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [3dem] Which resolution?
Gentlemen,
Please consider for a moment that by such intemperate
A very good point, Gerard, but maybe too late. It seems to me that a
lot of microscopists have already given up this abundantly discussed
question. They just call everything atomic resolution irrespective of
whatever numerical value they arrive at by whatever means.
All best.
Andreas
On
Gentlemen,
Please consider for a moment that by such intemperate language and
tone, you are making a topic of fundamental importance to both the MX and
the EM communities into a no-go area. This cannot be good for anyone's
reputation nor for the two fields in general. It has to be possible to
Hi Carlos Oscar and Jose-Maria,
I choose to answer you guys first, because it will take little of my time
to counter your criticism and because I have long since been less than
amused by your published, ill-conceived criticism:
“*Marin, I always suffer with your reference to sloppy statistics. If
AC.UK
Subject: Re: [ccp4bb] [3dem] Which resolution?
Hi all,
For those bewildered by Marin's insistence that everyone's been messing up
their stats since the bronze age, I'd like to offer what my understanding of
the situation. More details in this thread from a few years ago on t
Hi all,
For those bewildered by Marin's insistence that everyone's been messing up
their stats since the bronze age, I'd like to offer what my understanding
of the situation. More details in this thread from a few years ago on the
exact same topic:
https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-A
2019 CCP4 study weekend paper
Regards
Colin
From: Randy Read
Sent: 20 February 2020 11:45
To: Nave, Colin (DLSLtd,RAL,LSCI)
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] [3dem] Which resolution?
Dear Colin,
Over the last few years we've been implementing measures of information ga
f
> <http://www.mt-archive.info/50/SciAm-1949-Weaver.pdf>
>
> Sorry for the long reply – but at least some of it was requested!
>
> Colin
>
>
>
> From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of colin.n...@diamond.ac.uk
> <m
.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [3dem] Which resolution?
Hi All,
How is the 'correct' resolution estimation related to the estimated error on
some observed hydrogen bond length of interest, or an error on the estimated
occupancy of a ligand or conform
Hi Pawel,
We can indeed agree to disagree upon many basic things in life. We
apparently disagree on the basic assumptions upon which you choose to build
your science! What I am criticising is the very foundation you use to
construct your science, namely the flawed Frank & Al-Ali (1975) formula
r
restricted lens aperture.
>
>
>
> Good debate though.
>
>
>
> Colin
>
> *From:* John R Helliwell
> *Sent:* 17 February 2020 16:36
> *To:* Nave, Colin (DLSLtd,RAL,LSCI)
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolut
well
> Sent: 17 February 2020 16:36
> To: Nave, Colin (DLSLtd,RAL,LSCI)
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
> Hi Colin,
> Neutrons are applied to the uranyl hydrides so as to make their scattering
> lengths much more e
; FRC. If you can comment on this in your *Why-o-Why didactical crusade, I
> might even register for a twitter account!*
>
> *Regards*
>
> *Colin*
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Marin
> van Heel
> *Sent:* 17 February 2020 13:29
Sent: 17 February 2020 16:36
To: Nave, Colin (DLSLtd,RAL,LSCI)
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
Hi Colin,
Neutrons are applied to the uranyl hydrides so as to make their scattering
lengths much more equal than with X-rays, and so side step
t;>
On Behalf Of Marin van Heel
Sent: 17 February 2020 13:29
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [3dem] Which resolution?
Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)
Resolution in the sense of the Abbe Diffraction Limit
uraged from applying some I/sigI type cut off.
>
> Cheers
> Colin
>
>
>
> From: John R Helliwell
> Sent: 17 February 2020 12:09
> To: Nave, Colin (DLSLtd,RAL,LSCI)
> Subject: Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?
>
> Hi Colin,
> I think the ph
: [ccp4bb] [3dem] Which resolution?
Hi Colin,
I think the physics of the imaging and the crystal structure analysis,
respectively without and with Fourier termination ripples, are different. For
the MX re Fourier series for two types of difference map see our contribution:-
http://scripts.iucr.org/cgi
Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)
Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh
*Criterion
are part of what we would now call the theory of linear systems, and are
described by a “transfer function”. “Fourier Optics” covers the theory of
databases will simply search for
the structure with the highest named resolution. It might be difficult to send
these users to re-education camps.
Regards
Colin
From: CCP4 bulletin board On Behalf Of Petrus Zwart
Sent: 16 February 2020 21:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [3dem] Which
Hi All,
How is the 'correct' resolution estimation related to the estimated error
on some observed hydrogen bond length of interest, or an error on the
estimated occupancy of a ligand or conformation or anything else that has
structural significance?
In crystallography, it isn't really (only in s
Dear Pawel and All others
This 2010 review is - unfortunately - largely based on the flawed
statistics I mentioned before, namely on the a priori assumption that the
inner product of a signal vector and a noise vector are ZERO (an
orthogonality assumption). The (Frank & Al-Ali 1975) paper we
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