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 <http://staraniso.globalphasing.org/~itickle/staraniso_glossary.html>. 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 > > > > > > > > > > Confidentiality Note: This message is intended only for the use of the > named recipient(s) > > and may contain confidential and/or privileged information. If you are > not the intended > > recipient, please contact the sender and delete the message. Any > unauthorized use of > > the information contained in this message is prohibited. > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
