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

[Schreuder, Herman /DE]

Dear Bernard and other bulletin board members,

As Gerard mentioned, current data processing programs and table 1’s do not make 
this distinction, but of course, you are free to ask the community to introduce 
it.

My proposal to use “measurements per reflections” is not a joke. It exactly 
describes what is meant by the parameter and it is easily understood even by 
lay people like journal editors and referees, without the need of lengthy 
explanations like the ones we have seen in this thread.

I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread 
about completeness of data sets to be hijacked by a discussion on whether use 
the name multiplicity of redundancy for the number of measurements per 
reflection.

My 2 cents,
Herman



Von: CCP4 bulletin board  Im Auftrag von Bernhard Rupp
Gesendet: Dienstag, 30. Juni 2020 17:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

.…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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
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'.

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

[Schreuder, Herman /DE]

Dear Frank,

in general it is not possible to determine the intensity of a reflection from a 
single fine slice. One needs slices for the complete reflection.
Also, like Bernard, you are imposing criteria on the MPR, which are not imposed 
on the multiplicity/redundancy/abundancy.

All I ask the bulletin to think about my proposal as it is, without prejudices.

Best,
Herman



Von: Frank Von Delft 
Gesendet: Mittwoch, 1. Juli 2020 09:46
An: Schreuder, Herman /DE 
Betreff: Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
get a full dataset?


EXTERNAL : Real sender is 
frank.vonde...@sgc.ox.ac.uk

If I fine slice the data, does each frame measuring the same reflection (or a 
part of it) count as a measurement?

So that doesn't get us out of the woods, alas.

Sent from tiny silly touch screen

From: "Schreuder, Herman /DE" 
mailto:herman.schreu...@sanofi.com>>
Sent: Wednesday, 1 July 2020 08:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get 
a full dataset?

Dear Bernard and other bulletin board members,

As Gerard mentioned, current data processing programs and table 1’s do not make 
this distinction, but of course, you are free to ask the community to introduce 
it.

My proposal to use “measurements per reflections” is not a joke. It exactly 
describes what is meant by the parameter and it is easily understood even by 
lay people like journal editors and referees, without the need of lengthy 
explanations like the ones we have seen in this thread.

I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a thread 
about completeness of data sets to be hijacked by a discussion on whether use 
the name multiplicity of redundancy for the number of measurements per 
reflection.

My 2 cents,
Herman



Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Bernhard Rupp
Gesendet: Dienstag, 30. Juni 2020 17:50
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

.…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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
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

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

[John R Helliwell]

Good morning Jon,
Ah yes that is a good word from quantum mechanics but no it isn’t in the IUCr 
Dictionary, nor in the Statistical Descriptors section on Recommendations. 
http://ww1.iucr.org/iucr-top/comm/cnom/statdes/recomm.html 

In Laue mode, Xray or neutron, the MPR should be large enough to allow 
determination of the Lambda curve. This is achieved through repeated 
measurements of the same hkl at different wavelengths from more than one 
crystal orientation or its symmetry mates at the same or different crystal 
orientations. High completeness in Laue especially at low d spacings requires 
deconvolution of energy multiples and is also helped by repeat measurements at 
different crystal orientations and a high crystal symmetry. 

Treading hopefully deftly with my terminology,
John 

Emeritus Professor John R Helliwell DSc




> On 30 Jun 2020, at 18:13, "0c2488af9525-dmarc-requ...@jiscmail.ac.uk" 
> <0c2488af9525-dmarc-requ...@jiscmail.ac.uk wrote:
> 
> 
> Hello John
> 
> Does the IUCr dictionary list 'degeneracy'?
> 
> Jon Cooper
> 
> On 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 
> > 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  >  > 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 
> > 

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

[Dirk Kostrewa]

Dear Herman,

I think, your MPR proposal is a great idea and would like to second it! 
And I would also like to propose that data processing programs just 
average "identical" reflections measured under the same geometry and 
count them only once (*), so that, in the end, we will get a realistic 
number of truly independent measurements.


Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with 
the same geometry n-times and measuring it n-times as long (apart from, 
maybe, catching instabilities in the experimental setup). Just averaging 
such "identical" reflections would simplify the subsequent scaling 
process with equivalent reflections that were measured under different 
geometry.


On 01.07.20 09:32, Schreuder, Herman /DE wrote:


Dear Bernard and other bulletin board members,

As Gerard mentioned, current data processing programs and table 1’s do 
not make this distinction, but of course, you are free to ask the 
community to introduce it.


My proposal to use “measurements per reflections” is not a joke. It 
exactly describes what is meant by the parameter and it is easily 
understood even by lay people like journal editors and referees, 
without the need of lengthy explanations like the ones we have seen in 
this thread.


I really would like to ask you to consider replacing 
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a 
thread about completeness of data sets to be hijacked by a discussion 
on whether use the name multiplicity of redundancy for the number of 
measurements per reflection.


My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von 
*Bernhard Rupp

*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
get a full dataset?


*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 



.…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
enviro

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

[Gerard Bricogne]

Dear Dirk,

 Aren't you for getting about radiation damage? The n measurements of
the same hkl with the same geometry would not be equivalent, although they
would enable the tracking of radiation damage without the confounding with
absorption effects that comes from considering symmetry-related hkls. I
mentioned that in my second message yesterday.

 The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river". 


 With best wishes,

  Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:
> Dear Herman,
> 
> I think, your MPR proposal is a great idea and would like to second it! And
> I would also like to propose that data processing programs just average
> "identical" reflections measured under the same geometry and count them only
> once (*), so that, in the end, we will get a realistic number of truly
> independent measurements.
> 
> Cheers,
> 
> Dirk.
> 
> (*) I don't see a difference between measuring the same reflection with the
> same geometry n-times and measuring it n-times as long (apart from, maybe,
> catching instabilities in the experimental setup). Just averaging such
> "identical" reflections would simplify the subsequent scaling process with
> equivalent reflections that were measured under different geometry.
> 
> On 01.07.20 09:32, Schreuder, Herman /DE wrote:
> > 
> > Dear Bernard and other bulletin board members,
> > 
> > As Gerard mentioned, current data processing programs and table 1’s do
> > not make this distinction, but of course, you are free to ask the
> > community to introduce it.
> > 
> > My proposal to use “measurements per reflections” is not a joke. It
> > exactly describes what is meant by the parameter and it is easily
> > understood even by lay people like journal editors and referees, without
> > the need of lengthy explanations like the ones we have seen in this
> > thread.
> > 
> > I really would like to ask you to consider replacing
> > multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
> > thread about completeness of data sets to be hijacked by a discussion on
> > whether use the name multiplicity of redundancy for the number of
> > measurements per reflection.
> > 
> > My 2 cents,
> > 
> > Herman
> > 
> > *Von:* CCP4 bulletin board  *Im Auftrag von
> > *Bernhard Rupp
> > *Gesendet:* Dienstag, 30. Juni 2020 17:50
> > *An:* CCP4BB@JISCMAIL.AC.UK
> > *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
> > a full dataset?
> > 
> > *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
> > 
> > 
> > .…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  > > *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.
>

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

[Kay Diederichs]

Dear Dirk,

XDS_ASCII.HKL (and equivalent files from other processing software) gives you 
all the information that you're after, since every reflection is stored 
individually.
However when you analyze that, you will find that in a data set that comprises 
less than 360 degrees of rotation, there is not a single reflection that is 
identically (according to your definition) measured two or more times.
In other words, describing those "identical" reflections statistically will 
give you the statistics of (what I call) the unmerged data. 
And, as Gerard mentions, if you do have multiple measurements of "identical" 
reflections (i.e. if collecting more than 360°), they still differ in terms of 
radiation damage.

best,
Kay

On Wed, 1 Jul 2020 10:46:57 +0200, Dirk Kostrewa 
 wrote:

>Dear Herman,
>
>I think, your MPR proposal is a great idea and would like to second it! 
>And I would also like to propose that data processing programs just 
>average "identical" reflections measured under the same geometry and 
>count them only once (*), so that, in the end, we will get a realistic 
>number of truly independent measurements.
>
>Cheers,
>
>Dirk.
>
>(*) I don't see a difference between measuring the same reflection with 
>the same geometry n-times and measuring it n-times as long (apart from, 
>maybe, catching instabilities in the experimental setup). Just averaging 
>such "identical" reflections would simplify the subsequent scaling 
>process with equivalent reflections that were measured under different 
>geometry.
>
>On 01.07.20 09:32, Schreuder, Herman /DE wrote:
>>
>> Dear Bernard and other bulletin board members,
>>
>> As Gerard mentioned, current data processing programs and table 1’s do 
>> not make this distinction, but of course, you are free to ask the 
>> community to introduce it.
>>
>> My proposal to use “measurements per reflections” is not a joke. It 
>> exactly describes what is meant by the parameter and it is easily 
>> understood even by lay people like journal editors and referees, 
>> without the need of lengthy explanations like the ones we have seen in 
>> this thread.
>>
>> I really would like to ask you to consider replacing 
>> multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a 
>> thread about completeness of data sets to be hijacked by a discussion 
>> on whether use the name multiplicity of redundancy for the number of 
>> measurements per reflection.
>>
>> My 2 cents,
>>
>> Herman
>>
>> *Von:* CCP4 bulletin board  *Im Auftrag von 
>> *Bernhard Rupp
>> *Gesendet:* Dienstag, 30. Juni 2020 17:50
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to 
>> get a full dataset?
>>
>> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 
>> 
>>
>> .…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 > > *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“ a

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

[Dirk Kostrewa]

Dear Gerard and Kay,

yes, you are both right - I have totally forgotten radiation damage! And 
correcting for this really makes a difference!


However, if radiation damage is corrected for reflections measured at 
different time points under the same geometry, does anything speak 
against it, to average them and count them only once (say, for crystals 
measured multiple rounds of 360 degrees to find identical geometries)?


Best wishes,

Dirk.

On 01.07.20 11:02, Gerard Bricogne wrote:

Dear Dirk,

  Aren't you for getting about radiation damage? The n measurements of
the same hkl with the same geometry would not be equivalent, although they
would enable the tracking of radiation damage without the confounding with
absorption effects that comes from considering symmetry-related hkls. I
mentioned that in my second message yesterday.

  The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river".


  With best wishes,

   Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:

Dear Herman,

I think, your MPR proposal is a great idea and would like to second it! And
I would also like to propose that data processing programs just average
"identical" reflections measured under the same geometry and count them only
once (*), so that, in the end, we will get a realistic number of truly
independent measurements.

Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with the
same geometry n-times and measuring it n-times as long (apart from, maybe,
catching instabilities in the experimental setup). Just averaging such
"identical" reflections would simplify the subsequent scaling process with
equivalent reflections that were measured under different geometry.

On 01.07.20 09:32, Schreuder, Herman /DE wrote:

Dear Bernard and other bulletin board members,

As Gerard mentioned, current data processing programs and table 1’s do
not make this distinction, but of course, you are free to ask the
community to introduce it.

My proposal to use “measurements per reflections” is not a joke. It
exactly describes what is meant by the parameter and it is easily
understood even by lay people like journal editors and referees, without
the need of lengthy explanations like the ones we have seen in this
thread.

I really would like to ask you to consider replacing
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
thread about completeness of data sets to be hijacked by a discussion on
whether use the name multiplicity of redundancy for the number of
measurements per reflection.

My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von
*Bernhard Rupp
*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk


.…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 mailto:CCP4BB@JISCMAIL.AC.UK>> *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.

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

[Kay Diederichs]

Dear Dirk,

one cannot fully correct radiation damage. Normal scaling procedures take care 
of the average decay by a smooth resolution-dependant function. Zero-dose 
extrapolation goes beyond that but needs all symmetry mates - this does not 
fulfill your definition of "identical". 

If we really could correct radiation damage then we could collect data to high 
resolution from all crystals just by using very high dose, and solve structures 
much more easily.

How often you count a reflection is up to you; I don't see what you gain by 
this.

best,
Kay

Am 01.07.20 um 11:42 schrieb Dirk Kostrewa:
> Dear Gerard and Kay,
> 
> yes, you are both right - I have totally forgotten radiation damage! And 
> correcting for this really makes a difference!
> 
> However, if radiation damage is corrected for reflections measured at 
> different time points under the same geometry, does anything speak against 
> it, to average them and count them only once (say, for crystals measured 
> multiple rounds of 360 degrees to find identical geometries)?
> 
> Best wishes,
> 
> Dirk.
> 
> On 01.07.20 11:02, Gerard Bricogne wrote:
>> Dear Dirk,
>>
>>   Aren't you for getting about radiation damage? The n measurements of
>> the same hkl with the same geometry would not be equivalent, although they
>> would enable the tracking of radiation damage without the confounding with
>> absorption effects that comes from considering symmetry-related hkls. I
>> mentioned that in my second message yesterday.
>>
>>   The notion of "identical" reflections measurements is problematic for
>> the same reason that Heraclitus wrote (something like) "You cannot step
>> twice into the same river".
>>
>>
>>   With best wishes,
>>
>>    Gerard.
>>
>> -- 
>> On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:
>>> Dear Herman,
>>>
>>> I think, your MPR proposal is a great idea and would like to second it! And
>>> I would also like to propose that data processing programs just average
>>> "identical" reflections measured under the same geometry and count them only
>>> once (*), so that, in the end, we will get a realistic number of truly
>>> independent measurements.
>>>
>>> Cheers,
>>>
>>> Dirk.
>>>
>>> (*) I don't see a difference between measuring the same reflection with the
>>> same geometry n-times and measuring it n-times as long (apart from, maybe,
>>> catching instabilities in the experimental setup). Just averaging such
>>> "identical" reflections would simplify the subsequent scaling process with
>>> equivalent reflections that were measured under different geometry.
>>>
>>> On 01.07.20 09:32, Schreuder, Herman /DE wrote:
 Dear Bernard and other bulletin board members,

 As Gerard mentioned, current data processing programs and table 1’s do
 not make this distinction, but of course, you are free to ask the
 community to introduce it.

 My proposal to use “measurements per reflections” is not a joke. It
 exactly describes what is meant by the parameter and it is easily
 understood even by lay people like journal editors and referees, without
 the need of lengthy explanations like the ones we have seen in this
 thread.

 I really would like to ask you to consider replacing
 multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
 thread about completeness of data sets to be hijacked by a discussion on
 whether use the name multiplicity of redundancy for the number of
 measurements per reflection.

 My 2 cents,

 Herman

 *Von:* CCP4 bulletin board  *Im Auftrag von
 *Bernhard Rupp
 *Gesendet:* Dienstag, 30. Juni 2020 17:50
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
 a full dataset?

 *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
 

 .…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>>

[ccp4bb] Cryo-EM beamline scientist permanent position at CBI / IGBMC, Strasbourg

[Bruno KLAHOLZ]

Dear all,

here is an announcement for a permanent position as cryo-EM beamline scientist 
at the Centre for Integrative Biology, Strasbourg, France.
Deadline is tomorrow 2.7.2020 12 am CET.

With best regards,

Bruno Klaholz



Cryo-EM beamline scientist (permanent position):
The IGBMC/CBI is seeking a experienced scientist to participate in running the 
cutting-edge EM facilities at the Centre for Integrative Biology (CBI) at 
IGBMC, Illkirch/Strasbourg, France, while also participating in the on-site 
scientific projects.


The CBI provides a leading-edge scientific and technological environment in 
integrated structural biology to address the structure and function of 
biological systems, notably on gene expression, from the atomic, molecular to 
the tissue scales. The CBI http://www.igbmc.fr/grandesstructures/cbi/, hosts 
the French and European Infrastructures for Integrated Structural Biology, 
FRISBI http://frisbi.eu/, Instruct https://www.structuralbiology.eu/ and 
iNext-Discovery  https://inext-discovery.eu/network/inext-d/home which 
comprises advanced electron microscopy facilities equipped with cutting-edge 
instrumentation such as Titan Krios, Polara and Glacios (installation 2020) 
cryo electron microscopes, cryo Focused Ion Beam Scanning Electron Microscope 
(FIB/SEM) and super-resolution fluorescence microscopy 
http://frisbi.eu/centers/instruct-center-france-1-igbmc/cryo-electron-microscopy/.
 The Titan Krios microscope is equipped with Cs corrector, Falcon 3 camera, GIF 
energy filter, K3 camera and phase plate. In addition, the EM facility has a 
suite of associated equipments for sample preparation and dedicated computing 
resources for image processing and 3D reconstruction by single particle cryo-EM 
and cryo electron tomography (cryo-ET). For projects and publications of the 
associated teams see http://igbmc.fr/research/department/3/

Applications should be sent via the CNRS 
portal:
1) to see the description of the position: 
https://www.dgdr.cnrs.fr/drhita/concoursita/
Please click on "Consulter les offres"
Tick: Biologie & Doctorat, validate
Click on offer #4

2) to apply: https://www.dgdr.cnrs.fr/drhita/concoursita/
Click on "Poser sa candidature"
Please create login and follow procedure

Guidelines for the application:  
https://www.dgdr.cnrs.fr/drhita/concoursita/Guide-candidat-IT_2020.pdf

Deadline is tomorrow 2.7.2020 12 am CET.

Please include CV, list of publications, names of 3 referees and motivation 
letter and contact me at klah...@igbmc.fr if you have 
any questions.


###
Bruno P. Klaholz
Centre for Integrative Biology
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 1258
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
Tel. from abroad: 0033.369.48.52.78
Tel. inside France: 03.69.48.52.78
websites:
http://igbmc.fr/Klaholz
http://www.igbmc.fr/grandesstructures/cbi
http://frisbi.eu
http://instruct-eric.eu




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

[Dirk Kostrewa]

Dear Kay & Gerard,

the only reason, why I want to count differently, is to distinguish 
between true and pseudo-multiplicity. Apparently, I get on thin ice by 
trying to define "identical" reflections ... maybe, instead, we should 
start working with unmerged data in all programs. If I remember 
correctly, this is something that Gerard proposed long time ago for 
phasing programs.


Best wishes,

Dirk.

On 01.07.20 11:52, Kay Diederichs wrote:

Dear Dirk,

one cannot fully correct radiation damage. Normal scaling procedures take care of the 
average decay by a smooth resolution-dependant function. Zero-dose extrapolation goes 
beyond that but needs all symmetry mates - this does not fulfill your definition of 
"identical".

If we really could correct radiation damage then we could collect data to high 
resolution from all crystals just by using very high dose, and solve structures 
much more easily.

How often you count a reflection is up to you; I don't see what you gain by 
this.

best,
Kay

Am 01.07.20 um 11:42 schrieb Dirk Kostrewa:

Dear Gerard and Kay,

yes, you are both right - I have totally forgotten radiation damage! And 
correcting for this really makes a difference!

However, if radiation damage is corrected for reflections measured at different 
time points under the same geometry, does anything speak against it, to average 
them and count them only once (say, for crystals measured multiple rounds of 
360 degrees to find identical geometries)?

Best wishes,

Dirk.

On 01.07.20 11:02, Gerard Bricogne wrote:

Dear Dirk,

   Aren't you for getting about radiation damage? The n measurements of
the same hkl with the same geometry would not be equivalent, although they
would enable the tracking of radiation damage without the confounding with
absorption effects that comes from considering symmetry-related hkls. I
mentioned that in my second message yesterday.

   The notion of "identical" reflections measurements is problematic for
the same reason that Heraclitus wrote (something like) "You cannot step
twice into the same river".


   With best wishes,

    Gerard.

--
On Wed, Jul 01, 2020 at 10:46:57AM +0200, Dirk Kostrewa wrote:

Dear Herman,

I think, your MPR proposal is a great idea and would like to second it! And
I would also like to propose that data processing programs just average
"identical" reflections measured under the same geometry and count them only
once (*), so that, in the end, we will get a realistic number of truly
independent measurements.

Cheers,

Dirk.

(*) I don't see a difference between measuring the same reflection with the
same geometry n-times and measuring it n-times as long (apart from, maybe,
catching instabilities in the experimental setup). Just averaging such
"identical" reflections would simplify the subsequent scaling process with
equivalent reflections that were measured under different geometry.

On 01.07.20 09:32, Schreuder, Herman /DE wrote:

Dear Bernard and other bulletin board members,

As Gerard mentioned, current data processing programs and table 1’s do
not make this distinction, but of course, you are free to ask the
community to introduce it.

My proposal to use “measurements per reflections” is not a joke. It
exactly describes what is meant by the parameter and it is easily
understood even by lay people like journal editors and referees, without
the need of lengthy explanations like the ones we have seen in this
thread.

I really would like to ask you to consider replacing
multiplicity/redundancy/abundancy by MPR. At minimum, it may prevent a
thread about completeness of data sets to be hijacked by a discussion on
whether use the name multiplicity of redundancy for the number of
measurements per reflection.

My 2 cents,

Herman

*Von:* CCP4 bulletin board  *Im Auftrag von
*Bernhard Rupp
*Gesendet:* Dienstag, 30. Juni 2020 17:50
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get
a full dataset?

*EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk


.…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 mailto:CCP4BB@JISCMAIL.AC.UK>> *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:

  

[ccp4bb] Open position in biophysics/structural biology at Merck Healthcare KGaA

[Djordje Musil]

Dear colleagues,

There is an open position in biophysics/structural biology at Merck Healthcare 
KGaA in Darmstadt, Germany:

https://jobs.vibrantm.com/merck/job/Darmstadt-Scientist-(all-genders)-HE-64293/605907601/?locale=de_DE
Could you please forward the link to the colleagues you think might be 
interested into the position?

Best regards,
Djordje

Dr. Djordje Musil
Lab Head Protein Crystallography Darmstadt
MIB, DSPD, Discovery Technologies

Merck

Merck KGaA | Frankfurter Straße 250 | Postcode A022/001 | 64293 Darmstadt | 
Germany
Phone +49 6151 72 5855 | Mobile +49 151 14545855 | Fax +49 6151 72 915855
Email: djordje.mu...@merckgroup.com | 
www.merckgroup.com
Pflichtangaben finden Sie unter 
http://www.merckgroup.com/mandatories
Mandatory information can be found at 
http://www.merckgroup.com/mandatories




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otherwise protected from disclosure. If you are not the intended recipient, you 
must not copy this message or attachment or disclose the contents to any other 
person. If you have received this transmission in error, please notify the 
sender immediately and delete the message and any attachment from your system. 
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept 
liability for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any unauthorized 
changes of the content of this message and any attachment thereto. Merck KGaA, 
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message is free of viruses and does not accept liability for any damages caused 
by any virus transmitted therewith.



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Spanish and Portuguese versions of this disclaimer.



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[ccp4bb] Beamline scientist position - MX3 beamline at the Australian Synchrotron. [SEC=UNCLASSIFIED]

[CARADOC-DAVIES, Tom]

Hi All,

We need a new beamline scientist in the MX team at the Australian Synchrotron 
in Melbourne. This position is on the new microfocus MX3 beamline which is 
currently being designed and is scheduled for first users July 2023. This is a 
new 4-year fixed-term position in the MX3 build team. There is a potential for 
this role to contribute in the post-implementation phase of the project and 
possibly be a long-term appointment.

More information regarding the position can be found here:
https://anstocareers.nga.net.au/cp/index.cfm?event=jobs.checkJobDetailsNewApplication&returnToEvent=jobs.listJobs&jobid=98D57AD1-F1AB-4854-B6E7-ABE20074257C&CurATC=EXT&CurBID=0AC9%2DCFC1%2D4622%2D9710%2D9DB401354878&JobListID=22FC4F47%2DE994%2D46A3%2DB8C9%2D9BC901269F43&jobsListKey=03cad9eb%2Df31c%2D413a%2Db26a%2D339020bc5fa8&persistVariables=CurATC,CurBID,JobListID,jobsListKey,JobID&lid=58599540062

If you know anyone you think may be interested could you please let them know? 
Applications close on the 19th of July.

Cheers,

Tom

Tom Caradoc-Davies
Lead Scientist – MX3
Australian Synchrotron – ANSTO
Melbourne, VIC 3168




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

[Ian Tickle]

Yes this seems to be a common misunderstanding, that the meanings of words
such as 'redundancy' have to be the same in an informal non-scientific
context and in a formal technical/scientific context.

So we can say that in an informal context, 'redundancy' means "unnecessary
duplication (or multiplication) without a purpose", and in a formal context
it has come to mean, ever since John von Neumann pioneered the idea in the
1950s, "duplication / multiplication with the express purpose of improving
the reliability of the outcome".  'Multiplicity / multiplication' is
neutral with regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and
also not surprisingly the informal meaning tends to be rather ill-defined,
for example 'theory' used informally means "hypothesis, hunch, speculation,
conjecture etc.", whereas in a scientific context it has the precise
meaning "A coherent  statement
 or set of ideas that explains
 observed
 facts
 or phenomena
 and correctly predicts new
facts or phenomena not previously observed, or which sets out the laws
 and principles of something known or
observed; a hypothesis confirmed by observation, experiment etc." (
https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, 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'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

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

[Hughes, Jonathan]

hi ian,
oh no! all those trump fans across the pond will love the "hypothesis of 
evolution" idea. they won't know the word "hypothesis" of course, but 
unfortunately you might get famous for it anyhow.
cheers
jon

Von: CCP4 bulletin board  Im Auftrag von Ian Tickle
Gesendet: Mittwoch, 1. Juli 2020 17:39
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full 
dataset?


Yes this seems to be a common misunderstanding, that the meanings of words such 
as 'redundancy' have to be the same in an informal non-scientific context and 
in a formal technical/scientific context.

So we can say that in an informal context, 'redundancy' means "unnecessary 
duplication (or multiplication) without a purpose", and in a formal context it 
has come to mean, ever since John von Neumann pioneered the idea in the 1950s, 
"duplication / multiplication with the express purpose of improving the 
reliability of the outcome".  'Multiplicity / multiplication' is neutral with 
regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and 
also not surprisingly the informal meaning tends to be rather ill-defined, for 
example 'theory' used informally means "hypothesis, hunch, speculation, 
conjecture etc.", whereas in a scientific context it has the precise meaning "A 
coherent 
statement or set of ideas that 
explains 
observed 
facts or 
phenomena and correctly predicts new 
facts or phenomena not previously observed, or which sets out the 
laws and principles of something known or 
observed; a hypothesis confirmed by observation, experiment etc." 
(https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> 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 
> mailto: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 

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

[Goldman, Adrian]

I find, when discussing definitions of words, it’s always good to look in the 
OED (well, the SOED, I don’t have the big one).  For redundant (redundancy 
being defined as the state or quality of being redundant), we find:

1. Superabundant, superfluous, excessive. b. Characterised by superfluity or 
excess in some respect.
2. Abounding to excess or fullness; plentiful, copious, ((my itals), exuberant
 b Characterised by copiousness, fullness, or abundance (my itals).
As an example of (1), it gives “The employment of redundant capital (Macaulay).

- so we are employing the redundant observations (the ones above that minimal 
number (1) needed to say anything at all about the value of Ihkl).

I think it’s fair to see that the way it is used in x-ray crystallography is a 
subset of the meanings above, which is just fine.

Adrian


On 1 Jul 2020, at 16:38, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


Yes this seems to be a common misunderstanding, that the meanings of words such 
as 'redundancy' have to be the same in an informal non-scientific context and 
in a formal technical/scientific context.

So we can say that in an informal context, 'redundancy' means "unnecessary 
duplication (or multiplication) without a purpose", and in a formal context it 
has come to mean, ever since John von Neumann pioneered the idea in the 1950s, 
"duplication / multiplication with the express purpose of improving the 
reliability of the outcome".  'Multiplicity / multiplication' is neutral with 
regard to purpose.

This divergence of meanings should hardly come as a surprise to anyone, and 
also not surprisingly the informal meaning tends to be rather ill-defined, for 
example 'theory' used informally means "hypothesis, hunch, speculation, 
conjecture etc.", whereas in a scientific context it has the precise meaning "A 
coherent 
statement or set of ideas that 
explains 
observed 
facts or 
phenomena and correctly predicts new 
facts or phenomena not previously observed, or which sets out the 
laws and principles of something known or 
observed; a hypothesis confirmed by observation, experiment etc." 
(https://en.wiktionary.org/wiki/theory).

"The Hypothesis of Evolution" anyone ?

Cheers

-- Ian




On Tue, 30 Jun 2020 at 14:30, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> 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 
> mailto: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 

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

[John R Helliwell]

Dear Ian,
I take issue with your assertion below that “the totally precise **scientific** 
meaningis an  **engineering**” definition. 
Science and engineering are not the same. Health and safety leads to the need 
in engineering for redundancy and indeed safety factors. In essence, in 
engineering terms, one feels safest on a Brunel bridge than a Boris Johnson 
“across the Thames” walkway.  
The matter for science is encapsulated in Hermann’s excellent proposal, now 
seconded twice, MPR, measurements per hkl reflection. Even with Xray damage hkl 
as a label is the constant. Also XFELs offer Xray damage free reflection 
intensity measurements of an hkl reflection. Likewise neutrons offer damage 
free intensity measurements of an hkl.

Best regards,
John 

Emeritus Professor John R Helliwell DSc




> 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 th

[ccp4bb] Two Group Leader positions available@EMBL Hamburg

[Margret Fischer]

Dear colleagues,

I would like to inform you that EMBL Hamburg is currently advertising 
for two Group Leader positions.


*Reference Number HH00190*: Group leader - New approaches in electron 
microscopy


/Closing date: 13th August 2020/

*Reference Number HH00191:* Group Leader - X-ray imaging of biological 
samples


/Closing date: 13th August 2020/

Further detailed information can be found under the following links:

http://s.embl.org/HH00190

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Best wishes,

Margret

--

Margret Fischer
European Molecular Biology Laboratory
Senior Administrative Officer
Notkestrasse 85
22607 Hamburg
Germany
Tel: +49 40 89902110
Mob: +49 1754105760



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

[James Holton]

Sorry to take this thread on a detour/diversion: What I was attempting 
to point out below, perhaps unclearly, is that the different 
interpretations of the word "redundant" are a cultural difference.  As a 
student of multiple English languages perhaps I can explain:


Few US English speakers know that in UK/European/Australian English the 
word "redundant" has a strong negative connotation. I, for one, was 
surprised to learn that the phrase "made redundant" is used in the UK to 
describe loss of employment.  That is, a layoff, firing or perhaps a 
furlough. So, I think it important to spell out for my fellow US English 
speakers that the emotional ties to this negative connotation can be 
strong ones.


Conversely, many UK English speakers do not know that in US English the 
word "redundant" has a strong positive connotation.  We never use the 
phrase "made redundant" to describe a lost job.  Most Americans I think 
would be confused by such a turn of phrase. If a US English speaker was 
told their jobs was "made redundant" they would most likely think that a 
new hire was onboarded to back them up.  This would imply that their job 
was so important that the company wanted at least two people doing it, 
just in case you got hit by a bus. This strong positive connotation also 
has emotional roots.


Personally, I prefer the positive connotation. Perhaps that is my 
cultural bias, or perhaps I just generally believe that positivity is 
better than negativity. Maybe I'm just a "nice" guy. The meaning of the 
word "nice" has changed enormously over the last few hundred years, and 
I don't think we're going to change that any more than we are going to 
change the meaning of "redundant" in these two major forms of English.


However, just because a word has slightly different meanings in two 
slightly different languages does not mean we should abandon it. Are we 
going to stop eating "chips" just because we are not sure if our fried 
potato will come as sliced wedges or thin crispy wafers? If you are 
unhappy with your meal, is it the fault of the culture you are visiting? 
or the customer for forgetting where they are? Context is everything.


So, for those unfamiliar with one or more of the major English-speaking 
cultures, here are a few other important differences to be aware of:

"Football" may not be the game you think it is.
If you are offered a "biscuit" in the US, do not expect it to be sweet.
If you want to leave a building you should take the "lift" to the 
"ground floor", but if you take an "elevator" get off on the "1st floor".
A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it 
only means an unintelligent person, or a plastic replica of one.
"please" and "thank you" are considered baseline politeness in some 
English cultures, but their excessive use in others, such as the US, can 
be seen as rude.

A "tap" in the US dispenses beer, water comes out of a "faucet".
A "flat" in the US is not a place to live, but rather where we test 
rocket cars.

"Gas" can be a liquid in the US.
"Rubber" is a substance in both languages, but in the US a lump of it 
meant for erasing pencil marks is an "eraser". Do not ask for a "rubber" 
at the shop unless you are sure which country you are in.
A "holiday" in the US is a special day on the calendar when everyone 
gets off work, not just when an individual takes a "vacation".
If you go walking down the "pavement" you are risking getting hit by a 
car in the US, because that is what we call the road bed, not the 
"sidewalk".
A "torch", is a handheld electric light in the UK, but in the US it is a 
flaming stick of wood.
A "queue" is a line of people in the UK, but in the US it is known only 
to computer scientists submitting jobs on a cluster.


Then there are words like "capillary", which means the same thing in 
both languages but the alternate pronunciations never fail to enrage 
someone. It is perhaps odd that since US English and UK English are 
spoken with many different accents we pronounce essentially every word 
at least slightly differently, but for some reason "capillary" makes 
people angry.  Same with "schedule". Equally emotional responses arise 
from how you pronounce the letter "z".  Go figure.


Similar ire is risen for spelling. My favourite/favorite is 
aluminum/aluminium, but equally divisive are colour/color, tire/tyre, 
cheque/check, gray/grey, theatre/theater, pyjamas/pajamas, and many others.


It is at this stage when you will find people of another culture trying 
to "correct" you on how to speak or write your own language. This can be 
confusing because you will probably not be corrected for calling a 
"courgette" a "zucchini", especially if you are Italian. However, a 
native Hindi speaker might feel compelled to correct your pronunciation 
of "shampoo".  I am not singling out any one culture here, we have all 
given in to the temptation to "correct" someone, perhaps even while 
visiting their home.  Ahh, the erro

[ccp4bb] Postdoc position in the Fesik Lab at Vanderbilt University

[Phan, Jason]

Please post:

Advertisement for a postdoctoral structural biologist position at Vanderbilt 
University Medical Center, Department of Biochemistry

A postdoc position is available in the laboratory of Dr. Stephen Fesik 
(https://lab.vanderbilt.edu/fesik-lab/)
 for a structural biologist with experience in protein NMR or X-ray 
crystallography.  Responsibilities will include protein 
expression/purification, conducting fragment screens using NMR, and all aspects 
of x-ray crystallography, including preparation of protein-inhibitor complexes, 
crystallization, home/synchrotron data collection, and structure determination. 
Experience in cloning, site-directed mutagenesis, and the use of robots are 
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communicate effectively in a highly collaborative environment.




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

[jp d]

since i am not getting shit/shite done may i also point out aluminium/aluminum






On Wednesday, July 1, 2020, 11:52:21 AM PDT, James Holton  
wrote: 






Sorry to take this thread on a detour/diversion: What I was attempting to point 
out below, perhaps unclearly, is that the different interpretations of the word 
"redundant" are a cultural difference.  As a student of multiple English 
languages perhaps I can explain:

Few US English speakers know that in UK/European/Australian English the word 
"redundant" has a strong negative connotation. I, for one, was surprised to 
learn that the phrase "made redundant" is used in the UK to describe loss of 
employment.  That is, a layoff, firing or perhaps a furlough. So, I think it 
important to spell out for my fellow US English speakers that the emotional 
ties to this negative connotation can be strong ones.

Conversely, many UK English speakers do not know that in US English the word 
"redundant" has a strong positive connotation.  We never use the phrase "made 
redundant" to describe a lost job.  Most Americans I think would be confused by 
such a turn of phrase. If a US English speaker was told their jobs was "made 
redundant" they would most likely think that a new hire was onboarded to back 
them up.  This would imply that their job was so important that the company 
wanted at least two people doing it, just in case you got hit by a bus. This 
strong positive connotation also has emotional roots.

Personally, I prefer the positive connotation. Perhaps that is my cultural 
bias, or perhaps I just generally believe that positivity is better than 
negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has 
changed enormously over the last few hundred years, and I don't think we're 
going to change that any more than we are going to change the meaning of 
"redundant" in these two major forms of English.

However, just because a word has slightly different meanings in two slightly 
different languages does not mean we should abandon it.  Are we going to stop 
eating "chips" just because we are not sure if our fried potato will come as 
sliced wedges or thin crispy wafers? If you are unhappy with your meal, is it 
the fault of the culture you are visiting? or the customer for forgetting where 
they are? Context is everything. 

So, for those unfamiliar with one or more of the major English-speaking 
cultures, here are a few other important differences to be aware of: 
"Football" may not be the game you think it is. 
If you are offered a "biscuit" in the US, do not expect it to be sweet. 
If you want to leave a building you should take the "lift" to the "ground 
floor", but if you take an "elevator" get off on the "1st floor". 
A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it only 
means an unintelligent person, or a plastic replica of one. 
"please" and "thank you" are considered baseline politeness in some English 
cultures, but their excessive use in others, such as the US, can be seen as 
rude.
A "tap" in the US dispenses beer, water comes out of a "faucet".
A "flat" in the US is not a place to live, but rather where we test rocket 
cars. 
"Gas" can be a liquid in the US.  
"Rubber" is a substance in both languages, but in the US a lump of it meant for 
erasing pencil marks is an "eraser". Do not ask for a "rubber" at the shop 
unless you are sure which country you are in. 
A "holiday" in the US is a special day on the calendar when everyone gets off 
work, not just when an individual takes a "vacation". 
If you go walking down the "pavement" you are risking getting hit by a car in 
the US, because that is what we call the road bed, not the "sidewalk".  
A "torch", is a handheld electric light in the UK, but in the US it is a 
flaming stick of wood. 
A "queue" is a line of people in the UK, but in the US it is known only to 
computer scientists submitting jobs on a cluster. 

Then there are words like "capillary", which means the same thing in both 
languages but the alternate pronunciations never fail to enrage someone. It is 
perhaps odd that since US English and UK English are spoken with many different 
accents we pronounce essentially every word at least slightly differently, but 
for some reason "capillary" makes people angry.  Same with "schedule". Equally 
emotional responses arise from how you pronounce the letter "z".  Go figure.

Similar ire is risen for spelling. My favourite/favorite is aluminum/aluminium, 
but equally divisive are colour/color, tire/tyre, cheque/check, gray/grey, 
theatre/theater, pyjamas/pajamas, and many others. 

It is at this stage when you will find people of another culture trying to 
"correct" you on how to speak or write your own language. This can be confusing 
because you will probably not be corrected for calling a "courgette" a 
"zucchini", especially if you are Italian. However, a native Hindi speaker 
might feel compelled to correct your pronunciation of "shampoo".  I a

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

[Jose Brandao-Neto]

Hi Ian, good to hear! Hi everyone, thanks for the etymological - and 
etiological - discussion. I'm good whatever the choice.

John, I beg to differ with the absolute statement that xfels offer damage free 
hkls - back in 2016 yet another great experimental work, by Inoue et al 
(https://www.pnas.org/content/113/6/1492), showed global loss of diffraction in 
a protein crystal analog as soon as 10 fs from exposure start (later estimated 
in Mx experiments by I. Schlichting's team).

Cheers,
José
-> Digression: And I expect neutrons will do a similar job exciting the crystal 
with some phonon-magnetic moment coupling and changing the magnetisation state 
of the electronic structure pretty fast. 
-> Digressing even further, this might be a mechanism that underpins allosteric 
effects, so neutron mx might be a way to tease them.



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

[Ethan A Merritt]

On Wednesday, 1 July 2020 18:50:57 PDT Jose Brandao-Neto wrote:
> Hi Ian, good to hear! Hi everyone, thanks for the etymological - and 
> etiological - discussion. I'm good whatever the choice.
> 
> John, I beg to differ with the absolute statement that xfels offer damage 
> free hkls - back in 2016 yet another great experimental work, by Inoue et al 
> (https://www.pnas.org/content/113/6/1492), showed global loss of diffraction 
> in a protein crystal analog as soon as 10 fs from exposure start (later 
> estimated in Mx experiments by I. Schlichting's team).

That's the "destroy" part of "diffract and destroy".

Since an XFEL pulse can be shorter than 10 fs,
that observation does not contradict the idea that the measured
diffraction occurs faster than the damage.

Ethan

> Cheers,
> José

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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[ccp4bb] PostDoctoral Position in Membrane Protein Structural Biology at USC, Los Angeles

[Cornelius Gati]

PostDoctoral Position in Membrane Protein Structural Biology at USC, Los Angeles

The position is available starting January 2021 in the Department of Biological 
Sciences at the University of Southern California and is initially limited to 2 
years, with possible extension.

Our research focuses on the structural biology of important membrane proteins, 
using single particle cryoEM and X-ray crystallography. We are working in close 
collaboration with the group of Prof. Vadim Cherezov (USC) on the structural 
biology of GPCRs. External collaborations include the group of Prof. Dirk 
Slotboom (Univ. of Groningen) and Prof. K. Chris Garcia (Stanford University).

USC has a suite of research facilities and is in the process of installing a 
new CryoEM center:

  *   Electron microscopy suite: Titan Krios with GIF Quantum energy filter and 
K3 detector, Glacios with Falcon 4 detector, Talos Arctica with CCD/side entry 
holder for NS and screening
  *   Core facility for insect- and mammalian cell expression
  *   High performance computing for data processing/analysis

Qualified candidates must have a Ph.D. degree with a solid background in 
structural biology and biophysics/biochemistry. Previous work with membrane 
proteins is a plus. A successful candidate is expected to be highly skilled and 
self-motivated and is willing to work in a collaborative environment. The 
Postdoctoral salary depends on qualifications and relevant experiences 
according to USC standards.

Interested candidates should apply directly with Cornelius Gati at 
cornelius.gati[at]gmail.com. Please attach a 
cover letter, Curriculum Vitae, research statement, publication list and a 
reference letter. The deadline for the application is September 30th 2020.


Current group website: https://gati-lab.slac.stanford.edu/

Recent work from our group includes:

H Shaye, A Ishchenko, JH Lam, GW Han, L Xue, P Rondard, JP Pin, V Katritch, C 
Gati*, V. Cherezov*
Structural basis of the activation of a metabotropic GABA receptor. Nature. 
2020.

S Rempel, C Gati*, M Nijland, C Thangaratnarajah, A Karyolaimos, JW de Gier, A 
Guskov*, DJ Slotboom*.
A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds. 
Nature. 2020.



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