Hi David,
you are right, the M in MPR is just a count of “whatever” is averaged to get
the final intensities.
However, from this “inexhaustible thread” it is also clear that there will be
no agreement on what to call this “whatever”
Best, Herman
Von: David Waterman
Gesendet: Freitag, 3.
Dear Herman and David,
This thread seems inexhaustible :-) .
On the matter of "measurement" vs. "observation", we seem again to be
in a situation described by the British idiom "half of one and half-a-dozen"
of the other, i.e. distinct but synonymous terms between which a choice is
Dear Colleagues,
Now that Herman has announced a quietude I thought you might enjoy this quite
short report on a synchrotron radiation issue that came up some years back via
the JSR Main Editors into the IUCr Nomenclature Committee, chaired by Andre
Authier, Past President of the IUCr:-
Hi Herman,
I started googling and ended up completely lost down a rabbit hole (have a
look here if you want to see what I mean:
https://plato.stanford.edu/entries/measurement-science/). As a result I'm
no longer sure I know what the word "measurement" means! I tried to
simplify things with a
Dear David,
Thank you for your reaction. It has become clear to me that although most
people understand what I intended with “measurement”, in practice it is very
much in the eye of the beholder. It was suggested in the BB to use observation
instead, but I am fairly sure that some people will
Dear Ian,
I stand corrected: I should have realized before writing rather than
afterwards that you were surely stressing the formalization (or
formalisation) part.
Cheers,
Navdeep
---
On 02.07.20 22:09, Ian Tickle wrote:
>
> Hi Navdeep
>
> Yes good point, the principle of redundancy (though
Hi Herman,
I like the idea of MPR, but I continue to worry about the term
"measurement". The intensity associated with a particular reflection is a
fit based on a scaling model, and ultimately, depending on your integration
software, may be linked to a weighted sum of two raw measurements: the
Thanks Ian - I think you raise some excellent points - while I think the
general reader (TM) would understand that redundancy and multiplicity mean
broadly the same thing in Table 1, I think having program developers document
_precisely_ what they mean by those values would be very valuable. I
Dear Ian,
Since some very advanced countries still use miles, Fahrenheit and inches, I
did not expect anything to change. It was an escalating discussion in this
thread on data completeness(!) on the use of multiplicity vs redundancy that
made me suggest a different term. Except for an
Well I very much doubt that many software developers are going to trawl
through all their code, comments, output statements & documentation to
change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
agreed on (assuming of course we do manage to come to an agreement, which I
Hi Navdeep
Yes good point, the principle of redundancy (though they wouldn't have used
that term!) has a very long history, but von Neumann did more than anyone
before him to formalise it:
There is probably some justification for the absence of 'reflection' (as used
in crystallography) - in 'purist' Physics. The process
itself is not a 'reflection', despite that it can be macroscopically described
(in first approximation at least, and good enough for finding diffraction spot
Dear Ian,
You seem to be slightly off there: The successful use of repeating
observations to reduce (especially systematic) observational error
predates von Neumann by at least 4 centuries.
One of the first instances of its use was in the 1500s, due to a migrant
scientist working in Denmark and
Dear all
I’ve been persuaded that MPR is a useful name (and see that there are
shortcomings with both “multiplicity” and “redundancy") and I agree with much
of what’s been said most recently in this thread.
BTW, just because the Physics definition of a measurement/quantity/whatever is
given
Dear all,
While following the development of this thread, I am truly amazed how people
cling to names for the number of measurements per reflection whose meaning:
* Depends on the cultural/engineering/scientific context
* Can only be understood by experts
* Where the experts, as
It is hard for us to rise above these cultural differences, so perhaps the
adoption of a third, precisely-defined, and neutral term is indeed
warranted. MPR seems a good start, but it forces us to think about what we
mean by measurement. My feeling is that a diffraction spot can be
measured in
Good morning Jose,
The devil is always on the detail:-
You are of course correct that I had presumed, as Ethan pointed out, a sub 10
fsec pulse.
Neutrons creating magnetic waves, you are again correct, “spin echo“ does
occur, but without damage though as neutrons have such gentle energies
On Wednesday, 1 July 2020 18:50:57 PDT Jose Brandao-Neto wrote:
> Hi Ian, good to hear! Hi everyone, thanks for the etymological - and
> etiological - discussion. I'm good whatever the choice.
>
> John, I beg to differ with the absolute statement that xfels offer damage
> free hkls - back in
Hi Ian, good to hear! Hi everyone, thanks for the etymological - and
etiological - discussion. I'm good whatever the choice.
John, I beg to differ with the absolute statement that xfels offer damage free
hkls - back in 2016 yet another great experimental work, by Inoue et al
since i am not getting shit/shite done may i also point out aluminium/aluminum
On Wednesday, July 1, 2020, 11:52:21 AM PDT, James Holton
wrote:
Sorry to take this thread on a detour/diversion: What I was attempting to point
out below, perhaps unclearly, is that the different
Sorry to take this thread on a detour/diversion: What I was attempting
to point out below, perhaps unclearly, is that the different
interpretations of the word "redundant" are a cultural difference. As a
student of multiple English languages perhaps I can explain:
Few US English speakers
Dear Ian,
I take issue with your assertion below that “the totally precise **scientific**
meaningis an **engineering**” definition.
Science and engineering are not the same. Health and safety leads to the need
in engineering for redundancy and indeed safety factors. In essence, in
I find, when discussing definitions of words, it’s always good to look in the
OED (well, the SOED, I don’t have the big one). For redundant (redundancy
being defined as the state or quality of being redundant), we find:
1. Superabundant, superfluous, excessive. b. Characterised by superfluity
hi ian,
oh no! all those trump fans across the pond will love the "hypothesis of
evolution" idea. they won't know the word "hypothesis" of course, but
unfortunately you might get famous for it anyhow.
cheers
jon
Von: CCP4 bulletin board Im Auftrag von Ian Tickle
Gesendet: Mittwoch, 1. Juli
Yes this seems to be a common misunderstanding, that the meanings of words
such as 'redundancy' have to be the same in an informal non-scientific
context and in a formal technical/scientific context.
So we can say that in an informal context, 'redundancy' means "unnecessary
duplication (or
Dear Kay & Gerard,
the only reason, why I want to count differently, is to distinguish
between true and pseudo-multiplicity. Apparently, I get on thin ice by
trying to define "identical" reflections ... maybe, instead, we should
start working with unmerged data in all programs. If I remember
Dear Dirk,
one cannot fully correct radiation damage. Normal scaling procedures take care
of the average decay by a smooth resolution-dependant function. Zero-dose
extrapolation goes beyond that but needs all symmetry mates - this does not
fulfill your definition of "identical".
If we really
Dear Gerard and Kay,
yes, you are both right - I have totally forgotten radiation damage! And
correcting for this really makes a difference!
However, if radiation damage is corrected for reflections measured at
different time points under the same geometry, does anything speak
against it,
Dear Dirk,
XDS_ASCII.HKL (and equivalent files from other processing software) gives you
all the information that you're after, since every reflection is stored
individually.
However when you analyze that, you will find that in a data set that comprises
less than 360 degrees of rotation, there
Dear Dirk,
Aren't you for getting about radiation damage? The n measurements of
the same hkl with the same geometry would not be equivalent, although they
would enable the tracking of radiation damage without the confounding with
absorption effects that comes from considering
Dear Herman,
I think, your MPR proposal is a great idea and would like to second it!
And I would also like to propose that data processing programs just
average "identical" reflections measured under the same geometry and
count them only once (*), so that, in the end, we will get a realistic
Good morning Jon,
Ah yes that is a good word from quantum mechanics but no it isn’t in the IUCr
Dictionary, nor in the Statistical Descriptors section on Recommendations.
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html
In Laue mode, Xray or neutron, the MPR should be large enough to
Dear Frank,
in general it is not possible to determine the intensity of a reflection from a
single fine slice. One needs slices for the complete reflection.
Also, like Bernard, you are imposing criteria on the MPR, which are not imposed
on the multiplicity/redundancy/abundancy.
All I ask the
Dear Bernard and other bulletin board members,
As Gerard mentioned, current data processing programs and table 1’s do not make
this distinction, but of course, you are free to ask the community to introduce
it.
My proposal to use “measurements per reflections” is not a joke. It exactly
I think it is quite an interesting question in principle for Laue crystallography (now probably only relevant in the neutron world?) since, for example, if one had a crystal in the 432 point group, you could collect an essentially complete dataset with one 'image'. Given that each image can take
Dear Ed,
Concerning your remark that "use of terms redundancy and multiplicity
to describe the same concept is by itself redundant", one could perhaps say
that redundancy is an abstract property of a dataset, while multiplicity is
a numerical attribute. Redundancy is desirable because if
Hello JohnDoes the IUCr dictionary list 'degeneracy'?Jon CooperOn 30 Jun 2020 17:11, Gerard Bricogne wrote:Dear Bernhard,
That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones
Dear Bernhard,
That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones (e.g. in terms of radiation damage only, while the
others would also involve absorption effects). However I am
Gerard, fantastic proposal - let's call it "abundancy"!!!
Which developer will be the first to change their logfile?
On 30/06/2020 16:38, Gerard Bricogne wrote:
Dear Phil,
I would like to make an attempt to not let this question get mired in
exchanges of well-researched linguistic
.…but there is a difference whether I measure the same identical hkl over again
or ‘preferably in more than one symmetry-equivalent position’, to quote the
IUCr. So do we have a MPSR for the same reflection and a MPRR for the related
reflections?
Cacophonically yours,
BR
From: CCP4
Dear Phil,
I would like to make an attempt to not let this question get mired in
exchanges of well-researched linguistic arguments at risk of being drowned
in a cacophony of sound bites :-) .
You refer to the days of SCALA, at which time data were collected on
CCD detectors, whose
Dear Herman,
I think that MPR is a very neat and tidy, excellent, proposal.
Moreover it uses the word “measurements”, and we are an experimental based
science.
I support it.
Great.
Greetings,
John
Emeritus Professor John R Helliwell DSc
> On 30 Jun 2020, at 15:10, Schreuder, Herman /DE
>
Replicate is a good option with its own problems as it can be seen as
referring to exact copy which multiple measurements clearly aren't. It does
have an advantage of being the word used by non-crystallographers though.
As a lame attempt at joke, use of terms redundancy and multiplicity to
Dear BB,
Since there does not seem a generally accepted term for the subject of this
discussions, and since even the IUCR scriptures do not give any guidance, I
would propose to introduce a completely new term:
Measurements per reflection or MPR
This term is politically neutral, should
I changed the annotation from “Redundancy” to “Multiplicity” in Scala, later in
Aimless, after I was taken to task by Elspeth Garman with the argument as
stated, that if it’s redundant why did you bother to measure it?
(this one could run and run …)
Phil
> On 30 Jun 2020, at 14:07, Ian Tickle
I agree about RAID but I would go a lot further. There seems to be some
confusion here over the correct meaning of 'redundant' as used in a
scientific context. I don't think looking it up in an English dictionary
is very helpful. So as has been mentioned the non-scientific and rather
imprecise
By all means, if you still have "disks" you should get rid of them, and
replace them with some modern storage.
On 2020-06-29 21:17, Edward A. Berry wrote:
Now can we get rid of all the superfluous disks in our RAID? Or at
least not replace them when they fail?
On 06/29/2020 06:24 PM,
Dear Colleagues,
In an effort to break this naming deadlock, and with Massimo and Ian not
showing up as yet, I checked the IUCr Dictionary.
“Redundancy“ and “Multiplicity“ are not listed.
The more generic term “Statistical Descriptors“ is though and even offers
Recommendations:-
The people that already use multiplicity are going to find reasons why
it's the superior naming scheme - although the underlying reason has a
lot to do with negative associations with 'redundant', perhaps hightened
in the current environment. And conversely redundant works for many
others -
Or, we could accept the fact that crystallographers are kinda used to
multiplicity of an individual Miller index being different to multiplicity of
observations, and in Table 1 know which one you mean? Given that they add new
information (at the very least to the scaling model) they are
Ok, the analogy is not great because most reflection data sets have some
"fault tolerance" whereas RAID 0 does not. But the point is that anything
that is not an exact copy and brings actual information should not be
considered "redundant"
On Tue, 30 Jun 2020, 09:00 David Waterman, wrote:
>
Reflections are as "redundant" as the disks in a RAID 0 array
On Tue, 30 Jun 2020, 02:49 James Holton, wrote:
> What could possibly go wrong?
>
> -James Holton
> MAD Scientist
>
> On 6/29/2020 6:17 PM, Edward A. Berry wrote:
> > Now can we get rid of all the superfluous disks in our RAID? Or at
What could possibly go wrong?
-James Holton
MAD Scientist
On 6/29/2020 6:17 PM, Edward A. Berry wrote:
Now can we get rid of all the superfluous disks in our RAID? Or at
least not replace them when they fail?
On 06/29/2020 06:24 PM, Andreas Förster wrote:
I like to think that the reflections
Now can we get rid of all the superfluous disks in our RAID? Or at least not
replace them when they fail?
On 06/29/2020 06:24 PM, Andreas Förster wrote:
I like to think that the reflections I carefully measured at high multiplicity are not redundant, which the
dictionary on my computer
Ah…the rise of the replicants …
https://www.youtube.com/watch?v=yWPyRSURYFQ
…and don’t forget the and the Voight-Kampff Test results in Table 1.
Best, BR
From: Pierre Rizkallah
Sent: Monday, June 29, 2020 15:46
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: RE:
You’re missing out on a grand opportunity for iconoclasm here. Try out ‘Degree
of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’. Any other
offerings!
P.
***
Dr Pierre Rizkallah, Senior Lecturer Structural Biology
Institute of
I think it is time to escalate that discussion to crystallographic definition
purists like Massimo or to a logical consistency proponent like Ian who abhors
definitional vacuum
Cheers, BR
From: CCP4 bulletin board On Behalf Of Andreas Förster
Sent: Monday, June 29, 2020 15:24
To:
I like to think that the reflections I carefully measured at high
multiplicity are not redundant, which the dictionary on my computer defines
as "not or no longer needed or useful; superfluous" and the American
Heritage Dictionary as "exceeding what is necessary or natural;
superfluous" and
I have found that the use of "redundancy" vs "multiplicity" correlates
very well with the speaker's favorite processing software. The
Denzo/HKL program scalepack outputs "redundancy", whereas scala/aimless
and other more Europe-centric programs output "multiplicity".
At least it is not as
Phil Jefferey was right about the point group (432), which looks like it represents about 0.7 % of the PDB! I tested the completeness with MOSFLM strategy for various sporadic missetting angles and 11 degrees of data does give you around 90 % completeness or more with redundancy close to 2,
> Oh, and some of us prefer the word 'multiplicity' ;-0
Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive, and not
uniquely defined. It can refer to
a. the position multiplicity (number of equivalent sites per unit cell,
aka Wyckoff-Multiplicity), the only (!) cif
To improve both multiplicity, anomalous signal and dose-proofing from a single
crystal - complementing the thread and papers suggested so far and thinking of
a strategy that covers low symmetry - the excellent approach introduced at the
SLS (Basu et al,
I have no disagreement that anomalous is helpful and very useful data to have.
So I’m in agreement with you and Bernhard without any reservations whatsoever.
It just so happens that 360 degrees of data in the P1 spacegroup does not give
you very good anomalous signal. In my limited experience,
Well, it can still help. I used to be a great fan of inverse-beam expts! Oh, and some of us prefer the word 'multiplicity' ;-0Jon CooperOn 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" wrote:
I would just like to point out that for those of us who have worked too many times with P1
Tom makes a good point. The minimum RS coverage necessary to obtain a unique
data set is just a simple calculation
that involves no experimental reality.
To judge the expected usefulness of the data, you need to have some idea
about the possible errors, random and systematic.
Random is
I would just like to point out that for those of us who have worked too many
times with P1 or P21 that even 360 degrees will not give you 'super' anomalous
differences.
I'm not a minimalist when it comes to data- redundancy is a good thing to have.
cheers, tom
Tom Peat
Proteins Group
Biomedical
1/48th of reciprocal space is the minimum in certain SGs..
Table 6.6 in BMC or
http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
Best, BR
From: CCP4 bulletin board On Behalf Of
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Tuesday, June 23, 2020 08:11
To:
Someone told me there is a cubic space group where you can get away with something like 11 degrees of data. It would be interesting if that's correct. These minimum ranges for data collection rely on the crystal being pre-oriented, which is unheard-of these days, although they can help if someone
Hi Murpholino,
in my opinion (*), the question is neither number of frames nor degrees.
The only thing that matters to your crystal is dose. How many photons does
your crystal take before it dies? Consequently, the question to ask is How
best to use photons. Some people have done exactly that.
The old saying was degrees, not frames. If your frame width is not 1
degree, the result will differ accordingly.
One factor is whether the detector is centered or offset, and whether it
is large enough to get the entire pattern. If the detector is offset,
you are not getting the full
There are lots of places where you could find this information (many textbooks,
articles, etc.) but one that I use for classes is quite good due to ease of
understanding. It’s part of the Proceedings of the CCP4 Study Weekend on Data
Collection and Processing. There are other quite excellent
Well, its not no. of frames but minimum degree of crystal rotation. A goggle
search gave me this article.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557013/
Dhiraj
From: CCP4 bulletin board on behalf of Murpholino
Peligro
Sent: Monday, June 22, 2020 5:03
Hi.
Quick question...
I have seen *somewhere* that to get a 'full dataset we need to collect n
frames':
at least 180 frames if symmetry is X
at least 90 frames if symmetry is Y
at least 45 frames if symmetry is Z
Can somebody point where is *somewhere*?
...also...
what other factors can change
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