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 <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' 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 <dgwater...@gmail.com> wrote:
Reflections are as "redundant" as the disks in a RAID 0 array
On Tue, 30 Jun 2020, 02:49 James Holton, <jmhol...@lbl.gov> 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 <jmhol...@lbl.gov
<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
<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)"
<tom.p...@csiro.au <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 <mailto:tom.p...@csiro.au> ____
__ __
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*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of
00000c2488af9525-dmarc-requ...@jiscmail.ac.uk
<mailto:00000c2488af9525-dmarc-requ...@jiscmail.ac.uk>
<00000c2488af9525-dmarc-requ...@jiscmail.ac.uk
<mailto:00000c2488af9525-dmarc-requ...@jiscmail.ac.uk>>
*Sent:* Wednesday, June 24, 2020 1:10 AM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
<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,
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 <mailto: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.com/v3/__https://doi.org/10.1107/S2059798319003528__;!!GobTDDpD7A!Z-SrnEqSZwQOXWOwbMCkZ1GB3fvdFuQ5lzYUYwQdUVTCALc3j9O3xqX7-hiQXkxe$>____
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 <mailto: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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