There is probably some justification for the absence of 'reflection' (as used
in crystallography) - in 'purist' Physics. The process
itself is not a 'reflection', despite that it can be macroscopically described
(in first approximation at least, and good enough for finding diffraction spot
positions)
as the 'reflection' (as in mirror) on a lattice plane. The underlying single
scattering photon process itself - and the bb discussed this in multiple
threads - is
inherently quantum mechanical, and the 'reality' of that process is not readily
visualized in macroscopic, human-brain-derived terms.
Happy mpring, BR
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Harry Powell -
CCP4BB
Sent: Thursday, July 2, 2020 03:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a
full dataset?
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
>
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>
>
> --
> 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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