Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Navdeep Sidhu]

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 they wouldn't have
> used that term!) has a very long history, but von Neumann did more than
> anyone before him to formalise it:
> 
> http://www.cyclify.com/wiki/images/a/af/Von_Neumann_Probabilistic_Logics_and_the_Synthesis_of_Reliable_Organisms_from_Unreliable_Components.pdf
> 
> Cheers
> 
> -- Ian
> 
> 
> On Thu, 2 Jul 2020 at 11:58, Navdeep Sidhu  > wrote:
> 
> 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 Prague, Czech Republic: Tycho Brahe,
> whom "the divine goodness [had] given to us" (Kepler).
> 
> Best regards,
> Navdeep
> 
> 
> ---
> On 01.07.20 17:38, Ian Tickle wrote:
> >
> > 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 multiplication) without a purpose",
> and in
> > a formal context it has come to mean, ever since John von Neumann
> > pioneered the idea in the 1950s, "duplication / multiplication
> with the
> > express purpose of improving the reliability of the outcome". 
> > 'Multiplicity / multiplication' is neutral with regard to purpose.
> >
> > This divergence of meanings should hardly come as a surprise to
> anyone,
> > and also not surprisingly the informal meaning tends to be rather
> > ill-defined, for example 'theory' used informally means "hypothesis,
> > hunch, speculation, conjecture etc.", whereas in a scientific
> context it
> > has the precise meaning "A coherent
> >  statement
> >  or set of ideas
> that explains
> >  observed
> >  facts
> >  or phenomena
> >  and correctly predicts new
> > facts or phenomena not previously observed, or which sets out the laws
> >  and principles of something known
> > or observed; a hypothesis confirmed by observation, experiment etc."
> > (https://en.wiktionary.org/wiki/theory).
> >
> > "The Hypothesis of Evolution" anyone ?
> >
> > Cheers
> >
> > -- Ian
> >
> >
> >
> >
> > On Tue, 30 Jun 2020 at 14:30, Phil Evans  
> > >> wrote:
> >
> >     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  
> >     >> wrote:
> >     >
> >     >
> >     > 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 meanings are "not or no longer
> >     needed or useful; superfluous" or "exceeding what is necessary or
> >     natural; superfluous" and "needlessly repetitive; verbose". 
> In fact
> >     both redundant and abundant have the same Latin etymology, and
> >     redundant literally means 're' (again) + 'unda' (wave), i.e.
> >     'repeating as a wave'.  The original meaning in English is in fact
> >     'over-abundant' and is still used in poetry with that meaning
> (e.g.
> >     "as redundant as the poppies in the field").  There's of
> course also
> >     the meaning 'dismissal from a job due to a need to reduce the head
> >     count' and from there 'out of work', but that's relatively recent
> >     having been coined by a UK Government offic

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Winter, Graeme (DLSLtd,RAL,LSCI)]

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 also look 
hard at “completeness” which seems to vary from one program to the next and 
cause some confusion to end users.

I appreciate that some of this effort will also land on my desk and am happy to 
practice that which I preach

Best wishes Graeme

On 2 Jul 2020, at 21:05, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


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 doubt).  And 
good luck with persuading wwPDB to change 'redundancy' in their mmCIF 
dictionary!  That would be not only pointless but also a lot of work, partly 
because terms get abbreviated in code and in outputs (e.g. to 'redund' in mine, 
or 'mult').  And don't say I can keep the code & comments the same and only 
change the outputs and documentation: that will really tax my brain!  Also 
don't say this need only apply to new code: no code is ever completely new, and 
mixing up old & new terminology would be a disaster waiting to happen!  Also it 
won't end there: someone will always find terminology that they disagree with: 
I can think of plenty cans of worms that we could open, but I think one is 
already one too many!

By the way, "measurements per reflection" won't float, because some 
measurements will be rejected as outliers (that's why we need redundancy! - as 
opposed to simply measuring intensities for longer).  What I call redundancy is 
"the count of _contributing_ measurements per reflection" (CCMPR, sigh).  
Personally I think that adding one more term is going to confuse things even 
more since if I'm right most people will continue to use the old terms in 
parallel anyway.

IMO we should all be free to use the terminology we are most comfortable with, 
and it's up to the receivers of the information to perform the translation.  
That's how it always has been, and IMO always will be.  Of course it behoves 
(behooves?) the sender to point to or make available any necessary translation 
tools, such as a dictionary or glossary, but once that is done it is the 
responsibility of the receiver to make use of those tools.  Even better if you 
can point to formally-published information (i.e. book or peer-reviewed paper), 
since information on the web is so ephemeral.  As a receiver of information 
myself that's what my brain is doing constantly, i.e. converting others' 
terminology into concepts my brain can process.  If I'm forced to write code 
using a different set of terms it's inevitable that I will unconsciously lapse 
into my old bad ways and I'll end up with a dog's breakfast!  If I'm constantly 
having to convert my terminology into some standardised (standardized?) 
terminology before committing it to code, I'm going to use up what little 
brainpower I have left!

The absolutely critical thing surely is to DEFINE all terms that might be 
unfamiliar or ambiguous (yes Bernhard, I abhor a definitional vacuum for this 
very reason!).  That way the developers feel comfortable and the users can 
understand what's going on.  I'm very happy to put my head on the chopping 
block and add redundancy, multiplicity and whatever other terms people find 
unfamiliar or ambiguous in my outputs or documentation to my 
Glossary.  
Note that this covers only terms used on the STARANISO server; it is by no 
means intended as a replacement for the IUCr's Online Dictionary of 
Crystallography (or any other dictionary for that matter).

By the way, James, you left out my favourite (favorite?): "I could/couldn't 
care less", the positive one of which I always find illogical (if one could 
care less that means the amount of caring must be strictly positive since a 
negative amount is meaningless, whereas if one couldn't care less the amount of 
caring must already be exactly zero, which is surely what the expression is 
meant to convey).  I'm not suggesting at all that I don't care, quite the 
opposite: I think it's vital that terminology is universally understood 
("define your terms, Sir, or we'll never agree").

So my 2p's worth is: carry on as we are, but please, please, please DEFINE (and 
only argue about the definitions!).

https://www.brainyquote.com/quotes/dylan_moran_557269?src=t_please_everyone

Cheers

-- Ian


On Thu, 2 Jul 2020 at 11:11, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear all

I’ve been persuaded that MPR is a useful name 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Ian Tickle]

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:

http://www.cyclify.com/wiki/images/a/af/Von_Neumann_Probabilistic_Logics_and_the_Synthesis_of_Reliable_Organisms_from_Unreliable_Components.pdf

Cheers

-- Ian


On Thu, 2 Jul 2020 at 11:58, Navdeep Sidhu  wrote:

> 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 Prague, Czech Republic: Tycho Brahe,
> whom "the divine goodness [had] given to us" (Kepler).
>
> Best regards,
> Navdeep
>
>
> ---
> On 01.07.20 17:38, Ian Tickle wrote:
> >
> > 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 multiplication) without a purpose", and in
> > a formal context it has come to mean, ever since John von Neumann
> > pioneered the idea in the 1950s, "duplication / multiplication with the
> > express purpose of improving the reliability of the outcome".
> > 'Multiplicity / multiplication' is neutral with regard to purpose.
> >
> > This divergence of meanings should hardly come as a surprise to anyone,
> > and also not surprisingly the informal meaning tends to be rather
> > ill-defined, for example 'theory' used informally means "hypothesis,
> > hunch, speculation, conjecture etc.", whereas in a scientific context it
> > has the precise meaning "A coherent
> >  statement
> >  or set of ideas that explains
> >  observed
> >  facts
> >  or phenomena
> >  and correctly predicts new
> > facts or phenomena not previously observed, or which sets out the laws
> >  and principles of something known
> > or observed; a hypothesis confirmed by observation, experiment etc."
> > (https://en.wiktionary.org/wiki/theory).
> >
> > "The Hypothesis of Evolution" anyone ?
> >
> > Cheers
> >
> > -- Ian
> >
> >
> >
> >
> > On Tue, 30 Jun 2020 at 14:30, Phil Evans  > > wrote:
> >
> > 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  > > wrote:
> > >
> > >
> > > 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 meanings are "not or no longer
> > needed or useful; superfluous" or "exceeding what is necessary or
> > natural; superfluous" and "needlessly repetitive; verbose".  In fact
> > both redundant and abundant have the same Latin etymology, and
> > redundant literally means 're' (again) + 'unda' (wave), i.e.
> > 'repeating as a wave'.  The original meaning in English is in fact
> > 'over-abundant' and is still used in poetry with that meaning (e.g.
> > "as redundant as the poppies in the field").  There's of course also
> > the meaning 'dismissal from a job due to a need to reduce the head
> > count' and from there 'out of work', but that's relatively recent
> > having been coined by a UK Government official in the 1900s!
> > >
> > > The correct and totally precise scientific meaning which is
> > appropriate in the context of this discussion is to be found here:
> > https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that
> > it applies equally to both hardware and software engineering:
> > >
> > > Redundancy is the duplication of critical components or functions
> > of a system with the intention of increasing reliability of the
> > system, usually in the form of a backup or fail-safe, or to improve
> > actual system performance.
> > >
> > > Nothing there about not or no longer needed or useful,
> > superfluous, needlessly repetitive, verbose!  Note that
> > 'multiplicity' totally fails to carry the connotation of

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Navdeep Sidhu]

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 Prague, Czech Republic: Tycho Brahe,
whom "the divine goodness [had] given to us" (Kepler).

Best regards,
Navdeep


---
On 01.07.20 17:38, Ian Tickle wrote:
> 
> 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 multiplication) without a purpose", and in
> a formal context it has come to mean, ever since John von Neumann
> pioneered the idea in the 1950s, "duplication / multiplication with the
> express purpose of improving the reliability of the outcome". 
> 'Multiplicity / multiplication' is neutral with regard to purpose.
> 
> This divergence of meanings should hardly come as a surprise to anyone,
> and also not surprisingly the informal meaning tends to be rather
> ill-defined, for example 'theory' used informally means "hypothesis,
> hunch, speculation, conjecture etc.", whereas in a scientific context it
> has the precise meaning "A coherent
>  statement
>  or set of ideas that explains
>  observed
>  facts
>  or phenomena
>  and correctly predicts new
> facts or phenomena not previously observed, or which sets out the laws
>  and principles of something known
> or observed; a hypothesis confirmed by observation, experiment etc."
> (https://en.wiktionary.org/wiki/theory).
> 
> "The Hypothesis of Evolution" anyone ?
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> On Tue, 30 Jun 2020 at 14:30, Phil Evans  > wrote:
> 
> 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  > wrote:
> >
> >
> > 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 meanings are "not or no longer
> needed or useful; superfluous" or "exceeding what is necessary or
> natural; superfluous" and "needlessly repetitive; verbose".  In fact
> both redundant and abundant have the same Latin etymology, and
> redundant literally means 're' (again) + 'unda' (wave), i.e.
> 'repeating as a wave'.  The original meaning in English is in fact
> 'over-abundant' and is still used in poetry with that meaning (e.g.
> "as redundant as the poppies in the field").  There's of course also
> the meaning 'dismissal from a job due to a need to reduce the head
> count' and from there 'out of work', but that's relatively recent
> having been coined by a UK Government official in the 1900s!
> >
> > The correct and totally precise scientific meaning which is
> appropriate in the context of this discussion is to be found here:
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that
> it applies equally to both hardware and software engineering:
> >
> > Redundancy is the duplication of critical components or functions
> of a system with the intention of increasing reliability of the
> system, usually in the form of a backup or fail-safe, or to improve
> actual system performance.
> >
> > Nothing there about not or no longer needed or useful,
> superfluous, needlessly repetitive, verbose!  Note that
> 'multiplicity' totally fails to carry the connotation of increasing
> the system reliability by duplication (i.e. there are multiple
> copies but there's nothing that indicates the justification for
> them).  Redundancy occurs in TMR (triple modular redundancy) systems
> used (as I guess Bernhard knows well) in triplicated control systems
> in commercial aircraft.  I don't know about you but I wouldn't
> regard the extra two backup systems in TMR as 'not needed or useful'
> when I'm an airline passenger !
> >
> > https://en.wikipedia.org/wiki/Triple_modular_redundancy
> >
> > More is al

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

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 versus 
Xray photons. 

In re reading my “treading through the terminology carefully” email (hinting at 
“going where Angels fear to tread“) I had substituted d spacing for resolution, 
the latter term able to raise lengthy debates, which I sought to avoid, but 
should have changed low to large to read “large d spacings”. Apologies to all.

So, this lockdown is giving us time for considering such issues
Sam Horrell, Andrea Thorn and Dale Tronrud have been have carefully preparing 
via twitterdebate, and including a written document, their suggested options to 
resolve the issue of what to do in our pdb coordinate files where there is 
insufficient electron density for very mobile side chains. Over to you Sam, 
Andrea and Dale.

Greetings,
John 
Emeritus Professor John R Helliwell DSc




> On 2 Jul 2020, at 02:51, 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 2016 yet another great experimental work, by Inoue et al 
> (https://www.pnas.org/content/113/6/1492), showed global loss of diffraction 
> in a protein crystal analog as soon as 10 fs from exposure start (later 
> estimated in Mx experiments by I. Schlichting's team).
> 
> Cheers,
> José
> -> Digression: And I expect neutrons will do a similar job exciting the 
> crystal with some phonon-magnetic moment coupling and changing the 
> magnetisation state of the electronic structure pretty fast. 
> -> Digressing even further, this might be a mechanism that underpins 
> allosteric effects, so neutron mx might be a way to tease them.
> 
> 
> 
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> 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Ethan A Merritt]

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 2016 yet another great experimental work, by Inoue et al 
> (https://www.pnas.org/content/113/6/1492), showed global loss of diffraction 
> in a protein crystal analog as soon as 10 fs from exposure start (later 
> estimated in Mx experiments by I. Schlichting's team).

That's the "destroy" part of "diffract and destroy".

Since an XFEL pulse can be shorter than 10 fs,
that observation does not contradict the idea that the measured
diffraction occurs faster than the damage.

Ethan

> Cheers,
> José

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Jose Brandao-Neto]

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 
(https://www.pnas.org/content/113/6/1492), showed global loss of diffraction in 
a protein crystal analog as soon as 10 fs from exposure start (later estimated 
in Mx experiments by I. Schlichting's team).

Cheers,
José
-> Digression: And I expect neutrons will do a similar job exciting the crystal 
with some phonon-magnetic moment coupling and changing the magnetisation state 
of the electronic structure pretty fast. 
-> Digressing even further, this might be a mechanism that underpins allosteric 
effects, so neutron mx might be a way to tease them.



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

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 
engineering terms, one feels safest on a Brunel bridge than a Boris Johnson 
“across the Thames” walkway.  
The matter for science is encapsulated in Hermann’s excellent proposal, now 
seconded twice, MPR, measurements per hkl reflection. Even with Xray damage hkl 
as a label is the constant. Also XFELs offer Xray damage free reflection 
intensity measurements of an hkl reflection. Likewise neutrons offer damage 
free intensity measurements of an hkl.

Best regards,
John 

Emeritus Professor John R Helliwell DSc




> On 30 Jun 2020, at 14:07, Ian Tickle  wrote:
> 
> 
> 
> 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 meanings are "not or no longer needed or useful; superfluous" or 
> "exceeding what is necessary or natural; superfluous" and "needlessly 
> repetitive; verbose".  In fact both redundant and abundant have the same 
> Latin etymology, and redundant literally means 're' (again) + 'unda' (wave), 
> i.e. 'repeating as a wave'.  The original meaning in English is in fact 
> 'over-abundant' and is still used in poetry with that meaning (e.g. "as 
> redundant as the poppies in the field").  There's of course also the meaning 
> 'dismissal from a job due to a need to reduce the head count' and from there 
> 'out of work', but that's relatively recent having been coined by a UK 
> Government official in the 1900s!
> 
> The correct and totally precise scientific meaning which is appropriate in 
> the context of this discussion is to be found here: 
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it 
> applies equally to both hardware and software engineering:
> 
> Redundancy is the duplication of critical components or functions of a system 
> with the intention of increasing reliability of the system, usually in the 
> form of a backup or fail-safe, or to improve actual system performance.
> 
> Nothing there about not or no longer needed or useful, superfluous, 
> needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to 
> carry the connotation of increasing the system reliability by duplication 
> (i.e. there are multiple copies but there's nothing that indicates the 
> justification for them).  Redundancy occurs in TMR (triple modular 
> redundancy) systems used (as I guess Bernhard knows well) in triplicated 
> control systems in commercial aircraft.  I don't know about you but I 
> wouldn't regard the extra two backup systems in TMR as 'not needed or useful' 
> when I'm an airline passenger !
> 
> https://en.wikipedia.org/wiki/Triple_modular_redundancy
> 
> More is always better when it's critical:
> 
> https://www.isa.org/standards-and-publications/isa-publications/intech-magazine/2003/october/more-is-always-better-when-its-critical
> 
> There's also the question of the same word (redundancy, multiplicity or 
> whatever) having different meanings according to context.  That's unavoidable 
> given that the number of concepts that we might want to name far exceeds the 
> number of words available, so we have to rely heavily on context when 
> assigning meaning.  We don't say what the context is so the context must be 
> obvious and unambiguous.  Whether we're talking about RAID or losing one's 
> job it's obvious what the intended meaning is from the context because the 
> contexts are totally separate.  The important thing is that the contexts 
> should be well-separated so that no confusion is possible.  Graeme says he's 
> not confused by the various meanings of 'multiplicity' but 
> non-crystallographer consumers of Table 1 surely might be!  The various 
> contexts in which 'multiplicity' is used are certainly not well-separated and 
> overlap in program outputs and documentation, allowing plenty of scope for 
> confusion.
> 
> In a scientific context 'redundancy' has a unique precise meaning whereas 
> 'multiplicity' has a multiplicity!
> 
> BTW I use CCP4/Aimless and 'redundancy' (as you no doubt will have guessed, 
> because it's the word that unambiguously describes the concept), so 
> apparently I'm with you lot across the pond on this!
> 
> Cheers
> 
> -- Ian
>  
> 
> 
>> On Tue, 30 Jun 2020 at 09:01, 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 th

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Goldman, Adrian]

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 or 
excess in some respect.
2. Abounding to excess or fullness; plentiful, copious, ((my itals), exuberant
 b Characterised by copiousness, fullness, or abundance (my itals).
As an example of (1), it gives “The employment of redundant capital (Macaulay).

- so we are employing the redundant observations (the ones above that minimal 
number (1) needed to say anything at all about the value of Ihkl).

I think it’s fair to see that the way it is used in x-ray crystallography is a 
subset of the meanings above, which is just fine.

Adrian


On 1 Jul 2020, at 16:38, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


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 multiplication) without a purpose", and in a formal context it 
has come to mean, ever since John von Neumann pioneered the idea in the 1950s, 
"duplication / multiplication with the express purpose of improving the 
reliability of the outcome".  'Multiplicity / multiplication' is neutral with 
regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and 
also not surprisingly the informal meaning tends to be rather ill-defined, for 
example 'theory' used informally means "hypothesis, hunch, speculation, 
conjecture etc.", whereas in a scientific context it has the precise meaning "A 
coherent 
statement or set of ideas that 
explains 
observed 
facts or 
phenomena and correctly predicts new 
facts or phenomena not previously observed, or which sets out the 
laws and principles of something known or 
observed; a hypothesis confirmed by observation, experiment etc." 
(https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:
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 
> mailto:ianj...@gmail.com>> wrote:
>
>
> 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 meanings are "not or no longer needed or useful; superfluous" or 
> "exceeding what is necessary or natural; superfluous" and "needlessly 
> repetitive; verbose".  In fact both redundant and abundant have the same 
> Latin etymology, and redundant literally means 're' (again) + 'unda' (wave), 
> i.e. 'repeating as a wave'.  The original meaning in English is in fact 
> 'over-abundant' and is still used in poetry with that meaning (e.g. "as 
> redundant as the poppies in the field").  There's of course also the meaning 
> 'dismissal from a job due to a need to reduce the head count' and from there 
> 'out of work', but that's relatively recent having been coined by a UK 
> Government official in the 1900s!
>
> The correct and totally precise scientific meaning which is appropriate in 
> the context of this discussion is to be found here: 
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it 
> applies equally to both hardware and software engineering:
>
> Redundancy is the duplication of critical components or functions of a system 
> with the intention of increasing reliability of the system, usually in the 
> form of a backup or fail-safe, or to improve actual system performance.
>
> Nothing there about not or no longer needed or useful, superfluous, 
> needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to 
> carry the connotation of increasing the system reliability by duplication 
> (i.e. there are multiple copies but there's nothing that indicates the 
> justification for them).  Redundancy occurs in TMR (triple modular 
> redundancy) systems used (as I guess Bernhard knows well) in triplicated 
> control systems in commercial aircraft.  I don't know about you but I 
> wouldn't regard the 

[ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Hughes, Jonathan]

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 2020 17:39
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


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 multiplication) without a purpose", and in a formal context it 
has come to mean, ever since John von Neumann pioneered the idea in the 1950s, 
"duplication / multiplication with the express purpose of improving the 
reliability of the outcome".  'Multiplicity / multiplication' is neutral with 
regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and 
also not surprisingly the informal meaning tends to be rather ill-defined, for 
example 'theory' used informally means "hypothesis, hunch, speculation, 
conjecture etc.", whereas in a scientific context it has the precise meaning "A 
coherent<https://en.wiktionary.org/wiki/coherent> 
statement<https://en.wiktionary.org/wiki/statement> or set of ideas that 
explains<https://en.wiktionary.org/wiki/explain> 
observed<https://en.wiktionary.org/wiki/observe> 
facts<https://en.wiktionary.org/wiki/fact> or 
phenomena<https://en.wiktionary.org/wiki/phenomenon> and correctly predicts new 
facts or phenomena not previously observed, or which sets out the 
laws<https://en.wiktionary.org/wiki/law> and principles of something known or 
observed; a hypothesis confirmed by observation, experiment etc." 
(https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:
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 
> mailto:ianj...@gmail.com>> wrote:
>
>
> 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 meanings are "not or no longer needed or useful; superfluous" or 
> "exceeding what is necessary or natural; superfluous" and "needlessly 
> repetitive; verbose".  In fact both redundant and abundant have the same 
> Latin etymology, and redundant literally means 're' (again) + 'unda' (wave), 
> i.e. 'repeating as a wave'.  The original meaning in English is in fact 
> 'over-abundant' and is still used in poetry with that meaning (e.g. "as 
> redundant as the poppies in the field").  There's of course also the meaning 
> 'dismissal from a job due to a need to reduce the head count' and from there 
> 'out of work', but that's relatively recent having been coined by a UK 
> Government official in the 1900s!
>
> The correct and totally precise scientific meaning which is appropriate in 
> the context of this discussion is to be found here: 
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it 
> applies equally to both hardware and software engineering:
>
> Redundancy is the duplication of critical components or functions of a system 
> with the intention of increasing reliability of the system, usually in the 
> form of a backup or fail-safe, or to improve actual system performance.
>
> Nothing there about not or no longer needed or useful, superfluous, 
> needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to 
> carry the connotation of increasing the system reliability by duplication 
> (i.e. there are multiple copies but there's nothing that indicates the 
> justification for them).  Redundancy occurs in TMR (triple modular 
> redundancy) systems used (as I guess Bernhard knows well) in triplicated 
> control systems in commercial aircraft.  I don't know about you but I 
> wouldn't regard the extra two backup systems in TMR as 'not needed or useful

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Ian Tickle]

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 multiplication) without a purpose", and in a formal context
it has come to mean, ever since John von Neumann pioneered the idea in the
1950s, "duplication / multiplication with the express purpose of improving
the reliability of the outcome".  'Multiplicity / multiplication' is
neutral with regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and
also not surprisingly the informal meaning tends to be rather ill-defined,
for example 'theory' used informally means "hypothesis, hunch, speculation,
conjecture etc.", whereas in a scientific context it has the precise
meaning "A coherent  statement
 or set of ideas that explains
 observed
 facts
 or phenomena
 and correctly predicts new
facts or phenomena not previously observed, or which sets out the laws
 and principles of something known or
observed; a hypothesis confirmed by observation, experiment etc." (
https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, Phil Evans  wrote:

> 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  wrote:
> >
> >
> > 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 meanings are "not or no longer needed or useful; superfluous" or
> "exceeding what is necessary or natural; superfluous" and "needlessly
> repetitive; verbose".  In fact both redundant and abundant have the same
> Latin etymology, and redundant literally means 're' (again) + 'unda'
> (wave), i.e. 'repeating as a wave'.  The original meaning in English is in
> fact 'over-abundant' and is still used in poetry with that meaning (e.g.
> "as redundant as the poppies in the field").  There's of course also the
> meaning 'dismissal from a job due to a need to reduce the head count' and
> from there 'out of work', but that's relatively recent having been coined
> by a UK Government official in the 1900s!
> >
> > The correct and totally precise scientific meaning which is appropriate
> in the context of this discussion is to be found here:
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it
> applies equally to both hardware and software engineering:
> >
> > Redundancy is the duplication of critical components or functions of a
> system with the intention of increasing reliability of the system, usually
> in the form of a backup or fail-safe, or to improve actual system
> performance.
> >
> > Nothing there about not or no longer needed or useful, superfluous,
> needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to
> carry the connotation of increasing the system reliability by duplication
> (i.e. there are multiple copies but there's nothing that indicates the
> justification for them).  Redundancy occurs in TMR (triple modular
> redundancy) systems used (as I guess Bernhard knows well) in triplicated
> control systems in commercial aircraft.  I don't know about you but I
> wouldn't regard the extra two backup systems in TMR as 'not needed or
> useful' when I'm an airline passenger !
> >
> > https://en.wikipedia.org/wiki/Triple_modular_redundancy
> >
> > More is always better when it's critical:
> >
> >
> https://www.isa.org/standards-and-publications/isa-publications/intech-magazine/2003/october/more-is-always-better-when-its-critical
> >
> > There's also the question of the same word (redundancy, multiplicity or
> whatever) having different meanings according to context.  That's
> unavoidable given that the number of concepts that we might want to name
> far exceeds the number of words available, so we have to rely heavily on
> context when assigning meaning.  We don't say what the context is so the
> context must be obvious and unambiguous.  Whether we're talking about RAID
> or losing one's job it's obvious what the intended meaning is from the
> context because the contexts are totally separate.  The important thing is
> that the contexts should be

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Dirk Kostrewa]

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 
correctly, this is something that Gerard proposed long time ago for 
phasing programs.


Best wishes,

Dirk.

On 01.07.20 11:52, Kay Diederichs wrote:

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 could correct radiation damage then we could collect data to high 
resolution from all crystals just by using very high dose, and solve structures 
much more easily.

How often you count a reflection is up to you; I don't see what you gain by 
this.

best,
Kay

Am 01.07.20 um 11:42 schrieb Dirk Kostrewa:

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, to average 
them and count them only once (say, for crystals measured multiple rounds of 
360 degrees to find identical geometries)?

Best wishes,

Dirk.

On 01.07.20 11:02, Gerard Bricogne wrote:

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 symmetry-related hkls. I
mentioned that in my second message yesterday.

   The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river".


   With best wishes,

    Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:

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 number of truly
independent measurements.

Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with the
same geometry n-times and measuring it n-times as long (apart from, maybe,
catching instabilities in the experimental setup). Just averaging such
"identical" reflections would simplify the subsequent scaling process with
equivalent reflections that were measured under different geometry.

On 01.07.20 09:32, Schreuder, Herman /DE wrote:

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 describes what is meant by the parameter and it is easily
understood even by lay people like journal editors and referees, without
the need of lengthy explanations like the ones we have seen in this
thread.

I really would like to ask you to consider replacing
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
thread about completeness of data sets to be hijacked by a discussion on
whether use the name multiplicity of redundancy for the number of
measurements per reflection.

My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von
*Bernhard Rupp
*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
<mailto:owner-ccp...@jiscmail.ac.uk>

.…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 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell
*Sent:* Tuesday, June 30, 2020 08:36
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

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

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Kay Diederichs]

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 could correct radiation damage then we could collect data to high 
resolution from all crystals just by using very high dose, and solve structures 
much more easily.

How often you count a reflection is up to you; I don't see what you gain by 
this.

best,
Kay

Am 01.07.20 um 11:42 schrieb Dirk Kostrewa:
> 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, to average them and count them only once (say, for crystals measured 
> multiple rounds of 360 degrees to find identical geometries)?
> 
> Best wishes,
> 
> Dirk.
> 
> On 01.07.20 11:02, Gerard Bricogne wrote:
>> 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 symmetry-related hkls. I
>> mentioned that in my second message yesterday.
>>
>>   The notion of "identical" reflections measurements is problematic for
>> the same reason that Heraclitus wrote (something like) "You cannot step
>> twice into the same river".
>>
>>
>>   With best wishes,
>>
>>    Gerard.
>>
>> -- 
>> On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:
>>> 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 number of truly
>>> independent measurements.
>>>
>>> Cheers,
>>>
>>> Dirk.
>>>
>>> (*) I don't see a difference between measuring the same reflection with the
>>> same geometry n-times and measuring it n-times as long (apart from, maybe,
>>> catching instabilities in the experimental setup). Just averaging such
>>> "identical" reflections would simplify the subsequent scaling process with
>>> equivalent reflections that were measured under different geometry.
>>>
>>> On 01.07.20 09:32, Schreuder, Herman /DE wrote:
>>>> 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 describes what is meant by the parameter and it is easily
>>>> understood even by lay people like journal editors and referees, without
>>>> the need of lengthy explanations like the ones we have seen in this
>>>> thread.
>>>>
>>>> I really would like to ask you to consider replacing
>>>> multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
>>>> thread about completeness of data sets to be hijacked by a discussion on
>>>> whether use the name multiplicity of redundancy for the number of
>>>> measurements per reflection.
>>>>
>>>> My 2 cents,
>>>>
>>>> Herman
>>>>
>>>> *Von:* CCP4 bulletin board  *Im Auftrag von
>>>> *Bernhard Rupp
>>>> *Gesendet:* Dienstag, 30. Juni 2020 17:50
>>>> *An:* CCP4BB@JISCMAIL.AC.UK
>>>> *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
>>>> a full dataset?
>>>>
>>>> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>>>> <mailto:owner-ccp...@jiscmail.ac.uk>
>>>>
>>>> .…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

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Dirk Kostrewa]

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, to average them and count them only once (say, for crystals 
measured multiple rounds of 360 degrees to find identical geometries)?


Best wishes,

Dirk.

On 01.07.20 11:02, Gerard Bricogne wrote:

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 symmetry-related hkls. I
mentioned that in my second message yesterday.

  The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river".


  With best wishes,

   Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:

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 number of truly
independent measurements.

Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with the
same geometry n-times and measuring it n-times as long (apart from, maybe,
catching instabilities in the experimental setup). Just averaging such
"identical" reflections would simplify the subsequent scaling process with
equivalent reflections that were measured under different geometry.

On 01.07.20 09:32, Schreuder, Herman /DE wrote:

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 describes what is meant by the parameter and it is easily
understood even by lay people like journal editors and referees, without
the need of lengthy explanations like the ones we have seen in this
thread.

I really would like to ask you to consider replacing
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
thread about completeness of data sets to be hijacked by a discussion on
whether use the name multiplicity of redundancy for the number of
measurements per reflection.

My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von
*Bernhard Rupp
*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
<mailto:owner-ccp...@jiscmail.ac.uk>

.…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 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell
*Sent:* Tuesday, June 30, 2020 08:36
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

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
 mailto:herman.schreu...@sanofi.com>>
 wrote:

 

 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 adequately describe this
 particular statistic and is not associated with entrenched
 traditions at either side of the Atlantic.

 What do you think?

 Herman

 *Von:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *John R Helliwell
 *Gesendet:* Dienstag, 30. Juni 2020 14:34
 *An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
 *Betreff:* [EXTERNAL] Re: [ccp4bb] number of frames to get a full
 dataset?

 *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
 <mailto:owner-ccp...@jiscmail.ac.uk>

 Dear Colleagues,

 In an effort to break this naming 

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Kay Diederichs]

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 is not a single reflection that is 
identically (according to your definition) measured two or more times.
In other words, describing those "identical" reflections statistically will 
give you the statistics of (what I call) the unmerged data. 
And, as Gerard mentions, if you do have multiple measurements of "identical" 
reflections (i.e. if collecting more than 360°), they still differ in terms of 
radiation damage.

best,
Kay

On Wed, 1 Jul 2020 10:46:57 +0200, Dirk Kostrewa 
 wrote:

>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 
>number of truly independent measurements.
>
>Cheers,
>
>Dirk.
>
>(*) I don't see a difference between measuring the same reflection with 
>the same geometry n-times and measuring it n-times as long (apart from, 
>maybe, catching instabilities in the experimental setup). Just averaging 
>such "identical" reflections would simplify the subsequent scaling 
>process with equivalent reflections that were measured under different 
>geometry.
>
>On 01.07.20 09:32, Schreuder, Herman /DE wrote:
>>
>> 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 describes what is meant by the parameter and it is easily 
>> understood even by lay people like journal editors and referees, 
>> without the need of lengthy explanations like the ones we have seen in 
>> this thread.
>>
>> I really would like to ask you to consider replacing 
>> multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a 
>> thread about completeness of data sets to be hijacked by a discussion 
>> on whether use the name multiplicity of redundancy for the number of 
>> measurements per reflection.
>>
>> My 2 cents,
>>
>> Herman
>>
>> *Von:* CCP4 bulletin board  *Im Auftrag von 
>> *Bernhard Rupp
>> *Gesendet:* Dienstag, 30. Juni 2020 17:50
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
>> get a full dataset?
>>
>> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 
>> <mailto:owner-ccp...@jiscmail.ac.uk>
>>
>> .…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 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell
>> *Sent:* Tuesday, June 30, 2020 08:36
>> *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>> *Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
>> get a full dataset?
>>
>> 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
>> mailto:herman.schreu...@sanofi.com>>
>> wrote:
>>
>> 
>>
>> 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 adequately describe this
>> particular statistic and is not associated with entrenched
>> traditions at either side of the Atlantic.
>>
>> Wha

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

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 symmetry-related hkls. I
mentioned that in my second message yesterday.

 The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river". 


 With best wishes,

  Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:
> 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 number of truly
> independent measurements.
> 
> Cheers,
> 
> Dirk.
> 
> (*) I don't see a difference between measuring the same reflection with the
> same geometry n-times and measuring it n-times as long (apart from, maybe,
> catching instabilities in the experimental setup). Just averaging such
> "identical" reflections would simplify the subsequent scaling process with
> equivalent reflections that were measured under different geometry.
> 
> On 01.07.20 09:32, Schreuder, Herman /DE wrote:
> > 
> > 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 describes what is meant by the parameter and it is easily
> > understood even by lay people like journal editors and referees, without
> > the need of lengthy explanations like the ones we have seen in this
> > thread.
> > 
> > I really would like to ask you to consider replacing
> > multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
> > thread about completeness of data sets to be hijacked by a discussion on
> > whether use the name multiplicity of redundancy for the number of
> > measurements per reflection.
> > 
> > My 2 cents,
> > 
> > Herman
> > 
> > *Von:* CCP4 bulletin board  *Im Auftrag von
> > *Bernhard Rupp
> > *Gesendet:* Dienstag, 30. Juni 2020 17:50
> > *An:* CCP4BB@JISCMAIL.AC.UK
> > *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
> > a full dataset?
> > 
> > *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
> > <mailto:owner-ccp...@jiscmail.ac.uk>
> > 
> > .…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 bulletin board  > <mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell
> > *Sent:* Tuesday, June 30, 2020 08:36
> > *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> > *Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
> > a full dataset?
> > 
> > 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
> > mailto:herman.schreu...@sanofi.com>>
> > wrote:
> > 
> > 
> > 
> > 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 adequately describe this
> > particular statistic and is not associated with entrenched
> > traditions at either side of the Atlantic.
> > 
> > What do you think?
> > 
> > Her

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Dirk Kostrewa]

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 
number of truly independent measurements.


Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with 
the same geometry n-times and measuring it n-times as long (apart from, 
maybe, catching instabilities in the experimental setup). Just averaging 
such "identical" reflections would simplify the subsequent scaling 
process with equivalent reflections that were measured under different 
geometry.


On 01.07.20 09:32, Schreuder, Herman /DE wrote:


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 describes what is meant by the parameter and it is easily 
understood even by lay people like journal editors and referees, 
without the need of lengthy explanations like the ones we have seen in 
this thread.


I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a 
thread about completeness of data sets to be hijacked by a discussion 
on whether use the name multiplicity of redundancy for the number of 
measurements per reflection.


My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Bernhard Rupp

*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
get a full dataset?


*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 
<mailto:owner-ccp...@jiscmail.ac.uk>


.…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 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *John R Helliwell

*Sent:* Tuesday, June 30, 2020 08:36
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
get a full dataset?


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
mailto:herman.schreu...@sanofi.com>>
wrote:



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 adequately describe this
particular statistic and is not associated with entrenched
traditions at either side of the Atlantic.

What do you think?

Herman

*Von:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *Im Auftrag von *John R Helliwell
*Gesendet:* Dienstag, 30. Juni 2020 14:34
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] number of frames to get a full
dataset?

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
<mailto:owner-ccp...@jiscmail.ac.uk>

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:-

http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html

<https://urldefense.proofpoint.com/v2/url?u=http-3A__ww1.iucr.org_iucr-2Dtop_comm_cnom_statdes_recomm.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=vb2CFOGKla49hE2sbHAt6LCUz63K7uis9PmSUxUgMcM&s=-45HByHsLJPmc2KRmPKamiFNf1WFCI51GonllFyIRTE&e=>

Point 1, first sentence, fits the various wishes of this thread
succinctly, if not in a single word, and even not readily allowing
an easy acronym.

Greetings,

John

Emeritus Professor John R Helliwell DSc

On 30 Jun 2020, at 13:11, Phil Jeffrey mailto:pjeff...@princeton.edu>> wrote:

The people that already use multiplicity are going to find
reasons why it's the superior naming scheme - although the
underlyi

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

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 allow 
determination of the Lambda curve. This is achieved through repeated 
measurements of the same hkl at different wavelengths from more than one 
crystal orientation or its symmetry mates at the same or different crystal 
orientations. High completeness in Laue especially at low d spacings requires 
deconvolution of energy multiples and is also helped by repeat measurements at 
different crystal orientations and a high crystal symmetry. 

Treading hopefully deftly with my terminology,
John 

Emeritus Professor John R Helliwell DSc




> On 30 Jun 2020, at 18:13, "0c2488af9525-dmarc-requ...@jiscmail.ac.uk" 
> <0c2488af9525-dmarc-requ...@jiscmail.ac.uk wrote:
> 
> 
> Hello John
> 
> Does the IUCr dictionary list 'degeneracy'?
> 
> Jon Cooper
> 
> On 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 (e.g. in terms of radiation damage only, while the 
> others would also involve absorption effects). However I am not aware that 
> the existing data processing programs we use actually make and exploit this 
> distinction. 
> 
>  Going back to the initial topic of this thread, the main take-home 
> lesson for Murpholino should be: preoccupations about minimising the number 
> of frames to get completeness belong to a now obsolete age - instead use the 
> new paragigm of high-(redundancy/multiplicity) data collection with a low 
> transmission so that you can spread the dose your crystal can withstand over 
> the requisite angular range. No matter how you call the "abundance" property 
> of your final dataset, make sure it is high! 
> 
>  The case of low symmetry has been mentioned: the extra guidance for 
> Murpolino is that if you are in P1, you will never get completeness with a 
> single orientation, so make sure that you use a multi-axis goniometer and 
> collect data in at least two sufficiently different orientations. 
> 
> 
>  With best wishes, 
> 
>   Gerard. 
> 
> -- 
> On Tue, Jun 30, 2020 at 08:49:53AM -0700, Bernhard Rupp wrote: 
> > .…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 bulletin board  On Behalf Of John R 
> > Helliwell 
> > Sent: Tuesday, June 30, 2020 08:36 
> > To: CCP4BB@JISCMAIL.AC.UK 
> > Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a 
> > full dataset? 
> > 
> >  
> > 
> > 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 
> > mailto:herman.schreu...@sanofi.com> > wrote: 
> > 
> >  
> > 
> > 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 adequately describe this 
> > particular statistic and is not associated with entrenched traditions at 
> > either side of the Atlantic. 
> > 
> >  
> > 
> > What do you think? 
> > 
> > Herman 
> > 
> >  
> > 
> >  
> > 
> > Von: CCP4 bulletin board  > <mailto:CCP4BB@JISCMAIL.AC.UK> > Im Auftrag von John R Helliwell 
> > Gesendet: Dienstag, 30. Juni 202

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Schreuder, Herman /DE]

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 bulletin to think about my proposal as it is, without prejudices.

Best,
Herman



Von: Frank Von Delft 
Gesendet: Mittwoch, 1. Juli 2020 09:46
An: Schreuder, Herman /DE 
Betreff: Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
get a full dataset?


EXTERNAL : Real sender is 
frank.vonde...@sgc.ox.ac.uk<mailto:frank.vonde...@sgc.ox.ac.uk>

If I fine slice the data, does each frame measuring the same reflection (or a 
part of it) count as a measurement?

So that doesn't get us out of the woods, alas.

Sent from tiny silly touch screen

From: "Schreuder, Herman /DE" 
mailto:herman.schreu...@sanofi.com>>
Sent: Wednesday, 1 July 2020 08:33
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get 
a full dataset?

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 
describes what is meant by the parameter and it is easily understood even by 
lay people like journal editors and referees, without the need of lengthy 
explanations like the ones we have seen in this thread.

I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread 
about completeness of data sets to be hijacked by a discussion on whether use 
the name multiplicity of redundancy for the number of measurements per 
reflection.

My 2 cents,
Herman



Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Bernhard Rupp
Gesendet: Dienstag, 30. Juni 2020 17:50
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

.…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 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of John R Helliwell
Sent: Tuesday, June 30, 2020 08:36
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?

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 
mailto:herman.schreu...@sanofi.com>> wrote:

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 adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

What do you think?
Herman


Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

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:-
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__ww1.iucr.org_iucr-2Dtop_comm_cnom_statdes_recomm.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=vb2CFOGKla49hE2sbHAt6LCUz63K7uis9PmSUxUgMcM&s=-45HByHsLJPmc2KRmPKamiFNf1WFCI51GonllFyIRTE&e=>
Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym.
Greetings,
John

Emeritus Professor John R Helliwell DSc



On 30 J

[ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Schreuder, Herman /DE]

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 
describes what is meant by the parameter and it is easily understood even by 
lay people like journal editors and referees, without the need of lengthy 
explanations like the ones we have seen in this thread.

I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread 
about completeness of data sets to be hijacked by a discussion on whether use 
the name multiplicity of redundancy for the number of measurements per 
reflection.

My 2 cents,
Herman



Von: CCP4 bulletin board  Im Auftrag von Bernhard Rupp
Gesendet: Dienstag, 30. Juni 2020 17:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

.…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 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of John R Helliwell
Sent: Tuesday, June 30, 2020 08:36
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?

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 
mailto:herman.schreu...@sanofi.com>> wrote:

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 adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

What do you think?
Herman


Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

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:-
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__ww1.iucr.org_iucr-2Dtop_comm_cnom_statdes_recomm.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=vb2CFOGKla49hE2sbHAt6LCUz63K7uis9PmSUxUgMcM&s=-45HByHsLJPmc2KRmPKamiFNf1WFCI51GonllFyIRTE&e=>
Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym.
Greetings,
John

Emeritus Professor John R Helliwell DSc



On 30 Jun 2020, at 13:11, Phil Jeffrey 
mailto:pjeff...@princeton.edu>> wrote:
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 - Graeme's 
pragmatic defense of multiplicity actually works both ways - any person who 
takes the trouble to read the stats table, now exiled to Supplementary Data, 
knows what it means.  Surely, then, the only way forward on this almost totally 
irrelevant discussion is to come up with a universally-loathed nomenclature 
that pleases nobody, preferably an acronym whose origins will be lost to 
history and the dusty CCP4 archives (which contain threads similar to this 
one).  I humbly submit:

NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions of the 
inappropriateness of "R-factor" ?  I have a long history of rearguard action 
trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
from me on this for years.

(Personally I'm pining for 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[00000c2488af9525-dmarc-request]

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 (e.g. in terms of radiation damage only, while the

others would also involve absorption effects). However I am not aware that

the existing data processing programs we use actually make and exploit this

distinction.



 Going back to the initial topic of this thread, the main take-home

lesson for Murpholino should be: preoccupations about minimising the number

of frames to get completeness belong to a now obsolete age - instead use the

new paragigm of high-(redundancy/multiplicity) data collection with a low

transmission so that you can spread the dose your crystal can withstand over

the requisite angular range. No matter how you call the "abundance" property

of your final dataset, make sure it is high!



 The case of low symmetry has been mentioned: the extra guidance for

Murpolino is that if you are in P1, you will never get completeness with a

single orientation, so make sure that you use a multi-axis goniometer and

collect data in at least two sufficiently different orientations.





 With best wishes,



  Gerard.



--

On Tue, Jun 30, 2020 at 08:49:53AM -0700, Bernhard Rupp wrote:

> .…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 bulletin board  On Behalf Of John R Helliwell

> Sent: Tuesday, June 30, 2020 08:36

> To: CCP4BB@JISCMAIL.AC.UK

> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

> 

>  

> 

> 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  > wrote:

> 

>  

> 

> 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 adequately describe this particular statistic and is not associated with entrenched traditions at either side of the Atlantic.

> 

>  

> 

> What do you think?

> 

> Herman

> 

>  

> 

>  

> 

> Von: CCP4 bulletin board  > Im Auftrag von John R Helliwell

> Gesendet: Dienstag, 30. Juni 2020 14:34

> An: CCP4BB@JISCMAIL.AC.UK  

> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

> 

>  

> 

> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk   

> 

>  

> 

> 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:-

> 

> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html  

> 

> Point 1, first sentence, fits the various wishes of this thread succinctly, if not in a single word, and even not readily allowing an easy acronym. 

> 

> Greetings,

> 

> John 

> 

>  

> 

> Emeritus Professor John R Helliwell DSc

> 

>  

> 

>  

> 

> 

> 

> 

> 

> On 30 Jun 2020, at 13:11, Phil Jeffrey  > wrote:

> 

> 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 - Graeme's pragmatic defense of multiplicity actually works both ways - any person who takes the trouble to read the stats table, now exiled to Supplementary Data, knows what it means.  Surely, then, the only way forward on this almost totally irrelevant discussion is to come up with a universally-loathed nomenclature that pleases nobody, preferably an acronym

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

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 not aware that
the existing data processing programs we use actually make and exploit this
distinction.

 Going back to the initial topic of this thread, the main take-home
lesson for Murpholino should be: preoccupations about minimising the number
of frames to get completeness belong to a now obsolete age - instead use the
new paragigm of high-(redundancy/multiplicity) data collection with a low
transmission so that you can spread the dose your crystal can withstand over
the requisite angular range. No matter how you call the "abundance" property
of your final dataset, make sure it is high!

 The case of low symmetry has been mentioned: the extra guidance for
Murpolino is that if you are in P1, you will never get completeness with a
single orientation, so make sure that you use a multi-axis goniometer and
collect data in at least two sufficiently different orientations.


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2020 at 08:49:53AM -0700, Bernhard Rupp wrote:
> .…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 bulletin board  On Behalf Of John R 
> Helliwell
> Sent: Tuesday, June 30, 2020 08:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
> dataset?
> 
>  
> 
> 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  <mailto:herman.schreu...@sanofi.com> > wrote:
> 
>  
> 
> 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 adequately describe this particular 
> statistic and is not associated with entrenched traditions at either side of 
> the Atlantic.
> 
>  
> 
> What do you think?
> 
> Herman
> 
>  
> 
>  
> 
> Von: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK> > Im Auftrag von John R Helliwell
> Gesendet: Dienstag, 30. Juni 2020 14:34
> An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
> 
>  
> 
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
> <mailto:owner-ccp...@jiscmail.ac.uk>  
> 
>  
> 
> 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:-
> 
> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ww1.iucr.org_iucr-2Dtop_comm_cnom_statdes_recomm.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=vb2CFOGKla49hE2sbHAt6LCUz63K7uis9PmSUxUgMcM&s=-45HByHsLJPmc2KRmPKamiFNf1WFCI51GonllFyIRTE&e=>
>  
> 
> Point 1, first sentence, fits the various wishes of this thread succinctly, 
> if not in a single word, and even not readily allowing an easy acronym. 
> 
> Greetings,
> 
> John 
> 
>  
> 
> Emeritus Professor John R Helliwell DSc
> 
>  
> 
>  
> 
> 
> 
> 
> 
> On 30 Jun 2020, at 13:11, Phil Jeffrey  <mailto:pjeff...@princeton.edu> > wrote:
> 
> 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 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Frank von Delft]

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 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 lengthy read-out times led to designing data collection
strategies so that they would achieve completeness in the smallest number of
"frames", themselves chosen as thick-sliced as possible while avoiding
angular overlap because of the read-out noise added to each such frame. With
this mindset, measuring again a reflection that had already been measured
could have been viewed as a waste of effort, bringing water to the mill of
interpreting "redundancy" as a sign of sub-optimality. However, looking
again at the CCD datasets collected according to this paradigm, they are
dire! Minimal availability of symmetry-related measurements made internal
scaling fragile, the terrible corner effects in the 3x3 detectors could not
be corrected, and the tracking of radiation damage was beyond hope.

  A lot has happened since, namely pixel-array detectors, fine-sliced
images recorded at low transmission, aiming at recording symmetry-related
reflections "a large number of times" - whatever one ends up calling that.
Far from being superfluous, or "redundant" in the negative sense of the
term, these "abundant" measurements (to coin a phrase) are now recognised as
being absolutely crucial towards the rejection of outliers, a key process in
obtaining high-quality data. This would then bring us back to the positive,
even noble connotation of the term "redundancy", since an abundance of
symmetry-related measurements now allows the detection and rejection of the
dodgy ones. From that perspective, "redundant" is good in the sense Ian
mentioned in relation to aviation equipment: if a few of those measurements
are rotten, you can throw them away and still have some left to do the job.
If you have abundant measurements and just call them multiple, this sense of
allowing rescue in case of failure disappears, and with it an important
aspect of why one should go for strategies that harvest symmetry-related
measurement in high numbers. This is why I ceased to support the standard
term "multiplicity" in conversations with Ian and went along with his choice
of the term "redundancy" in the presentation of STARANISO results.


  With best wishes,

   Gerard.

--
On Tue, Jun 30, 2020 at 02:30:27PM +0100, Phil Evans wrote:

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  wrote:


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 meanings are "not or no longer needed or useful; 
superfluous" or "exceeding what is necessary or natural; superfluous" and "needlessly repetitive; 
verbose".  In fact both redundant and abundant have the same Latin etymology, and redundant literally means 're' 
(again) + 'unda' (wave), i.e. 'repeating as a wave'.  The original meaning in English is in fact 'over-abundant' and is 
still used in poetry with that meaning (e.g. "as redundant as the poppies in the field").  There's of course 
also the meaning 'dismissal from a job due to a need to reduce the head count' and from there 'out of work', but that's 
relatively recent having been coined by a UK Government official in the 1900s!

The correct and totally precise scientific meaning which is appropriate in the 
context of this discussion is to be found here: 
https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it applies 
equally to both hardware and software engineering:

Redundancy is the duplication of critical components or functions of a system 
with the intention of increasing reliability of the system, usually in the form 
of a backup or fail-safe, or to improve actual system performance.

Nothing there about not or no longer needed or useful, superfluous, needlessly 
repetitive, verbose!  Note that 'multiplicity' totally fails to carry the 
connotation of increasing the system reliability by duplication (i.e. there are 
multiple copies but there's nothing that indicates the justification for them). 
 Redundancy occurs in TMR (triple modular redundancy) systems used (as I guess 
Bernhard knows well) in triplicated control systems in commercial aircraft.  I 
don't know about you but I 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

.…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 bulletin board  On Behalf Of John R Helliwell
Sent: Tuesday, June 30, 2020 08:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?

 

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 mailto:herman.schreu...@sanofi.com> > wrote:

 

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 adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

 

What do you think?

Herman

 

 

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

 

EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk 
<mailto:owner-ccp...@jiscmail.ac.uk>  

 

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:-

http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 
<https://urldefense.proofpoint.com/v2/url?u=http-3A__ww1.iucr.org_iucr-2Dtop_comm_cnom_statdes_recomm.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=vb2CFOGKla49hE2sbHAt6LCUz63K7uis9PmSUxUgMcM&s=-45HByHsLJPmc2KRmPKamiFNf1WFCI51GonllFyIRTE&e=>
 

Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym. 

Greetings,

John 

 

Emeritus Professor John R Helliwell DSc

 

 





On 30 Jun 2020, at 13:11, Phil Jeffrey mailto:pjeff...@princeton.edu> > wrote:

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 - Graeme's 
pragmatic defense of multiplicity actually works both ways - any person who 
takes the trouble to read the stats table, now exiled to Supplementary Data, 
knows what it means.  Surely, then, the only way forward on this almost totally 
irrelevant discussion is to come up with a universally-loathed nomenclature 
that pleases nobody, preferably an acronym whose origins will be lost to 
history and the dusty CCP4 archives (which contain threads similar to this 
one).  I humbly submit:

NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions of the 
inappropriateness of "R-factor" ?  I have a long history of rearguard action 
trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
from me on this for years.

(Personally I'm pining for Gerard Kleywegt to resume his quest for overextended 
naming rationales, of which ValLigURL is a personal 'favo[u]rite'.  But I'm 
just old-fashioned.)

Ironically,
Phil Jeffrey
Princeton

[* I too have collected 540 degrees in P1 to solve a SAD structure, just 
because I could, hence "nearly"]
[** The actual answer to this thread is: history is written by the authors of 
scaling programs - and I think the Americans are currently losing at this game, 
thus perilously close to making themselves redundant.]

On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:



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 strictly not 
“redundant”.

The amount that anyone outside of methods development cares about the “epsilon” 
multiplicity of reflections is … negligible?

Sorry for chucking pragmatism into a dogmatic debate 😀

Cheerio 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

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 lengthy read-out times led to designing data collection
strategies so that they would achieve completeness in the smallest number of
"frames", themselves chosen as thick-sliced as possible while avoiding
angular overlap because of the read-out noise added to each such frame. With
this mindset, measuring again a reflection that had already been measured
could have been viewed as a waste of effort, bringing water to the mill of
interpreting "redundancy" as a sign of sub-optimality. However, looking
again at the CCD datasets collected according to this paradigm, they are
dire! Minimal availability of symmetry-related measurements made internal
scaling fragile, the terrible corner effects in the 3x3 detectors could not
be corrected, and the tracking of radiation damage was beyond hope.

 A lot has happened since, namely pixel-array detectors, fine-sliced
images recorded at low transmission, aiming at recording symmetry-related
reflections "a large number of times" - whatever one ends up calling that.
Far from being superfluous, or "redundant" in the negative sense of the
term, these "abundant" measurements (to coin a phrase) are now recognised as
being absolutely crucial towards the rejection of outliers, a key process in
obtaining high-quality data. This would then bring us back to the positive,
even noble connotation of the term "redundancy", since an abundance of
symmetry-related measurements now allows the detection and rejection of the
dodgy ones. From that perspective, "redundant" is good in the sense Ian
mentioned in relation to aviation equipment: if a few of those measurements
are rotten, you can throw them away and still have some left to do the job.
If you have abundant measurements and just call them multiple, this sense of
allowing rescue in case of failure disappears, and with it an important
aspect of why one should go for strategies that harvest symmetry-related
measurement in high numbers. This is why I ceased to support the standard
term "multiplicity" in conversations with Ian and went along with his choice
of the term "redundancy" in the presentation of STARANISO results.


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2020 at 02:30:27PM +0100, Phil Evans wrote:
> 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  wrote:
> > 
> > 
> > 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 meanings are "not or no longer needed or useful; superfluous" or 
> > "exceeding what is necessary or natural; superfluous" and "needlessly 
> > repetitive; verbose".  In fact both redundant and abundant have the same 
> > Latin etymology, and redundant literally means 're' (again) + 'unda' 
> > (wave), i.e. 'repeating as a wave'.  The original meaning in English is in 
> > fact 'over-abundant' and is still used in poetry with that meaning (e.g. 
> > "as redundant as the poppies in the field").  There's of course also the 
> > meaning 'dismissal from a job due to a need to reduce the head count' and 
> > from there 'out of work', but that's relatively recent having been coined 
> > by a UK Government official in the 1900s!
> > 
> > The correct and totally precise scientific meaning which is appropriate in 
> > the context of this discussion is to be found here: 
> > https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it 
> > applies equally to both hardware and software engineering:
> > 
> > Redundancy is the duplication of critical components or functions of a 
> > system with the intention of increasing reliability of the system, usually 
> > in the form of a backup or fail-safe, or to improve actual system 
> > performance.
> > 
> > Nothing there about not or no longer needed or useful, superfluous, 
> > needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to 
> > carry the connotation of increasing the system reliability by duplication 
> > (i.e. there are multiple copies but there's nothing that indicates the 
> > justification for them).  Redundancy occurs in TMR (triple modular 
> > redundancy) systems used (as I guess Bernhard knows well) in triplicated 
> > control systems in commercial aircraft.  I don't know about you but I 
> > wouldn

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

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  
> wrote:
> 
> 
> 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 adequately describe this particular 
> statistic and is not associated with entrenched traditions at either side of 
> the Atlantic.
>  
> What do you think?
> Herman
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von John R 
> Helliwell
> Gesendet: Dienstag, 30. Juni 2020 14:34
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> 
>  
> 
> 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:-
> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html
> Point 1, first sentence, fits the various wishes of this thread succinctly, 
> if not in a single word, and even not readily allowing an easy acronym. 
> Greetings,
> John 
>  
> 
> Emeritus Professor John R Helliwell DSc
>  
>  
> 
> 
> On 30 Jun 2020, at 13:11, Phil Jeffrey  wrote:
> 
> 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 - Graeme's 
> pragmatic defense of multiplicity actually works both ways - any person who 
> takes the trouble to read the stats table, now exiled to Supplementary Data, 
> knows what it means.  Surely, then, the only way forward on this almost 
> totally irrelevant discussion is to come up with a universally-loathed 
> nomenclature that pleases nobody, preferably an acronym whose origins will be 
> lost to history and the dusty CCP4 archives (which contain threads similar to 
> this one).  I humbly submit:
> 
> NFDOF: Nearly Futile Data Overcollection Factor ?
> [*]
> 
> Or, even better, could we not move on to equally pointless discussions of the 
> inappropriateness of "R-factor" ?  I have a long history of rearguard action 
> trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
> from me on this for years.
> 
> (Personally I'm pining for Gerard Kleywegt to resume his quest for 
> overextended naming rationales, of which ValLigURL is a personal 
> 'favo[u]rite'.  But I'm just old-fashioned.)
> 
> Ironically,
> Phil Jeffrey
> Princeton
> 
> [* I too have collected 540 degrees in P1 to solve a SAD structure, just 
> because I could, hence "nearly"]
> [** The actual answer to this thread is: history is written by the authors of 
> scaling programs - and I think the Americans are currently losing at this 
> game, thus perilously close to making themselves redundant.]
> 
> On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
> 
> 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 strictly 
> not “redundant”.
> The amount that anyone outside of methods development cares about the 
> “epsilon” multiplicity of reflections is … negligible?
> Sorry for chucking pragmatism into a dogmatic debate 😀
> Cheerio Graeme
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Phil Evans]

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  wrote:
> 
> 
> 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 meanings are "not or no longer needed or useful; superfluous" or 
> "exceeding what is necessary or natural; superfluous" and "needlessly 
> repetitive; verbose".  In fact both redundant and abundant have the same 
> Latin etymology, and redundant literally means 're' (again) + 'unda' (wave), 
> i.e. 'repeating as a wave'.  The original meaning in English is in fact 
> 'over-abundant' and is still used in poetry with that meaning (e.g. "as 
> redundant as the poppies in the field").  There's of course also the meaning 
> 'dismissal from a job due to a need to reduce the head count' and from there 
> 'out of work', but that's relatively recent having been coined by a UK 
> Government official in the 1900s!
> 
> The correct and totally precise scientific meaning which is appropriate in 
> the context of this discussion is to be found here: 
> https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it 
> applies equally to both hardware and software engineering:
> 
> Redundancy is the duplication of critical components or functions of a system 
> with the intention of increasing reliability of the system, usually in the 
> form of a backup or fail-safe, or to improve actual system performance.
> 
> Nothing there about not or no longer needed or useful, superfluous, 
> needlessly repetitive, verbose!  Note that 'multiplicity' totally fails to 
> carry the connotation of increasing the system reliability by duplication 
> (i.e. there are multiple copies but there's nothing that indicates the 
> justification for them).  Redundancy occurs in TMR (triple modular 
> redundancy) systems used (as I guess Bernhard knows well) in triplicated 
> control systems in commercial aircraft.  I don't know about you but I 
> wouldn't regard the extra two backup systems in TMR as 'not needed or useful' 
> when I'm an airline passenger !
> 
> https://en.wikipedia.org/wiki/Triple_modular_redundancy
> 
> More is always better when it's critical:
> 
> https://www.isa.org/standards-and-publications/isa-publications/intech-magazine/2003/october/more-is-always-better-when-its-critical
> 
> There's also the question of the same word (redundancy, multiplicity or 
> whatever) having different meanings according to context.  That's unavoidable 
> given that the number of concepts that we might want to name far exceeds the 
> number of words available, so we have to rely heavily on context when 
> assigning meaning.  We don't say what the context is so the context must be 
> obvious and unambiguous.  Whether we're talking about RAID or losing one's 
> job it's obvious what the intended meaning is from the context because the 
> contexts are totally separate.  The important thing is that the contexts 
> should be well-separated so that no confusion is possible.  Graeme says he's 
> not confused by the various meanings of 'multiplicity' but 
> non-crystallographer consumers of Table 1 surely might be!  The various 
> contexts in which 'multiplicity' is used are certainly not well-separated and 
> overlap in program outputs and documentation, allowing plenty of scope for 
> confusion.
> 
> In a scientific context 'redundancy' has a unique precise meaning whereas 
> 'multiplicity' has a multiplicity!
> 
> BTW I use CCP4/Aimless and 'redundancy' (as you no doubt will have guessed, 
> because it's the word that unambiguously describes the concept), so 
> apparently I'm with you lot across the pond on this!
> 
> Cheers
> 
> -- Ian
>  
> 
> 
> On Tue, 30 Jun 2020 at 09:01, 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 
> > 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 
> >> defines as "not or no longer needed or useful; superfluous" and the 
> >> American Heritage Dictionary as "exceeding what is necessary or 
> >> natural; superfluous" and "needlessly repetitive; verbose".
> >>
> >> Please don't use the term Needless repetitivity in your Table 1.  It 
> >

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[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 meanings are "not or no longer needed or useful; superfluous" or
"exceeding what is necessary or natural; superfluous" and "needlessly
repetitive; verbose".  In fact both redundant and abundant have the same
Latin etymology, and redundant literally means 're' (again) + 'unda'
(wave), i.e. 'repeating as a wave'.  The original meaning in English is in
fact 'over-abundant' and is still used in poetry with that meaning (e.g.
"as redundant as the poppies in the field").  There's of course also the
meaning 'dismissal from a job due to a need to reduce the head count' and
from there 'out of work', but that's relatively recent having been coined
by a UK Government official in the 1900s!

The correct and totally precise scientific meaning which is appropriate in
the context of this discussion is to be found here:
https://en.wikipedia.org/wiki/Redundancy_(engineering) .  Note that it
applies equally to both hardware and software engineering:

*R**edundancy* is the duplication of critical components or functions of a
system with the intention of increasing reliability of the system
, usually in the form of a backup or
fail-safe , or to improve actual
system performance.

Nothing there about not or no longer needed or useful, superfluous, needlessly
repetitive, verbose!  Note that 'multiplicity' totally fails to carry the
connotation of increasing the system reliability by duplication (i.e. there
are multiple copies but there's nothing that indicates the justification
for them).  Redundancy occurs in TMR (triple modular redundancy) systems
used (as I guess Bernhard knows well) in triplicated control systems in
commercial aircraft.  I don't know about you but I wouldn't regard the
extra two backup systems in TMR as 'not needed or useful' when I'm an
airline passenger !

https://en.wikipedia.org/wiki/Triple_modular_redundancy

More is always better when it's critical:

https://www.isa.org/standards-and-publications/isa-publications/intech-magazine/2003/october/more-is-always-better-when-its-critical

There's also the question of the same word (redundancy, multiplicity or
whatever) having different meanings according to context.  That's
unavoidable given that the number of concepts that we might want to name
far exceeds the number of words available, so we have to rely heavily on
context when assigning meaning.  We don't say what the context is so the
context must be obvious and unambiguous.  Whether we're talking about RAID
or losing one's job it's obvious what the intended meaning is from the
context because the contexts are totally separate.  The important thing is
that the contexts should be well-separated so that no confusion is
possible.  Graeme says he's not confused by the various meanings of
'multiplicity' but non-crystallographer consumers of Table 1 surely might
be!  The various contexts in which 'multiplicity' is used are certainly not
well-separated and overlap in program outputs and documentation, allowing
plenty of scope for confusion.

In a scientific context 'redundancy' has a unique precise meaning whereas
'multiplicity' has a multiplicity!

BTW I use CCP4/Aimless and 'redundancy' (as you no doubt will have guessed,
because it's the word that unambiguously describes the concept), so
apparently I'm with you lot across the pond on this!

Cheers

-- Ian



On Tue, 30 Jun 2020 at 09:01, 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
>> > 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
>> >> defines as "not or no longer needed or useful; superfluous" and the
>> >> American Heritage Dictionary as "exceeding what is necessary or
>> >> natural; superfluous" and "needlessly repetitive; verbose".
>> >>
>> >> Please don't use the term Needless repetitivity in your Table 1.  It
>> >> sends the wrong message.  Multiplicity is good.
>> >>
>> >> All best.
>> >>
>> >>
>> >> Andreas
>> >>
>> >>
>> >>
>> >> On Tue, Jun 30, 2020 at 12:03 AM James Holton > >> > wrote:
>> >>
>> >> 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

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Schuller]

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, 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 
defines as "not or no longer needed or useful; superfluous" and the 
American Heritage Dictionary as "exceeding what is necessary or 
natural; superfluous" and "needlessly repetitive; verbose".


Please don't use the term Needless repetitivity in your Table 1.  It 
sends the wrong message.  Multiplicity is good.


All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton > wrote:


    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 bad as "intensity", which is so ambiguous 
as to be almost useless as a word on its own.


    -James Holton
    MAD Scientist

    On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


    > 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 


 1. the position multiplicity (number of equivalent sites per 
unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of 
multiplicity
 2. the multiplicity of the reflection, which means the 
superposition of reflections with the same /d/  (mostly powder 
diffraction) 

 3. the multiplicity of observations, aka redundancy.

    While (a) and (b) are clearly defined, (c) is an arbitrary 
experimental number.


    How from (a) real space symmetry follows (b) in reciprocal space 
(including the epsilon zones, another ‘multiplicity’) is explained 
here 


    https://scripts.iucr.org/cgi-bin/paper?a14080 
 



    and also on page 306 in BMC.

    Too much multiplicity might create duplicity… 

    Cheers, BR

    __ __

    Jon Cooper

    __ __

    On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> wrote:


    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 Program, CSIRO
    343 Royal Parade
    Parkville, VIC, 3052
    +613 9662 7304
    +614 57 539 419
    tom.p...@csiro.au  

    __ __



--


    *From:*CCP4 bulletin board > on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
>

    *Sent:* Wednesday, June 24, 2020 1:10 AM
    *To:* CCP4BB@JISCMAIL.AC.UK  
mailto:CCP4BB@JISCMAIL.AC.UK>>
    *Subject:* Re: [ccp4bb] number of frames to get a full 
dataset? 


    

    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, altho

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Waterman]

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
>> > 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
>> >> defines as "not or no longer needed or useful; superfluous" and the
>> >> American Heritage Dictionary as "exceeding what is necessary or
>> >> natural; superfluous" and "needlessly repetitive; verbose".
>> >>
>> >> Please don't use the term Needless repetitivity in your Table 1.  It
>> >> sends the wrong message.  Multiplicity is good.
>> >>
>> >> All best.
>> >>
>> >>
>> >> Andreas
>> >>
>> >>
>> >>
>> >> On Tue, Jun 30, 2020 at 12:03 AM James Holton > >> > wrote:
>> >>
>> >> 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 bad as "intensity", which is so ambiguous
>> >> as to be almost useless as a word on its own.
>> >>
>> >> -James Holton
>> >> MAD Scientist
>> >>
>> >> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
>> >>>
>> >>> > 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 
>> >>>
>> >>>  1. the position multiplicity (number of equivalent sites per
>> >>> unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of
>> >>> multiplicity
>> >>>  2. the multiplicity of the reflection, which means the
>> >>> superposition of reflections with the same /d/  (mostly powder
>> >>> diffraction) 
>> >>>  3. the multiplicity of observations, aka redundancy.
>> >>>
>> >>> While (a) and (b) are clearly defined, (c) is an arbitrary
>> >>> experimental number.
>> >>>
>> >>> How from (a) real space symmetry follows (b) in reciprocal space
>> >>> (including the epsilon zones, another ‘multiplicity’) is explained
>> >>> here 
>> >>>
>> >>> https://scripts.iucr.org/cgi-bin/paper?a14080
>> >>> <
>> https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/paper?a14080__;!!GobTDDpD7A!Z-SrnEqSZwQOXWOwbMCkZ1GB3fvdFuQ5lzYUYwQdUVTCALc3j9O3xqX7-s72_nF7$>
>>
>> >>> 
>> >>>
>> >>> and also on page 306 in BMC.
>> >>>
>> >>> Too much multiplicity might create duplicity… 
>> >>>
>> >>> Cheers, BR
>> >>>
>> >>> __ __
>> >>>
>> >>> Jon Cooper
>> >>>
>> >>> __ __
>> >>>
>> >>> On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)"
>> >>> mailto:tom.p...@csiro.au>> wrote:
>> >>>
>> >>> 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 Program, CSIRO
>> >>> 343 Royal Parade
>> >>> Parkville, VIC, 3052
>> >>> +613 9662 7304
>> >>> +614 57 539 419
>> >>> tom.p...@csiro.au  
>> >>>
>> >>> __ __
>> >>>
>> >>>
>> 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Waterman]

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
> > 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
> >> defines as "not or no longer needed or useful; superfluous" and the
> >> American Heritage Dictionary as "exceeding what is necessary or
> >> natural; superfluous" and "needlessly repetitive; verbose".
> >>
> >> Please don't use the term Needless repetitivity in your Table 1.  It
> >> sends the wrong message.  Multiplicity is good.
> >>
> >> All best.
> >>
> >>
> >> Andreas
> >>
> >>
> >>
> >> On Tue, Jun 30, 2020 at 12:03 AM James Holton  >> > wrote:
> >>
> >> 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 bad as "intensity", which is so ambiguous
> >> as to be almost useless as a word on its own.
> >>
> >> -James Holton
> >> MAD Scientist
> >>
> >> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
> >>>
> >>> > 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 
> >>>
> >>>  1. the position multiplicity (number of equivalent sites per
> >>> unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of
> >>> multiplicity
> >>>  2. the multiplicity of the reflection, which means the
> >>> superposition of reflections with the same /d/  (mostly powder
> >>> diffraction) 
> >>>  3. the multiplicity of observations, aka redundancy.
> >>>
> >>> While (a) and (b) are clearly defined, (c) is an arbitrary
> >>> experimental number.
> >>>
> >>> How from (a) real space symmetry follows (b) in reciprocal space
> >>> (including the epsilon zones, another ‘multiplicity’) is explained
> >>> here 
> >>>
> >>> https://scripts.iucr.org/cgi-bin/paper?a14080
> >>> <
> https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/paper?a14080__;!!GobTDDpD7A!Z-SrnEqSZwQOXWOwbMCkZ1GB3fvdFuQ5lzYUYwQdUVTCALc3j9O3xqX7-s72_nF7$>
>
> >>> 
> >>>
> >>> and also on page 306 in BMC.
> >>>
> >>> Too much multiplicity might create duplicity… 
> >>>
> >>> Cheers, BR
> >>>
> >>> __ __
> >>>
> >>> Jon Cooper
> >>>
> >>> __ __
> >>>
> >>> On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)"
> >>> mailto:tom.p...@csiro.au>> wrote:
> >>>
> >>> 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 Program, CSIRO
> >>> 343 Royal Parade
> >>> Parkville, VIC, 3052
> >>> +613 9662 7304
> >>> +614 57 539 419
> >>> tom.p...@csiro.au  
> >>>
> >>> __ __
> >>>
> >>>
> 
> > --
> >>>
> >>> *From:*CCP4 bulletin board  >>> > on behalf of
> >>> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk
> >>> 
> >>> <0c2488af9525-dmarc-requ...@jiscmai

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[James Holton]

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 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 "needlessly repetitive; verbose".


Please don't use the term Needless repetitivity in your Table 1.  It 
sends the wrong message.  Multiplicity is good.


All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton > wrote:


    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 bad as "intensity", which is so ambiguous 
as to be almost useless as a word on its own.


    -James Holton
    MAD Scientist

    On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


    > 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 


 1. the position multiplicity (number of equivalent sites per 
unit cell, aka Wyckoff-Multiplicity), the only (!) cif use of 
multiplicity
 2. the multiplicity of the reflection, which means the 
superposition of reflections with the same /d/  (mostly powder 
diffraction) 

 3. the multiplicity of observations, aka redundancy.

    While (a) and (b) are clearly defined, (c) is an arbitrary 
experimental number.


    How from (a) real space symmetry follows (b) in reciprocal space 
(including the epsilon zones, another ‘multiplicity’) is explained 
here 


    https://scripts.iucr.org/cgi-bin/paper?a14080 
 



    and also on page 306 in BMC.

    Too much multiplicity might create duplicity… 

    Cheers, BR

    __ __

    Jon Cooper

    __ __

    On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" 
mailto:tom.p...@csiro.au>> wrote:


    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 Program, CSIRO
    343 Royal Parade
    Parkville, VIC, 3052
    +613 9662 7304
    +614 57 539 419
    tom.p...@csiro.au  

    __ __



--


    *From:*CCP4 bulletin board > on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
>

    *Sent:* Wednesday, June 24, 2020 1:10 AM
    *To:* CCP4BB@JISCMAIL.AC.UK  
mailto:CCP4BB@JISCMAIL.AC.UK>>
    *Subject:* Re: [ccp4bb] number of frames to get a full 
dataset? 


    

    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 is nagging 
you to get of

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Edward A. Berry]

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 defines as "not or no longer needed or useful; superfluous" and the 
American Heritage Dictionary as "exceeding what is necessary or natural; superfluous" and 
"needlessly repetitive; verbose".

Please don't use the term Needless repetitivity in your Table 1.  It sends the 
wrong message.  Multiplicity is good.

All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton mailto:jmhol...@lbl.gov>> wrote:

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 bad as "intensity", which is so ambiguous as to be 
almost useless as a word on its own.

-James Holton
MAD Scientist

On 6/24/2020 10:27 AM, Bernhard Rupp wrote:


> 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 

 1. the position multiplicity (number of equivalent sites per unit cell, 
aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
 2. the multiplicity of the reflection, which means the superposition of 
reflections with the same /d/  (mostly powder diffraction) 
 3. the multiplicity of observations, aka redundancy.

While (a) and (b) are clearly defined, (c) is an arbitrary experimental 
number.

How from (a) real space symmetry follows (b) in reciprocal space (including 
the epsilon zones, another ‘multiplicity’) is explained here 

https://scripts.iucr.org/cgi-bin/paper?a14080 

 

and also on page 306 in BMC.

Too much multiplicity might create duplicity… 

Cheers, BR

__ __

Jon Cooper

__ __

On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" mailto:tom.p...@csiro.au>> wrote:

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 Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au  

__ __




--


*From:*CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on 
behalf of 0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
>
*Sent:* Wednesday, June 24, 2020 1:10 AM
*To:* CCP4BB@JISCMAIL.AC.UK  
mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject:* Re: [ccp4bb] number of frames to get a full dataset? 



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 
is nagging you to get off the beam line or if your diffraction fades quickly. 
Going for 180 degrees always makes sense for a well-behaved crystal