Hi Herman, I started googling and ended up completely lost down a rabbit hole (have a look here if you want to see what I mean: https://plato.stanford.edu/entries/measurement-science/). As a result I'm no longer sure I know what the word "measurement" means! I tried to simplify things with a practical example. Let's say I take a set of clearly real world measurements (temperature values over time, say). I can take the mean of subsets of these values and maybe that is a "measurement" too - especially for readings taken in quick succession, expressly done to reduce measurement error. But what if I fit a line to a series of values, is the gradient of the line also a "measurement"? Maybe?
Anyway, for MPR it probably doesn't matter if the measurement is of a response variable, rather than something "raw". That's because MPR isn't actually affected by the values themselves (ignoring the thorny issue of outlier rejection), it is just a count of them. Cheers -- David On Fri, 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__staraniso.globalphasing.org_-7Eitickle_staraniso-5Fglossary.html&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=YOMbn7m3LdRKpXMxrwkn8Qfa99nEsioggRbgwTvMFtM&e=>. > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.brainyquote.com_quotes_dylan-5Fmoran-5F557269-3Fsrc-3Dt-5Fplease-5Feveryone&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=e3bL2Imbw_jrHBV5-UdMXDmTLVsgmIktLHjdQzF5Vjc&e=> > > > > 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) > <https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Reflection-5F-28physics-29&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=tj7dE-cxPqP4L8eRvjiu0CaZL3VNFn19dKa-9VTdVvM&e=> > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__scripts.iucr.org_cgi-2Dbin_paper-3Fa14080&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=uHL7oQAeeuh10DrZQvGksLGrkHsdGucSKMblCZGSeNU&e=> > > > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1107_S2059798319003528&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=7PsShgmbN7Lnfs9SMUFk6q3ICDcrjGvo6EtogE8dEMQ&e=> > > > > 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=UyX3RjiV2Rb1RpRMT1-smotYE-Q3U3G0d_9di9M2Im4&e=> > > > > > > > > -- > > 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 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dectris.com&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=rkv3VHbs8Bfme-xQfteNHrAgAmRdtVOsCD3ryGGQbTI&s=fv0w1arJi-7fEBkRYf5lb6cPy4Z--8ijD8AxBi19cvk&e=> > > > > > > > > > > Confidentiality Note: This message is intended only for the use of the > named recipient(s) > > and may contain confidential and/or privileged information. 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