Dear Colleagues,
Now that Herman has announced a quietude I thought you might enjoy this quite
short report on a synchrotron radiation issue that came up some years back via
the JSR Main Editors into the IUCr Nomenclature Committee, chaired by Andre
Authier, Past President of the IUCr:-
https://journals.iucr.org/s/issues/2005/03/00/es0344/es0344.pdf
Have a great weekend,
John
Emeritus Professor John R Helliwell DSc
> On 3 Jul 2020, at 11:22, Schreuder, Herman /DE <herman.schreu...@sanofi.com>
> wrote:
>
>
> Dear David,
>
> Thank you for your reaction. It has become clear to me that although most
> people understand what I intended with “measurement”, in practice it is very
> much in the eye of the beholder. It was suggested in the BB to use
> observation instead, but I am fairly sure that some people will also have
> issues with that.
>
> The advantage of multiplicity/redundancy is that it does not mention what is
> multiple or redundant and that one can refer to the program documentation for
> an exact definition. Since most people are happy with the
> multiplicity/redundancy they grew up with, that is the way it will stay.
>
> Best regards,
> Herman
>
>
>
>
> Von: David Waterman <dgwater...@gmail.com>
> Gesendet: Freitag, 3. Juli 2020 10:49
> An: Schreuder, Herman /DE <herman.schreu...@sanofi.com>
> Cc: CCP4BB@jiscmail.ac.uk
> Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of
> frames to get a full dataset?
>
> EXTERNAL : Real sender is dgwater...@gmail.com
>
>
>
> Hi Herman,
>
> I like the idea of MPR, but I continue to worry about the term "measurement".
> The intensity associated with a particular reflection is a fit based on a
> scaling model, and ultimately, depending on your integration software, may be
> linked to a weighted sum of two raw measurements: the summation and
> profile-fitted intensities. I think these are the measurements, not the
> intensity derived during the scaling procedure. Sure, anyone who wants to be
> even more pedantic than me will point out that these "raw measurements" are
> also the result of fitting procedures. However, to my eyes, the difference is
> that we don't consider the profile and summation integrated intensities to
> change as a result of the procedure that ultimately determines the statistic
> (MPR) of interest. During that procedure they are independent, not dependent
> variables.
>
> Maybe I am worrying about nothing. It agree it is fairly clear what you mean
> by MPR. I just wanted to explore if there was any opportunity for further
> reducing ambiguity.
>
> Cheers
> -- David
>
>
> On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE
> <herman.schreu...@sanofi.com> wrote:
> Dear Ian,
>
> Since some very advanced countries still use miles, Fahrenheit and inches, I
> did not expect anything to change. It was an escalating discussion in this
> thread on data completeness(!) on the use of multiplicity vs redundancy that
> made me suggest a different term. Except for an occasional discussion in the
> BB, there is nothing against people using the term they are most comfortable
> with.
>
> However, I insist that trying to impose a different definition of
> “measurement” for MPR vs the definition used for the calculation of
> redundancy/multiplicity is not a valid argument against MPR.
>
> Cheers,
> Herman
>
>
>
>
> Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Ian Tickle
> Gesendet: Donnerstag, 2. Juli 2020 22:06
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a
> full dataset?
>
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
>
> 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
> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear all
>
> I’ve been persuaded that MPR is a useful name (and see that there are
> shortcomings with both “multiplicity” and “redundancy") and I agree with much
> of what’s been said most recently in this thread.
>
> BTW, just because the Physics definition of a measurement/quantity/whatever
> is given on wikipedia (or elsewhere, for that matter), it doesn’t mean that’s
> what we (crystallographers, structural biologists, etc) should use without
> question. If you check
>
> https://en.wikipedia.org/wiki/Reflection_(physics)
>
> you will find no mention of diffraction maxima corresponding to reflections
> except a link to a page on diffraction. Or maybe we should slavishly follow
> the Physicists and use another term…
>
> H
>
> > On 2 Jul 2020, at 10:41, Schreuder, Herman /DE
> > <herman.schreu...@sanofi.com> wrote:
> >
> > Dear all,
> >
> > While following the development of this thread, I am truly amazed how
> > people cling to names for the number of measurements per reflection whose
> > meaning:
> > • Depends on the cultural/engineering/scientific context
> > • Can only be understood by experts
> > • Where the experts, as witnessed by the discussions in this thread,
> > do not agree on which name to use.
> >
> > What is wrong with the name “measurements per reflection”? The definition
> > for measurement is the same as is used to calculate the
> > multiplicity/redundancy.
> > The only disadvantage I see is that it can be understood by non-experts as
> > well, which reminds me of medical doctors, who invent complicated Latin
> > names for common ailments to prevent patients to understand where they are
> > talking about.
> >
> > Another 2 cents/pennies from my side,
> > Herman
> >
> >
> >
> > Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von James Holton
> > Gesendet: Mittwoch, 1. Juli 2020 20:52
> > 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
> >
> >
> >
> >
> > Sorry to take this thread on a detour/diversion: What I was attempting to
> > point out below, perhaps unclearly, is that the different interpretations
> > of the word "redundant" are a cultural difference. As a student of
> > multiple English languages perhaps I can explain:
> >
> > Few US English speakers know that in UK/European/Australian English the
> > word "redundant" has a strong negative connotation. I, for one, was
> > surprised to learn that the phrase "made redundant" is used in the UK to
> > describe loss of employment. That is, a layoff, firing or perhaps a
> > furlough. So, I think it important to spell out for my fellow US English
> > speakers that the emotional ties to this negative connotation can be strong
> > ones.
> >
> > Conversely, many UK English speakers do not know that in US English the
> > word "redundant" has a strong positive connotation. We never use the
> > phrase "made redundant" to describe a lost job. Most Americans I think
> > would be confused by such a turn of phrase. If a US English speaker was
> > told their jobs was "made redundant" they would most likely think that a
> > new hire was onboarded to back them up. This would imply that their job
> > was so important that the company wanted at least two people doing it, just
> > in case you got hit by a bus. This strong positive connotation also has
> > emotional roots.
> >
> > Personally, I prefer the positive connotation. Perhaps that is my cultural
> > bias, or perhaps I just generally believe that positivity is better than
> > negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has
> > changed enormously over the last few hundred years, and I don't think we're
> > going to change that any more than we are going to change the meaning of
> > "redundant" in these two major forms of English.
> >
> > However, just because a word has slightly different meanings in two
> > slightly different languages does not mean we should abandon it. Are we
> > going to stop eating "chips" just because we are not sure if our fried
> > potato will come as sliced wedges or thin crispy wafers? If you are unhappy
> > with your meal, is it the fault of the culture you are visiting? or the
> > customer for forgetting where they are? Context is everything.
> >
> > So, for those unfamiliar with one or more of the major English-speaking
> > cultures, here are a few other important differences to be aware of:
> > "Football" may not be the game you think it is.
> > If you are offered a "biscuit" in the US, do not expect it to be sweet.
> > If you want to leave a building you should take the "lift" to the "ground
> > floor", but if you take an "elevator" get off on the "1st floor".
> > A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it
> > only means an unintelligent person, or a plastic replica of one.
> > "please" and "thank you" are considered baseline politeness in some English
> > cultures, but their excessive use in others, such as the US, can be seen as
> > rude.
> > A "tap" in the US dispenses beer, water comes out of a "faucet".
> > A "flat" in the US is not a place to live, but rather where we test rocket
> > cars.
> > "Gas" can be a liquid in the US.
> > "Rubber" is a substance in both languages, but in the US a lump of it meant
> > for erasing pencil marks is an "eraser". Do not ask for a "rubber" at the
> > shop unless you are sure which country you are in.
> > A "holiday" in the US is a special day on the calendar when everyone gets
> > off work, not just when an individual takes a "vacation".
> > If you go walking down the "pavement" you are risking getting hit by a car
> > in the US, because that is what we call the road bed, not the "sidewalk".
> > A "torch", is a handheld electric light in the UK, but in the US it is a
> > flaming stick of wood.
> > A "queue" is a line of people in the UK, but in the US it is known only to
> > computer scientists submitting jobs on a cluster.
> >
> > Then there are words like "capillary", which means the same thing in both
> > languages but the alternate pronunciations never fail to enrage someone. It
> > is perhaps odd that since US English and UK English are spoken with many
> > different accents we pronounce essentially every word at least slightly
> > differently, but for some reason "capillary" makes people angry. Same with
> > "schedule". Equally emotional responses arise from how you pronounce the
> > letter "z". Go figure.
> >
> > Similar ire is risen for spelling. My favourite/favorite is
> > aluminum/aluminium, but equally divisive are colour/color, tire/tyre,
> > cheque/check, gray/grey, theatre/theater, pyjamas/pajamas, and many others.
> >
> > It is at this stage when you will find people of another culture trying to
> > "correct" you on how to speak or write your own language. This can be
> > confusing because you will probably not be corrected for calling a
> > "courgette" a "zucchini", especially if you are Italian. However, a native
> > Hindi speaker might feel compelled to correct your pronunciation of
> > "shampoo". I am not singling out any one culture here, we have all given
> > in to the temptation to "correct" someone, perhaps even while visiting
> > their home. Ahh, the errors of my youth.
> >
> > All that said, I don't think this forum is the place to discuss cultural
> > differences. This is especially true once we start using words like
> > "correct"/"incorrect" and "right"/"wrong", as these tend to generate far
> > more heat than light. However, I do think it important to identify and
> > describe cultural differences when they start to impede scientific
> > discussion. It is OK to disagree. But let it be over interpretation of
> > complete information that both parties possess, not preconceived notions
> > nor ignorance of the complete picture. If we understand WHY another person
> > thinks in a way we find disagreeable, then perhaps we have a better chance
> > of moving forward and enjoying the upcoming celebrations of
> > Independence/GoodRiddanceUngratefulColonials Day.
> >
> > Whatever you call it, an eggplant or an an aubergine, its odour/odor and
> > flavour/flavor are the same. I apologize/apologise to my
> > neighbours/neighbors across the Lake/Pond for my behaviour/behavior if you
> > are not enamoured/enamored with my endeavour/endeavor at humor/humour. It
> > is not my specialty/speciality. fullstop/period.
> >
> > -James Holton
> > MAD Scientist
> >
> >
> > On 6/29/2020 3:36 PM, Bernhard Rupp wrote:
> > I think it is time to escalate that discussion to crystallographic
> > definition purists like Massimo or to a logical consistency proponent like
> > Ian who abhors definitional vacuum 😊
> >
> > Cheers, BR
> >
> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Andreas
> > Förster
> > Sent: Monday, June 29, 2020 15:24
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] number of frames to get a full dataset?
> >
> > 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 <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
> >
> > • the position multiplicity (number of equivalent sites per unit
> > cell, aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
> > • the multiplicity of the reflection, which means the superposition
> > of reflections with the same d (mostly powder diffraction)
> > • 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)"
> > <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 <CCP4BB@JISCMAIL.AC.UK> on behalf of
> > 00000c2488af9525-dmarc-requ...@jiscmail.ac.uk
> > <00000c2488af9525-dmarc-requ...@jiscmail.ac.uk>
> > Sent: Wednesday, June 24, 2020 1:10 AM
> > To: CCP4BB@JISCMAIL.AC.UK <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, or 360 degrees if you want super anomalous differences. Hope this
> > helps a bit.
> >
> > Jon Cooper
> >
> > On 23 Jun 2020 07:29, Andreas Förster <andreas.foers...@dectris.com> wrote:
> > Hi Murpholino,
> >
> > in my opinion (*), the question is neither number of frames nor degrees.
> > The only thing that matters to your crystal is dose. How many photons does
> > your crystal take before it dies? Consequently, the question to ask is How
> > best to use photons. Some people have done exactly that.
> > https://doi.org/10.1107/S2059798319003528
> >
> > All best.
> >
> >
> > Andreas
> >
> >
> > (*) Disclaimer: I benefit when you use PILATUS or EIGER - but I want you
> > to use them to your advantage.
> >
> >
> >
> > On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro <murpholi...@gmail.com>
> > wrote:
> > Hi.
> > Quick question...
> > I have seen *somewhere* that to get a 'full dataset we need to collect n
> > frames':
> > at least 180 frames if symmetry is X
> > at least 90 frames if symmetry is Y
> > at least 45 frames if symmetry is Z
> > Can somebody point where is *somewhere*?
> >
> > ...also...
> > what other factors can change n... besides symmetry and radiation damage?
> >
> > Thanks
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >
> >
> > --
> > Andreas Förster, Ph.D.
> > Application Scientist Crystallography, Area Sales Manager Asia & Pacific
> > Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
> > andreas.foers...@dectris.com
> > DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
> > www.dectris.com
> >
> >
> >
> >
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