Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Waterman]

Reflections are as "redundant" as the disks in a RAID 0 array

On Tue, 30 Jun 2020, 02:49 James Holton,  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  >> > 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)"
> >>> 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  
> >>>
> >>> __ __
> >>>
> >>>
> 
> > --
> >>>
> >>> *From:*CCP4 bulletin board  >>> > on behalf of
> >>> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk
> >>> 
> >>> <0c2488af9525-dmarc-requ...@jiscmai

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Waterman]

Ok, the analogy is not great because most reflection data sets have some
"fault tolerance" whereas RAID 0 does not. But the point is that anything
that is not an exact copy and brings actual information should not be
considered "redundant"

On Tue, 30 Jun 2020, 09:00 David Waterman,  wrote:

> Reflections are as "redundant" as the disks in a RAID 0 array
>
> On Tue, 30 Jun 2020, 02:49 James Holton,  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 > >> > 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)"
>> >>> 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  
>> >>>
>> >>> __ __
>> >>>
>> >>>
>> 

Re: [ccp4bb] number of frames to get a full dataset?

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Or, we could accept the fact that crystallographers are kinda used to 
multiplicity of an individual Miller index being different to multiplicity of 
observations, and in Table 1 know which one you mean? 😉 Given that they add new 
information (at the very least to the scaling model) they are strictly not 
“redundant”.

The amount that anyone outside of methods development cares about the “epsilon” 
multiplicity of reflections is … negligible?

Sorry for chucking pragmatism into a dogmatic debate 😀

Cheerio Graeme

On 29 Jun 2020, at 23:36, Bernhard Rupp 
mailto:hofkristall...@gmail.com>> 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 mailto: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 
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
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)" 
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


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 24, 2020 1:10 AM
To: 
CCP4BB@JISCMAIL.AC.UKmailto: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 
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

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want yo

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[ccp4bb] insertion of a chemical

[Daniele Veggi]

Dear CCP4bb,

I'm trying to insert an Acetone molecule between two cysteine residues in
coot or modifying the pdb. I'm working on this modified molecule where the
disulfide bridge was chemichally opened and inserted an acetone molecule
between the two cysteine.

MS data confirm this modification (98% of molecules modified) but I can not
insert the acetone covalently linked to the S of both cysteine
(S-ACN-S).
Maybe what I think and what I am doing is not the right solution (the
disulfide bridge is still alive?) anyway i would like to know how to link
the acetone to the two cysteine
To better understand what I mean in attach you find a screenshot

I thank in advance all those who will have the courtesy to make a suggestion

Daniele Veggi



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Re: [ccp4bb] insertion of a chemical

[Lumbini Yadav]

Hi Daniele,
Do you see Fo-Fc density  near disuphide bond where you are trying to fit
acetone?

On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi 
wrote:

> Dear CCP4bb,
>
> I'm trying to insert an Acetone molecule between two cysteine residues in
> coot or modifying the pdb. I'm working on this modified molecule where the
> disulfide bridge was chemichally opened and inserted an acetone molecule
> between the two cysteine.
>
> MS data confirm this modification (98% of molecules modified) but I can
> not insert the acetone covalently linked to the S of both cysteine
> (S-ACN-S).
> Maybe what I think and what I am doing is not the right solution (the
> disulfide bridge is still alive?) anyway i would like to know how to link
> the acetone to the two cysteine
> To better understand what I mean in attach you find a screenshot
>
> I thank in advance all those who will have the courtesy to make a
> suggestion
>
> Daniele Veggi
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] insertion of a chemical

[Roger Rowlett]

The first step would be to verify consistent, convincing electron density
for the proposed thioketal adduct. A good way to start might be an "omit"
map of the region by mutating the Cys residues to Ala, truncating them to
the beta-carbon. The resulting difference density may be suggestive of a
thioketal adduct or a simple disulfide bridge. Building the thioketal, if
actually present, will require addition skill with ligand building and
Coot. You are essentially attaching an isopropyl group to the two Cys
sulfur atoms.

Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Dept. Of Chemisty
Colgate University

On Tue, Jun 30, 2020, 5:58 AM Daniele Veggi  wrote:

> Dear CCP4bb,
>
> I'm trying to insert an Acetone molecule between two cysteine residues in
> coot or modifying the pdb. I'm working on this modified molecule where the
> disulfide bridge was chemichally opened and inserted an acetone molecule
> between the two cysteine.
>
> MS data confirm this modification (98% of molecules modified) but I can
> not insert the acetone covalently linked to the S of both cysteine
> (S-ACN-S).
> Maybe what I think and what I am doing is not the right solution (the
> disulfide bridge is still alive?) anyway i would like to know how to link
> the acetone to the two cysteine
> To better understand what I mean in attach you find a screenshot
>
> I thank in advance all those who will have the courtesy to make a
> suggestion
>
> Daniele Veggi
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] insertion of a chemical

[Daniele Veggi]

Hi Yadav,
yes, this is only a representation of what I would like to do. If during
the refinement will continue to appear density, probably I'm on the good
track..but currently my big issue is inserting the ACN
covalently linked to both cys.

many thanks

Daniele Veggi
GSK Vaccines Siena Italy





Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav 
ha scritto:

> Hi Daniele,
> Do you see Fo-Fc density  near disuphide bond where you are trying to fit
> acetone?
>
> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi 
> wrote:
>
>> Dear CCP4bb,
>>
>> I'm trying to insert an Acetone molecule between two cysteine residues in
>> coot or modifying the pdb. I'm working on this modified molecule where the
>> disulfide bridge was chemichally opened and inserted an acetone molecule
>> between the two cysteine.
>>
>> MS data confirm this modification (98% of molecules modified) but I can
>> not insert the acetone covalently linked to the S of both cysteine
>> (S-ACN-S).
>> Maybe what I think and what I am doing is not the right solution (the
>> disulfide bridge is still alive?) anyway i would like to know how to link
>> the acetone to the two cysteine
>> To better understand what I mean in attach you find a screenshot
>>
>> I thank in advance all those who will have the courtesy to make a
>> suggestion
>>
>> Daniele Veggi
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] insertion of a chemical

[Lumbini Yadav]

As also suggested by Dr. Roger you should first see the density then the
next step of molecule addition is suggested.  Omit is also a good idea for
further confirmation.

On Tue, Jun 30, 2020 at 4:55 PM Daniele Veggi 
wrote:

> Hi Yadav,
> yes, this is only a representation of what I would like to do. If during
> the refinement will continue to appear density, probably I'm on the good
> track..but currently my big issue is inserting the ACN
> covalently linked to both cys.
>
> many thanks
>
> Daniele Veggi
> GSK Vaccines Siena Italy
>
>
>
>
>
> Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav <
> lumbin...@gmail.com> ha scritto:
>
>> Hi Daniele,
>> Do you see Fo-Fc density  near disuphide bond where you are trying to fit
>> acetone?
>>
>> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi 
>> wrote:
>>
>>> Dear CCP4bb,
>>>
>>> I'm trying to insert an Acetone molecule between two cysteine residues
>>> in coot or modifying the pdb. I'm working on this modified molecule where
>>> the disulfide bridge was chemichally opened and inserted an acetone
>>> molecule between the two cysteine.
>>>
>>> MS data confirm this modification (98% of molecules modified) but I can
>>> not insert the acetone covalently linked to the S of both cysteine
>>> (S-ACN-S).
>>> Maybe what I think and what I am doing is not the right solution (the
>>> disulfide bridge is still alive?) anyway i would like to know how to link
>>> the acetone to the two cysteine
>>> To better understand what I mean in attach you find a screenshot
>>>
>>> I thank in advance all those who will have the courtesy to make a
>>> suggestion
>>>
>>> Daniele Veggi
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>



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Re: [ccp4bb] insertion of a chemical

[Roger Rowlett]

To verify the presence of a non protein ligand, you need to come at this
from an unbiased perspective.

1. Remove what you think is not there (e.g. disulfide bond) by truncating
the Cys residues
2. Examine the difference density map to see if it conforms to your
expectations of what is proposed to be there (or does not)
3. If appropriate, build and attach ligand and re-refine. I am assuming
that you are proposing a thioketal adduct, which is not the same as
inserting an acetone molecule in the structure.

You can find generic instructions for these types of tasks on my
XRD-protocols site, https://sites.google.com/colgate.edu/xrd-protocols.

Roger Rowlett

On Tue, Jun 30, 2020, 7:25 AM Daniele Veggi  wrote:

> Hi Yadav,
> yes, this is only a representation of what I would like to do. If during
> the refinement will continue to appear density, probably I'm on the good
> track..but currently my big issue is inserting the ACN
> covalently linked to both cys.
>
> many thanks
>
> Daniele Veggi
> GSK Vaccines Siena Italy
>
>
>
>
>
> Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav <
> lumbin...@gmail.com> ha scritto:
>
>> Hi Daniele,
>> Do you see Fo-Fc density  near disuphide bond where you are trying to fit
>> acetone?
>>
>> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi 
>> wrote:
>>
>>> Dear CCP4bb,
>>>
>>> I'm trying to insert an Acetone molecule between two cysteine residues
>>> in coot or modifying the pdb. I'm working on this modified molecule where
>>> the disulfide bridge was chemichally opened and inserted an acetone
>>> molecule between the two cysteine.
>>>
>>> MS data confirm this modification (98% of molecules modified) but I can
>>> not insert the acetone covalently linked to the S of both cysteine
>>> (S-ACN-S).
>>> Maybe what I think and what I am doing is not the right solution (the
>>> disulfide bridge is still alive?) anyway i would like to know how to link
>>> the acetone to the two cysteine
>>> To better understand what I mean in attach you find a screenshot
>>>
>>> I thank in advance all those who will have the courtesy to make a
>>> suggestion
>>>
>>> Daniele Veggi
>>>
>>> --
>>>
>>> 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
>



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Re: [ccp4bb] number of frames to get a full dataset?

[Phil Jeffrey]

The people that already use multiplicity are going to find reasons why 
it's the superior naming scheme - although the underlying reason has a 
lot to do with negative associations with 'redundant', perhaps hightened 
in the current environment.  And conversely redundant works for many 
others - Graeme's pragmatic defense of multiplicity actually works both 
ways - any person who takes the trouble to read the stats table, now 
exiled to Supplementary Data, knows what it means.  Surely, then, the 
only way forward on this almost totally irrelevant discussion is to come 
up with a universally-loathed nomenclature that pleases nobody, 
preferably an acronym whose origins will be lost to history and the 
dusty CCP4 archives (which contain threads similar to this one).  I 
humbly submit:


NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions 
of the inappropriateness of "R-factor" ?  I have a long history of 
rearguard action trying to give stupid acronyms a wider audience, so 
you're guaranteed to hear from me on this for years.


(Personally I'm pining for Gerard Kleywegt to resume his quest for 
overextended naming rationales, of which ValLigURL is a personal 
'favo[u]rite'.  But I'm just old-fashioned.)


Ironically,
Phil Jeffrey
Princeton

[* I too have collected 540 degrees in P1 to solve a SAD structure, just 
because I could, hence "nearly"]
[** The actual answer to this thread is: history is written by the 
authors of scaling programs - and I think the Americans are currently 
losing at this game, thus perilously close to making themselves redundant.]


On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Or, we could accept the fact that crystallographers are kinda used to 
multiplicity of an individual Miller index being different to 
multiplicity of observations, and in Table 1 know which one you mean? 😉 
Given that they add new information (at the very least to the scaling 
model) they are strictly not “redundant”.


The amount that anyone outside of methods development cares about the 
“epsilon” multiplicity of reflections is … negligible?


Sorry for chucking pragmatism into a dogmatic debate 😀

Cheerio Graeme





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Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

Dear Colleagues,
In an effort to break this naming deadlock, and with Massimo and Ian not 
showing up as yet, I checked the IUCr Dictionary.
“Redundancy“ and “Multiplicity“ are not listed.
The more generic term “Statistical Descriptors“ is though and even offers 
Recommendations:-
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html
Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym. 
Greetings,
John 


Emeritus Professor John R Helliwell DSc



> On 30 Jun 2020, at 13:11, Phil Jeffrey  wrote:
> 
> The people that already use multiplicity are going to find reasons why it's 
> the superior naming scheme - although the underlying reason has a lot to do 
> with negative associations with 'redundant', perhaps hightened in the current 
> environment.  And conversely redundant works for many others - Graeme's 
> pragmatic defense of multiplicity actually works both ways - any person who 
> takes the trouble to read the stats table, now exiled to Supplementary Data, 
> knows what it means.  Surely, then, the only way forward on this almost 
> totally irrelevant discussion is to come up with a universally-loathed 
> nomenclature that pleases nobody, preferably an acronym whose origins will be 
> lost to history and the dusty CCP4 archives (which contain threads similar to 
> this one).  I humbly submit:
> 
> NFDOF: Nearly Futile Data Overcollection Factor ?
> [*]
> 
> Or, even better, could we not move on to equally pointless discussions of the 
> inappropriateness of "R-factor" ?  I have a long history of rearguard action 
> trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
> from me on this for years.
> 
> (Personally I'm pining for Gerard Kleywegt to resume his quest for 
> overextended naming rationales, of which ValLigURL is a personal 
> 'favo[u]rite'.  But I'm just old-fashioned.)
> 
> Ironically,
> Phil Jeffrey
> Princeton
> 
> [* I too have collected 540 degrees in P1 to solve a SAD structure, just 
> because I could, hence "nearly"]
> [** The actual answer to this thread is: history is written by the authors of 
> scaling programs - and I think the Americans are currently losing at this 
> game, thus perilously close to making themselves redundant.]
> 
>> On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
>> Or, we could accept the fact that crystallographers are kinda used to 
>> multiplicity of an individual Miller index being different to multiplicity 
>> of observations, and in Table 1 know which one you mean? 😉 Given that they 
>> add new information (at the very least to the scaling model) they are 
>> strictly not “redundant”.
>> The amount that anyone outside of methods development cares about the 
>> “epsilon” multiplicity of reflections is … negligible?
>> Sorry for chucking pragmatism into a dogmatic debate 😀
>> Cheerio Graeme
> 
> 
> 
> 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 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[David Schuller]

By all means, if you still have "disks" you should get rid of them, and 
replace them with some modern storage.




On 2020-06-29 21:17, 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 > 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 
 



    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)" 
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  

    __ __



--


    *From:*CCP4 bulletin board > on behalf of 
0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk 
>

    *Sent:* Wednesday, June 24, 2020 1:10 AM
    *To:* 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, altho

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Ian Tickle]

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:

*R**edundancy* 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  wrote:

> Reflections are as "redundant" as the disks in a RAID 0 array
>
> On Tue, 30 Jun 2020, 02:49 James Holton,  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 > >> > 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

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Phil Evans]

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  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  wrote:
> Reflections are as "redundant" as the disks in a RAID 0 array
> 
> On Tue, 30 Jun 2020, 02:49 James Holton,  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 
> >

Re: [ccp4bb] insertion of a chemical

[Paul Emsley]

On 30/06/2020 10:51, Daniele Veggi wrote:

Dear CCP4bb,

I'm trying to insert an Acetone molecule between two cysteine residues 
in coot or modifying the pdb. I'm working on this modified molecule 
where the disulfide bridge was chemichally opened and inserted an 
acetone molecule between the two cysteine.


MS data confirm this modification (98% of molecules modified) but I 
can not insert the acetone covalently linked to the S of both cysteine

(S-ACN-S).
Maybe what I think and what I am doing is not the right solution (the 
disulfide bridge is still alive?) anyway i would like to know how to 
link the acetone to the two cysteine




Here's how to make a link between a ligand and the protein using Coot 
and Acedrg:


https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html

Making a link from a ligand to two protein residues is tricky (I 
wouldn't know how to do it off the top of my head).


Paul.



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Schreuder, Herman /DE]

Dear BB,

Since there does not seem a generally accepted term for the subject of this 
discussions, and since even the IUCR scriptures do not give any guidance, I 
would propose to introduce a completely new term:

Measurements per reflection or MPR

This term is politically neutral, should adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

What do you think?
Herman


Von: CCP4 bulletin board  Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
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

Dear Colleagues,
In an effort to break this naming deadlock, and with Massimo and Ian not 
showing up as yet, I checked the IUCr Dictionary.
“Redundancy“ and “Multiplicity“ are not listed.
The more generic term “Statistical Descriptors“ is though and even offers 
Recommendations:-
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html
Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym.
Greetings,
John

Emeritus Professor John R Helliwell DSc




On 30 Jun 2020, at 13:11, Phil Jeffrey 
mailto:pjeff...@princeton.edu>> wrote:
The people that already use multiplicity are going to find reasons why it's 
the superior naming scheme - although the underlying reason has a lot to do 
with negative associations with 'redundant', perhaps hightened in the current 
environment.  And conversely redundant works for many others - Graeme's 
pragmatic defense of multiplicity actually works both ways - any person who 
takes the trouble to read the stats table, now exiled to Supplementary Data, 
knows what it means.  Surely, then, the only way forward on this almost totally 
irrelevant discussion is to come up with a universally-loathed nomenclature 
that pleases nobody, preferably an acronym whose origins will be lost to 
history and the dusty CCP4 archives (which contain threads similar to this 
one).  I humbly submit:

NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions of the 
inappropriateness of "R-factor" ?  I have a long history of rearguard action 
trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
from me on this for years.

(Personally I'm pining for Gerard Kleywegt to resume his quest for overextended 
naming rationales, of which ValLigURL is a personal 'favo[u]rite'.  But I'm 
just old-fashioned.)

Ironically,
Phil Jeffrey
Princeton

[* I too have collected 540 degrees in P1 to solve a SAD structure, just 
because I could, hence "nearly"]
[** The actual answer to this thread is: history is written by the authors of 
scaling programs - and I think the Americans are currently losing at this game, 
thus perilously close to making themselves redundant.]

On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:

Or, we could accept the fact that crystallographers are kinda used to 
multiplicity of an individual Miller index being different to multiplicity of 
observations, and in Table 1 know which one you mean? 😉 Given that they add new 
information (at the very least to the scaling model) they are strictly not 
“redundant”.
The amount that anyone outside of methods development cares about the “epsilon” 
multiplicity of reflections is … negligible?
Sorry for chucking pragmatism into a dogmatic debate 😀
Cheerio Graeme



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Re: [ccp4bb] number of frames to get a full dataset?

[Edwin Pozharski]

Replicate is a good option with its own problems as it can be seen as
referring to exact copy which multiple measurements clearly aren't. It does
have an advantage of being the word used by non-crystallographers though.

As a lame attempt at joke, use of terms redundancy and multiplicity to
describe the same concept is by itself redundant.

On Mon, Jun 29, 2020, 7:21 PM Bernhard Rupp 
wrote:

> Ah…the rise of the replicants …
>
>
>
> https://www.youtube.com/watch?v=yWPyRSURYFQ
>
>
>
> …and don’t forget the and the Voight-Kampff Test results in Table 1.
>
>
>
> Best, BR
>
>
>
> *From:* Pierre Rizkallah 
> *Sent:* Monday, June 29, 2020 15:46
> *To:* b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
> *Subject:* RE: [ccp4bb] number of frames to get a full dataset?
>
>
>
> You’re missing out on a grand opportunity for iconoclasm here. Try out
> ‘Degree of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’.
> Any other offerings!
>
>
>
> P.
>
> ***
>
> Dr Pierre Rizkallah, Senior Lecturer Structural Biology
>
> Institute of Infection & Immunology, Sir Geraint Evans Building,
>
> School of Medicine, Heath Campus, Cardiff, CF14 4XN
>
> email: rizkall...@cardiff.ac.ukphone: +44 29 2074 2248
>
> http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Bernhard
> Rupp
> *Sent:* 29 June 2020 23:36
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] number of frames to get a full dataset?
>
>
>
> 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  *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  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
> 
>
> 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  on behalf of
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk <
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Wednesday, June 24, 2020 1:10 A

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[John R Helliwell]

Dear Herman,
I think that MPR is a very neat and tidy, excellent, proposal.
Moreover it uses the word “measurements”, and we are an experimental based 
science.
I support it.
Great.
Greetings,
John 

Emeritus Professor John R Helliwell DSc




> On 30 Jun 2020, at 15:10, Schreuder, Herman /DE  
> wrote:
> 
> 
> Dear BB,
>  
> Since there does not seem a generally accepted term for the subject of this 
> discussions, and since even the IUCR scriptures do not give any guidance, I 
> would propose to introduce a completely new term:
>  
> Measurements per reflection or MPR
>  
> This term is politically neutral, should adequately describe this particular 
> statistic and is not associated with entrenched traditions at either side of 
> the Atlantic.
>  
> What do you think?
> Herman
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von John R 
> Helliwell
> Gesendet: Dienstag, 30. Juni 2020 14:34
> 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
> 
>  
> 
> Dear Colleagues,
> In an effort to break this naming deadlock, and with Massimo and Ian not 
> showing up as yet, I checked the IUCr Dictionary.
> “Redundancy“ and “Multiplicity“ are not listed.
> The more generic term “Statistical Descriptors“ is though and even offers 
> Recommendations:-
> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html
> Point 1, first sentence, fits the various wishes of this thread succinctly, 
> if not in a single word, and even not readily allowing an easy acronym. 
> Greetings,
> John 
>  
> 
> Emeritus Professor John R Helliwell DSc
>  
>  
> 
> 
> On 30 Jun 2020, at 13:11, Phil Jeffrey  wrote:
> 
> The people that already use multiplicity are going to find reasons why it's 
> the superior naming scheme - although the underlying reason has a lot to do 
> with negative associations with 'redundant', perhaps hightened in the current 
> environment.  And conversely redundant works for many others - Graeme's 
> pragmatic defense of multiplicity actually works both ways - any person who 
> takes the trouble to read the stats table, now exiled to Supplementary Data, 
> knows what it means.  Surely, then, the only way forward on this almost 
> totally irrelevant discussion is to come up with a universally-loathed 
> nomenclature that pleases nobody, preferably an acronym whose origins will be 
> lost to history and the dusty CCP4 archives (which contain threads similar to 
> this one).  I humbly submit:
> 
> NFDOF: Nearly Futile Data Overcollection Factor ?
> [*]
> 
> Or, even better, could we not move on to equally pointless discussions of the 
> inappropriateness of "R-factor" ?  I have a long history of rearguard action 
> trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
> from me on this for years.
> 
> (Personally I'm pining for Gerard Kleywegt to resume his quest for 
> overextended naming rationales, of which ValLigURL is a personal 
> 'favo[u]rite'.  But I'm just old-fashioned.)
> 
> Ironically,
> Phil Jeffrey
> Princeton
> 
> [* I too have collected 540 degrees in P1 to solve a SAD structure, just 
> because I could, hence "nearly"]
> [** The actual answer to this thread is: history is written by the authors of 
> scaling programs - and I think the Americans are currently losing at this 
> game, thus perilously close to making themselves redundant.]
> 
> On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
> 
> Or, we could accept the fact that crystallographers are kinda used to 
> multiplicity of an individual Miller index being different to multiplicity of 
> observations, and in Table 1 know which one you mean? 😉 Given that they add 
> new information (at the very least to the scaling model) they are strictly 
> not “redundant”.
> The amount that anyone outside of methods development cares about the 
> “epsilon” multiplicity of reflections is … negligible?
> Sorry for chucking pragmatism into a dogmatic debate 😀
> Cheerio Graeme
> 
> 
> 
> 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 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

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  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

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Bernhard Rupp]

.…but there is a difference whether I measure the same identical hkl over again 
or ‘preferably in more than one symmetry-equivalent position’, to quote the

IUCr. So do we have a MPSR for the same reflection and a MPRR for the related 
reflections?

 

Cacophonically yours,

 

BR

 

From: CCP4 bulletin board  On Behalf Of John R Helliwell
Sent: Tuesday, June 30, 2020 08:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?

 

Dear Herman,

I think that MPR is a very neat and tidy, excellent, proposal.

Moreover it uses the word “measurements”, and we are an experimental based 
science.

I support it.

Great.

Greetings,

John 

Emeritus Professor John R Helliwell DSc

 

 

 

 

On 30 Jun 2020, at 15:10, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com> > wrote:

 

Dear BB,

 

Since there does not seem a generally accepted term for the subject of this 
discussions, and since even the IUCR scriptures do not give any guidance, I 
would propose to introduce a completely new term:

 

Measurements per reflection or MPR

 

This term is politically neutral, should adequately describe this particular 
statistic and is not associated with entrenched traditions at either side of 
the Atlantic.

 

What do you think?

Herman

 

 

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> Im Auftrag von John R Helliwell
Gesendet: Dienstag, 30. Juni 2020 14:34
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 
  

 

Dear Colleagues,

In an effort to break this naming deadlock, and with Massimo and Ian not 
showing up as yet, I checked the IUCr Dictionary.

“Redundancy“ and “Multiplicity“ are not listed.

The more generic term “Statistical Descriptors“ is though and even offers 
Recommendations:-

http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 

 

Point 1, first sentence, fits the various wishes of this thread succinctly, if 
not in a single word, and even not readily allowing an easy acronym. 

Greetings,

John 

 

Emeritus Professor John R Helliwell DSc

 

 





On 30 Jun 2020, at 13:11, Phil Jeffrey mailto:pjeff...@princeton.edu> > wrote:

The people that already use multiplicity are going to find reasons why it's 
the superior naming scheme - although the underlying reason has a lot to do 
with negative associations with 'redundant', perhaps hightened in the current 
environment.  And conversely redundant works for many others - Graeme's 
pragmatic defense of multiplicity actually works both ways - any person who 
takes the trouble to read the stats table, now exiled to Supplementary Data, 
knows what it means.  Surely, then, the only way forward on this almost totally 
irrelevant discussion is to come up with a universally-loathed nomenclature 
that pleases nobody, preferably an acronym whose origins will be lost to 
history and the dusty CCP4 archives (which contain threads similar to this 
one).  I humbly submit:

NFDOF: Nearly Futile Data Overcollection Factor ?
[*]

Or, even better, could we not move on to equally pointless discussions of the 
inappropriateness of "R-factor" ?  I have a long history of rearguard action 
trying to give stupid acronyms a wider audience, so you're guaranteed to hear 
from me on this for years.

(Personally I'm pining for Gerard Kleywegt to resume his quest for overextended 
naming rationales, of which ValLigURL is a personal 'favo[u]rite'.  But I'm 
just old-fashioned.)

Ironically,
Phil Jeffrey
Princeton

[* I too have collected 540 degrees in P1 to solve a SAD structure, just 
because I could, hence "nearly"]
[** The actual answer to this thread is: history is written by the authors of 
scaling programs - and I think the Americans are currently losing at this game, 
thus perilously close to making themselves redundant.]

On 6/30/20 4:14 AM, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:



Or, we could accept the fact that crystallographers are kinda used to 
multiplicity of an individual Miller index being different to multiplicity of 
observations, and in Table 1 know which one you mean? 😉 Given that they add new 
information (at the very least to the scaling model) they are strictly not 
“redundant”.

The amount that anyone outside of methods development cares about the “epsilon” 
multiplicity of reflections is … negligible?

Sorry for chucking pragmatism into a dogmatic debate 😀

Cheerio Graeme




To unsubscribe from the CCP4BB list, click the 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Frank von Delft]

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  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 

[ccp4bb] 60th Anniversary Meeting of The British Biophysical Society 14-17 September via Zoom

[Dave Scott]

Update: 60th Anniversary Meeting of The British Biophysical Society 14-17 
September via Zoom

Registration is now OPEN and is FREE. 

Please register at: REGISTER URL: https://bit.ly/31p61xC

The British Biophysical Society Biennial meeting is the largest national 
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as it celebrates the 60th Anniversary of the creation of the society.

‘Biophysics through time and space: The BBS@60’ will be on Zoom 14-17 September 
2020.

We invite participants to submit posters (in the form of a powerpoint slide or 
pdf) to bbsa...@gmail.com. Poster titles and contact email addresses will be 
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Finally, if you would like to suggest or host a satellite event in the morning 
or evening of either 14-17 September 2020, please contact Dave Scott 
(david.sc...@nottingham.ac.uk)

Speakers
Richard Henderson FRS, MRC Laboratory of Molecular Biology, Cambridge.
Banafshe Larijani, University of Bath.
Perdita Barran, University of Manchester.
Allen Orville, Diamond Light Source, Harwell.
Amanda Wright, University of Nottingham.
Tim Knowles, University of Birmingham.
Tom Clarke, University of East Anglia.
David Brockwell, University of Leeds.
Mike Fried, University of Kentucky.
Ben Luisi, University of Cambridge.
Peter Crowley, NUI Galway, Ireland.
Corinne Smith, University of Warwick
Alison Rodger, Macquarie University, Sydney, Australia.
Marcello Nollmann, CNRS, Montepellier, France.
Phil Biggin, University of Oxford




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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

Dear Bernhard,

 That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones (e.g. in terms of radiation damage only, while the
others would also involve absorption effects). However I am not aware that
the existing data processing programs we use actually make and exploit this
distinction.

 Going back to the initial topic of this thread, the main take-home
lesson for Murpholino should be: preoccupations about minimising the number
of frames to get completeness belong to a now obsolete age - instead use the
new paragigm of high-(redundancy/multiplicity) data collection with a low
transmission so that you can spread the dose your crystal can withstand over
the requisite angular range. No matter how you call the "abundance" property
of your final dataset, make sure it is high!

 The case of low symmetry has been mentioned: the extra guidance for
Murpolino is that if you are in P1, you will never get completeness with a
single orientation, so make sure that you use a multi-axis goniometer and
collect data in at least two sufficiently different orientations.


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2020 at 08:49:53AM -0700, Bernhard Rupp wrote:
> .…but there is a difference whether I measure the same identical hkl over 
> again or ‘preferably in more than one symmetry-equivalent position’, to quote 
> the
> 
> IUCr. So do we have a MPSR for the same reflection and a MPRR for the related 
> reflections?
> 
>  
> 
> Cacophonically yours,
> 
>  
> 
> BR
> 
>  
> 
> From: CCP4 bulletin board  On Behalf Of John R 
> Helliwell
> Sent: Tuesday, June 30, 2020 08:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
> dataset?
> 
>  
> 
> Dear Herman,
> 
> I think that MPR is a very neat and tidy, excellent, proposal.
> 
> Moreover it uses the word “measurements”, and we are an experimental based 
> science.
> 
> I support it.
> 
> Great.
> 
> Greetings,
> 
> John 
> 
> Emeritus Professor John R Helliwell DSc
> 
>  
> 
>  
> 
>  
> 
>  
> 
> On 30 Jun 2020, at 15:10, Schreuder, Herman /DE   > wrote:
> 
>  
> 
> Dear BB,
> 
>  
> 
> Since there does not seem a generally accepted term for the subject of this 
> discussions, and since even the IUCR scriptures do not give any guidance, I 
> would propose to introduce a completely new term:
> 
>  
> 
> Measurements per reflection or MPR
> 
>  
> 
> This term is politically neutral, should adequately describe this particular 
> statistic and is not associated with entrenched traditions at either side of 
> the Atlantic.
> 
>  
> 
> What do you think?
> 
> Herman
> 
>  
> 
>  
> 
> Von: CCP4 bulletin board   > Im Auftrag von John R Helliwell
> Gesendet: Dienstag, 30. Juni 2020 14:34
> 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 
>   
> 
>  
> 
> Dear Colleagues,
> 
> In an effort to break this naming deadlock, and with Massimo and Ian not 
> showing up as yet, I checked the IUCr Dictionary.
> 
> “Redundancy“ and “Multiplicity“ are not listed.
> 
> The more generic term “Statistical Descriptors“ is though and even offers 
> Recommendations:-
> 
> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 
> 
>  
> 
> Point 1, first sentence, fits the various wishes of this thread succinctly, 
> if not in a single word, and even not readily allowing an easy acronym. 
> 
> Greetings,
> 
> John 
> 
>  
> 
> Emeritus Professor John R Helliwell DSc
> 
>  
> 
>  
> 
> 
> 
> 
> 
> On 30 Jun 2020, at 13:11, Phil Jeffrey   > wrote:
> 
> The people that already use multiplicity are going to find reasons why it's 
> the superior naming scheme - although the underlying reason has a lot to do 
> with negative associations with 'redundant', perhaps hightened in the current 
> environment.  And conversely redundant works for many others - Graeme's 
> pragmatic defense of multiplicity actually works both ways - any person who 
> takes the trouble to read the stats table, now exiled to Supplementary Data, 
> knows what it means.  Surely, then, the only way forward on this almost 
> totally irrelevant discussion is to come up with a universally-loathed 
> nomenclature that pleases nobody, preferably an acronym whose origins will be 
> lost to history and the dusty CCP4 archives (which contain threads similar to 
> this

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[00000c2488af9525-dmarc-request]

Hello JohnDoes the IUCr dictionary list 'degeneracy'?Jon CooperOn 30 Jun 2020 17:11, Gerard Bricogne  wrote:Dear Bernhard,



 That is true, and the discrepancies between repeated measurements of

the same hkl would have to be parametrised differently from those between

symmetry-related ones (e.g. in terms of radiation damage only, while the

others would also involve absorption effects). However I am not aware that

the existing data processing programs we use actually make and exploit this

distinction.



 Going back to the initial topic of this thread, the main take-home

lesson for Murpholino should be: preoccupations about minimising the number

of frames to get completeness belong to a now obsolete age - instead use the

new paragigm of high-(redundancy/multiplicity) data collection with a low

transmission so that you can spread the dose your crystal can withstand over

the requisite angular range. No matter how you call the "abundance" property

of your final dataset, make sure it is high!



 The case of low symmetry has been mentioned: the extra guidance for

Murpolino is that if you are in P1, you will never get completeness with a

single orientation, so make sure that you use a multi-axis goniometer and

collect data in at least two sufficiently different orientations.





 With best wishes,



  Gerard.



--

On Tue, Jun 30, 2020 at 08:49:53AM -0700, Bernhard Rupp wrote:

> .…but there is a difference whether I measure the same identical hkl over again or ‘preferably in more than one symmetry-equivalent position’, to quote the

> 

> IUCr. So do we have a MPSR for the same reflection and a MPRR for the related reflections?

> 

>  

> 

> Cacophonically yours,

> 

>  

> 

> BR

> 

>  

> 

> From: CCP4 bulletin board  On Behalf Of John R Helliwell

> Sent: Tuesday, June 30, 2020 08:36

> To: CCP4BB@JISCMAIL.AC.UK

> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

> 

>  

> 

> Dear Herman,

> 

> I think that MPR is a very neat and tidy, excellent, proposal.

> 

> Moreover it uses the word “measurements”, and we are an experimental based science.

> 

> I support it.

> 

> Great.

> 

> Greetings,

> 

> John 

> 

> Emeritus Professor John R Helliwell DSc

> 

>  

> 

>  

> 

>  

> 

>  

> 

> On 30 Jun 2020, at 15:10, Schreuder, Herman /DE  > wrote:

> 

>  

> 

> Dear BB,

> 

>  

> 

> Since there does not seem a generally accepted term for the subject of this discussions, and since even the IUCR scriptures do not give any guidance, I would propose to introduce a completely new term:

> 

>  

> 

> Measurements per reflection or MPR

> 

>  

> 

> This term is politically neutral, should adequately describe this particular statistic and is not associated with entrenched traditions at either side of the Atlantic.

> 

>  

> 

> What do you think?

> 

> Herman

> 

>  

> 

>  

> 

> Von: CCP4 bulletin board  > Im Auftrag von John R Helliwell

> Gesendet: Dienstag, 30. Juni 2020 14:34

> 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   

> 

>  

> 

> Dear Colleagues,

> 

> In an effort to break this naming deadlock, and with Massimo and Ian not showing up as yet, I checked the IUCr Dictionary.

> 

> “Redundancy“ and “Multiplicity“ are not listed.

> 

> The more generic term “Statistical Descriptors“ is though and even offers Recommendations:-

> 

> http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html  

> 

> Point 1, first sentence, fits the various wishes of this thread succinctly, if not in a single word, and even not readily allowing an easy acronym. 

> 

> Greetings,

> 

> John 

> 

>  

> 

> Emeritus Professor John R Helliwell DSc

> 

>  

> 

>  

> 

> 

> 

> 

> 

> On 30 Jun 2020, at 13:11, Phil Jeffrey  > wrote:

> 

> The people that already use multiplicity are going to find reasons why it's the superior naming scheme - although the underlying reason has a lot to do with negative associations with 'redundant', perhaps hightened in the current environment.  And conversely redundant works for many others - Graeme's pragmatic defense of multiplicity actually works both ways - any person who takes the trouble to read the stats table, now exiled to Supplementary Data, knows what it means.  Surely, then, the only way forward on this almost totally irrelevant discussion is to come up with a universally-loathed nomenclature that pleases nobody, preferably an acronym whose origins will be lost to history and the dusty CCP4 archives (which contain threads similar to this one).  I humbly submit:

> 

> NFDOF: Nearly Futile Data Overcollection Factor ?

> [*]

> 

> Or, even better, could we not move on to equally pointless discussions of the inappropriateness of "R-factor" ?  I have a long history of rearguard action trying to give stupid acronyms a wider audien

Re: [ccp4bb] number of frames to get a full dataset?

[Gerard Bricogne]

Dear Ed,

 Concerning your remark that "use of terms redundancy and multiplicity
to describe the same concept is by itself redundant", one could perhaps say
that redundancy is an abstract property of a dataset, while multiplicity is
a numerical attribute. Redundancy is desirable because if some measurements
turn out to be corrupted, there are spare ones to salvage completeness. In
this form it is an aspect of quality, without being in itself a numerical
entity. That property of redundancy is conferred by high multiplicity of
measurement, which is very much a numerical entity. The two terms are
threfore not redundant, but are made so in practice by the shorthand of
giving the numerical attribute the name of the abstract property it gives
rise to.

 Regarding the relation to replication, I can remember Peter Mueller's
book on refinement with SHELX quoting George Sheldrick's point that simply
repeating a measurement is of limited usefulness, because one repeats its
systematic errors, and advocating that what is truly valuable is to make
multiple measurements in conditions such that their systematic errors are
likely to be different. This diversity of conditions gives rise to what he
called "true multiplicity". There is clearly a close affinity between this
concept and that of redundancy viewed as a protection against corrupted
individual measurements.

 The essential thing, though, is not the choice of terminology but the
practical decision of abjuring the pernicious mindset alluded to by the
Subject line of this thread :-) .


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2020 at 11:19:38AM -0400, Edwin Pozharski wrote:
> Replicate is a good option with its own problems as it can be seen as
> referring to exact copy which multiple measurements clearly aren't. It does
> have an advantage of being the word used by non-crystallographers though.
> 
> As a lame attempt at joke, use of terms redundancy and multiplicity to
> describe the same concept is by itself redundant.
> 
> On Mon, Jun 29, 2020, 7:21 PM Bernhard Rupp 
> wrote:
> 
> > Ah…the rise of the replicants …
> >
> >
> >
> > https://www.youtube.com/watch?v=yWPyRSURYFQ
> >
> >
> >
> > …and don’t forget the and the Voight-Kampff Test results in Table 1.
> >
> >
> >
> > Best, BR
> >
> >
> >
> > *From:* Pierre Rizkallah 
> > *Sent:* Monday, June 29, 2020 15:46
> > *To:* b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
> > *Subject:* RE: [ccp4bb] number of frames to get a full dataset?
> >
> >
> >
> > You’re missing out on a grand opportunity for iconoclasm here. Try out
> > ‘Degree of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’.
> > Any other offerings!
> >
> >
> >
> > P.
> >
> > ***
> >
> > Dr Pierre Rizkallah, Senior Lecturer Structural Biology
> >
> > Institute of Infection & Immunology, Sir Geraint Evans Building,
> >
> > School of Medicine, Heath Campus, Cardiff, CF14 4XN
> >
> > email: rizkall...@cardiff.ac.ukphone: +44 29 2074 2248
> >
> > http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
> >
> >
> >
> > *From:* CCP4 bulletin board  *On Behalf Of *Bernhard
> > Rupp
> > *Sent:* 29 June 2020 23:36
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* Re: [ccp4bb] number of frames to get a full dataset?
> >
> >
> >
> > 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  *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  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 n

Re: [ccp4bb] number of frames to get a full dataset?

[00000c2488af9525-dmarc-request]

I think it is quite an interesting question in principle for Laue crystallography (now probably only relevant in the neutron world?) since, for example, if one had a crystal in the 432 point group, you could collect an essentially complete dataset with one 'image'. Given that each image can take several hours to collect, the number of them would seem to be important...Jon CooperOn 30 Jun 2020 20:24, Gerard Bricogne  wrote:Dear Ed,

 Concerning your remark that "use of terms redundancy and multiplicity
to describe the same concept is by itself redundant", one could perhaps say
that redundancy is an abstract property of a dataset, while multiplicity is
a numerical attribute. Redundancy is desirable because if some measurements
turn out to be corrupted, there are spare ones to salvage completeness. In
this form it is an aspect of quality, without being in itself a numerical
entity. That property of redundancy is conferred by high multiplicity of
measurement, which is very much a numerical entity. The two terms are
threfore not redundant, but are made so in practice by the shorthand of
giving the numerical attribute the name of the abstract property it gives
rise to.

 Regarding the relation to replication, I can remember Peter Mueller's
book on refinement with SHELX quoting George Sheldrick's point that simply
repeating a measurement is of limited usefulness, because one repeats its
systematic errors, and advocating that what is truly valuable is to make
multiple measurements in conditions such that their systematic errors are
likely to be different. This diversity of conditions gives rise to what he
called "true multiplicity". There is clearly a close affinity between this
concept and that of redundancy viewed as a protection against corrupted
individual measurements.

 The essential thing, though, is not the choice of terminology but the
practical decision of abjuring the pernicious mindset alluded to by the
Subject line of this thread :-) .


 With best wishes,

  Gerard.

--
On Tue, Jun 30, 2020 at 11:19:38AM -0400, Edwin Pozharski wrote:
> Replicate is a good option with its own problems as it can be seen as
> referring to exact copy which multiple measurements clearly aren't. It does
> have an advantage of being the word used by non-crystallographers though.
> 
> As a lame attempt at joke, use of terms redundancy and multiplicity to
> describe the same concept is by itself redundant.
> 
> On Mon, Jun 29, 2020, 7:21 PM Bernhard Rupp 
> wrote:
> 
> > Ah…the rise of the replicants …
> >
> >
> >
> > https://www.youtube.com/watch?v=yWPyRSURYFQ
> >
> >
> >
> > …and don’t forget the and the Voight-Kampff Test results in Table 1.
> >
> >
> >
> > Best, BR
> >
> >
> >
> > *From:* Pierre Rizkallah 
> > *Sent:* Monday, June 29, 2020 15:46
> > *To:* b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
> > *Subject:* RE: [ccp4bb] number of frames to get a full dataset?
> >
> >
> >
> > You’re missing out on a grand opportunity for iconoclasm here. Try out
> > ‘Degree of Replication’ or ‘Average Replication’ or ‘Replicate Frequency’.
> > Any other offerings!
> >
> >
> >
> > P.
> >
> > ***
> >
> > Dr Pierre Rizkallah, Senior Lecturer Structural Biology
> >
> > Institute of Infection & Immunology, Sir Geraint Evans Building,
> >
> > School of Medicine, Heath Campus, Cardiff, CF14 4XN
> >
> > email: rizkall...@cardiff.ac.uk    phone: +44 29 2074 2248
> >
> > http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
> >
> >
> >
> > *From:* CCP4 bulletin board  *On Behalf Of *Bernhard
> > Rupp
> > *Sent:* 29 June 2020 23:36
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* Re: [ccp4bb] number of frames to get a full dataset?
> >
> >
> >
> > 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  *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  wrote:
> >
> > I have f