Re: [ccp4bb] Protein-DNA covalent bond refinement

[Robert Nicholls]

Dear Cristina,

In CCP4 you've got two options that use the modern approach (Acedrg):

(1) CCP4i2 -> Ligands -> Make Covalent Link.

(2) Coot -> Calculate -> Modules -> CCP4. This will make a "CCP4" menu appear 
that contains the option: Make Link via Acedrg.

Hopefully it's pretty self-explanatory from there - you'll end up with a CIF 
dictionary containing the link description, which you can then pass to your 
refinement program. Both of these options require the latest version of CCP4 
(7.1).

Regards,
Rob


> On 2 Jul 2020, at 15:59, Cristina Machon  wrote:
> 
> Dear all,
> 
> I am writing regarding a problem we are facing with the refinement of a 
> structure. We would really appreciate it if anybody could suggest how to set 
> up geometrical restraints for a protein-DNA covalent bond in Refmac or 
> Phenix? 
> 
> Thanks in advance,
> 
> Best wishes,
> 
> Cristina
> 
> 
> -- 
> Cristina Machón Sobrado, PhD
> Instituto de Biología Molecular Barcelona-CSIC
> Parc Científic de Barcelona
> c/ Baldiri Reixac 10
> 08028 Barcelona
> Spain
> 
> Phone: +34934034957
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] Protein-DNA covalent bond refinement

[Eleanor Dodson]

You can create a link in COOT..
Eleanor

On Thu, 2 Jul 2020 at 16:10, Cristina Machon  wrote:

> Dear all,
>
> I am writing regarding a problem we are facing with the refinement of a
> structure. We would really appreciate it if anybody could suggest how to
> set up geometrical restraints for a protein-DNA covalent bond in Refmac or
> Phenix?
>
> Thanks in advance,
>
> Best wishes,
>
> Cristina
>
>
> --
> Cristina Machón Sobrado, PhD
> Instituto de Biología Molecular Barcelona-CSIC
> Parc Científic de Barcelona
> c/ Baldiri Reixac 10
> 08028 Barcelona
> Spain
>
> Phone: +34934034957
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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

[Schreuder, Herman /DE]

Dear Ian,

Since some very advanced countries still use miles, Fahrenheit and inches, I 
did not expect anything to change. It was an escalating discussion in this 
thread on data completeness(!) on the use of multiplicity vs redundancy that 
made me suggest a different term. Except for an occasional discussion in the 
BB, there is nothing against people using the term they are most comfortable 
with.

However, I insist that trying to impose a different definition of “measurement” 
for MPR vs the definition used for the calculation of redundancy/multiplicity 
is not a valid argument against MPR.

Cheers,
Herman




Von: CCP4 bulletin board  Im Auftrag von Ian Tickle
Gesendet: Donnerstag, 2. Juli 2020 22:06
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a 
full dataset?


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


Well I very much doubt that many software developers are going to trawl through 
all their code, comments, output statements & documentation to change 
'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is agreed on 
(assuming of course we do manage to come to an agreement, which I doubt).  And 
good luck with persuading wwPDB to change 'redundancy' in their mmCIF 
dictionary!  That would be not only pointless but also a lot of work, partly 
because terms get abbreviated in code and in outputs (e.g. to 'redund' in mine, 
or 'mult').  And don't say I can keep the code & comments the same and only 
change the outputs and documentation: that will really tax my brain!  Also 
don't say this need only apply to new code: no code is ever completely new, and 
mixing up old & new terminology would be a disaster waiting to happen!  Also it 
won't end there: someone will always find terminology that they disagree with: 
I can think of plenty cans of worms that we could open, but I think one is 
already one too many!

By the way, "measurements per reflection" won't float, because some 
measurements will be rejected as outliers (that's why we need redundancy! - as 
opposed to simply measuring intensities for longer).  What I call redundancy is 
"the count of _contributing_ measurements per reflection" (CCMPR, sigh).  
Personally I think that adding one more term is going to confuse things even 
more since if I'm right most people will continue to use the old terms in 
parallel anyway.

IMO we should all be free to use the terminology we are most comfortable with, 
and it's up to the receivers of the information to perform the translation.  
That's how it always has been, and IMO always will be.  Of course it behoves 
(behooves?) the sender to point to or make available any necessary translation 
tools, such as a dictionary or glossary, but once that is done it is the 
responsibility of the receiver to make use of those tools.  Even better if you 
can point to formally-published information (i.e. book or peer-reviewed paper), 
since information on the web is so ephemeral.  As a receiver of information 
myself that's what my brain is doing constantly, i.e. converting others' 
terminology into concepts my brain can process.  If I'm forced to write code 
using a different set of terms it's inevitable that I will unconsciously lapse 
into my old bad ways and I'll end up with a dog's breakfast!  If I'm constantly 
having to convert my terminology into some standardised (standardized?) 
terminology before committing it to code, I'm going to use up what little 
brainpower I have left!

The absolutely critical thing surely is to DEFINE all terms that might be 
unfamiliar or ambiguous (yes Bernhard, I abhor a definitional vacuum for this 
very reason!).  That way the developers feel comfortable and the users can 
understand what's going on.  I'm very happy to put my head on the chopping 
block and add redundancy, multiplicity and whatever other terms people find 
unfamiliar or ambiguous in my outputs or documentation to my 
Glossary.
  Note that this covers only terms used on the STARANISO server; it is by no 
means intended as a replacement for the IUCr's Online Dictionary of 
Crystallography (or any other dictionary for that matter).

By the way, James, you left out my favourite (favorite?): "I could/couldn't 
care less", the positive one of which I always find illogical (if one could 
care less that means the amount of caring must be strictly positive since a 
negative amount is meaningless, whereas if one couldn't care less the amount of 
caring must already be exactly zero, which is surely what the expression is 
meant to convey).  I'm not suggesting at all that I don't care, quite the 
opposite: I think 

[ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

[Nicholas Keep]

We are going to be doing a data collection for an MRes student at 
Diamond in the next couple of weeks.  These are his first crystals.  It 
would be good if he could be involved in watching it.


I was wondering if anyone had tried sharing screen and voice via moodle 
collaborate or Microsoft Teams while doing a data collection?  Zoom is 
deprecated by our institution but if anyone had succeeded on zoom that 
would also be interesting.


I am on Virgin media 100 MB broadband which is pretty much achieving 
that (upload is only around 9 MB though).


Alternatively we can try and set him up to connect via nx and watch, but 
that would lose the sound connection unless I have a phone tucked under 
my chin.


We could just record my screen and sound and he could watch later.

Any tips?

Best wishes

Nick



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

Dean Email; scid...@bbk.ac.uk
Dept email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] flow rate for cooling stream?

[Schreuder, Herman /DE]

Dear Patrick,
if I recall correctly, our systems run at 10-15 ml/min (gas). I will check on 
Monday when I am back in the lab.
The original cryostreams would run for several day's on a tank of liquid 
nitrogen. However, they had significant hardware to dry the nitrogen and to 
ensure a constant flow.

Best, Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Patrick Loll
Gesendet: Donnerstag, 2. Juli 2020 22:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] flow rate for cooling stream?

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



Sorry, way off topic:

Does anyone have an estimate for the flow rate one would typically use for the 
cold nitrogen stream passing over a protein crystal in a standard data 
collection?

Background: Our nitrogen “generator” has gone belly-up and the vendor no longer 
services it, so I’m testing the feasibility of using the boil-off from a liquid 
nitrogen tank to provide the gas to support a short data collection (this 
nitrogen gas would serve as the feedstock into our helium cryostat). But I 
don’t know the flow rate required, so I can’t calculate if one tank has enough 
nitrogen to support a day or so of data collection. There are flow meters for 
the warm and cold stream on the nitrogen generator, but these flow meters have 
no apparent units anywhere on them, so I have no idea of the rate at which the 
gas would be consumed.

Thanks for any useful tidbits. 

And for those of you in the US, best wishes for a happy “Holy crap, even MORE 
fireworks?!?!!” Day 

Pat


---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology Drexel University College of 
Medicine Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu


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Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

[Sandy, James (DLSLtd,RAL,LSCI)]

Hi all,

I have had problems trying to share my screen using Teams when using the NX 
client. I have experienced the screen flashing in a manner which may induce 
fits! This may be related to sharing a window rather than the whole desktop but 
something to be aware of. I have taken to using Zoom if I want to work with 
others sharing an NX session.

Cheers,

James


-Original Message-
From: CCP4 bulletin board  On Behalf Of Winter, Graeme 
(DLSLtd,RAL,LSCI)
Sent: 03 July 2020 09:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Relaying a remote data collection on using moodle 
collaborate or Microsoft Teams

Hi Nick

I’ll offer a vote in favour of teams, as it is possible with the desktop 
application to hand over control as well for a shared window (e.g. NX) so your 
student could perform the collection themselves under your supervision rather 
than just watching.

I’ve not tried teams + NX as a combination but I can see no reason why this 
would not work, it’s not like the network load will be much different to 
watching a room full of happy faces… you could also try this out in advance, 
connecting to nx.diamond for e.g. processing and confirming that the screen 
share works so you lose no time on data collection day. 

FWIW I prefer zoom for meetings as it’s got better sound & copes better with 
large groups (IMHO) however for small groups / 1:1 teams has worked quite well 
in my experience, and I was particularly impressed with the screen sharing. 

Best wishes Graeme



> On 3 Jul 2020, at 09:18, Nicholas Keep  wrote:
> 
> We are going to be doing a data collection for an MRes student at Diamond in 
> the next couple of weeks.  These are his first crystals.  It would be good if 
> he could be involved in watching it.
> 
> I was wondering if anyone had tried sharing screen and voice via moodle 
> collaborate or Microsoft Teams while doing a data collection?  Zoom is 
> deprecated by our institution but if anyone had succeeded on zoom that would 
> also be interesting.
> 
> I am on Virgin media 100 MB broadband which is pretty much achieving that 
> (upload is only around 9 MB though).
> 
> Alternatively we can try and set him up to connect via nx and watch, but that 
> would lose the sound connection unless I have a phone tucked under my chin.
> 
> We could just record my screen and sound and he could watch later.
> 
> Any tips?
> 
> Best wishes
> 
> Nick
> 
> 
> 
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology, 
> Department of Biological Sciences Birkbeck,  University of London, 
> Malet Street, Bloomsbury LONDON WC1E 7HX
> 
> Dean Email;   scid...@bbk.ac.uk
> Dept email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>  020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the 
> crystallography entrance and ring me or the department office from the 
> internal phone by the door
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

[Navdeep Sidhu]

Dear Ian,

I stand corrected: I should have realized before writing rather than
afterwards that you were surely stressing the formalization (or
formalisation) part.

Cheers,
Navdeep


---
On 02.07.20 22:09, Ian Tickle wrote:
> 
> Hi Navdeep
> 
> Yes good point, the principle of redundancy (though they wouldn't have
> used that term!) has a very long history, but von Neumann did more than
> anyone before him to formalise it:
> 
> http://www.cyclify.com/wiki/images/a/af/Von_Neumann_Probabilistic_Logics_and_the_Synthesis_of_Reliable_Organisms_from_Unreliable_Components.pdf
> 
> Cheers
> 
> -- Ian
> 
> 
> On Thu, 2 Jul 2020 at 11:58, Navdeep Sidhu  > wrote:
> 
> Dear Ian,
> 
> You seem to be slightly off there: The successful use of repeating
> observations to reduce (especially systematic) observational error
> predates von Neumann by at least 4 centuries.
> 
> One of the first instances of its use was in the 1500s, due to a migrant
> scientist working in Denmark and Prague, Czech Republic: Tycho Brahe,
> whom "the divine goodness [had] given to us" (Kepler).
> 
> Best regards,
> Navdeep
> 
> 
> ---
> On 01.07.20 17:38, Ian Tickle 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  
> > >> 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 

[ccp4bb] flow rate for cooling stream?

[Marcus Winter]

Dear Patrick, Herman,



Regarding the Cryostream, then referring to the Cryostream 800 brochure 
indicates that the N2 (gas) flow rates employed are in the range of 5 - 10 
litres / minute, … and, I guess, therefore something similar for the outer dry 
air 'shield' stream.   Obviously, it’s best to check directly with the 
manufacturers (Oxford Cryosystems) directly on the details.



All The Best,



Marcus Winter

(Rigaku)





 -Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Schreuder, Herman /DE
Sent: Friday, July 03, 2020 7:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [EXTERNAL] [ccp4bb] flow rate for cooling stream?



Dear Patrick,

if I recall correctly, our systems run at 10-15 ml/min (gas). I will check on 
Monday when I am back in the lab.

The original cryostreams would run for several day's on a tank of liquid 
nitrogen. However, they had significant hardware to dry the nitrogen and to 
ensure a constant flow.



Best, Herman



-Ursprüngliche Nachricht-

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Patrick Loll

Gesendet: Donnerstag, 2. Juli 2020 22:03

An: CCP4BB@JISCMAIL.AC.UK

Betreff: [EXTERNAL] [ccp4bb] flow rate for cooling stream?



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







Sorry, way off topic:



Does anyone have an estimate for the flow rate one would typically use for the 
cold nitrogen stream passing over a protein crystal in a standard data 
collection?



Background: Our nitrogen “generator” has gone belly-up and the vendor no longer 
services it, so I’m testing the feasibility of using the boil-off from a liquid 
nitrogen tank to provide the gas to support a short data collection (this 
nitrogen gas would serve as the feedstock into our helium cryostat). But I 
don’t know the flow rate required, so I can’t calculate if one tank has enough 
nitrogen to support a day or so of data collection. There are flow meters for 
the warm and cold stream on the nitrogen generator, but these flow meters have 
no apparent units anywhere on them, so I have no idea of the rate at which the 
gas would be consumed.



Thanks for any useful tidbits.



And for those of you in the US, best wishes for a happy “Holy crap, even MORE 
fireworks?!?!!” Day



Pat





---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology Drexel University College of 
Medicine Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA  19102  USA



(215) 762-7706

pjl...@gmail.com

pj...@drexel.edu





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

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

Thanks Ian - I think you raise some excellent points - while I think the 
general reader (TM) would understand that redundancy and multiplicity mean 
broadly the same thing in Table 1, I think having program developers document 
_precisely_ what they mean by those values would be very valuable. I also look 
hard at “completeness” which seems to vary from one program to the next and 
cause some confusion to end users.

I appreciate that some of this effort will also land on my desk and am happy to 
practice that which I preach

Best wishes Graeme

On 2 Jul 2020, at 21:05, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:


Well I very much doubt that many software developers are going to trawl through 
all their code, comments, output statements & documentation to change 
'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is agreed on 
(assuming of course we do manage to come to an agreement, which I doubt).  And 
good luck with persuading wwPDB to change 'redundancy' in their mmCIF 
dictionary!  That would be not only pointless but also a lot of work, partly 
because terms get abbreviated in code and in outputs (e.g. to 'redund' in mine, 
or 'mult').  And don't say I can keep the code & comments the same and only 
change the outputs and documentation: that will really tax my brain!  Also 
don't say this need only apply to new code: no code is ever completely new, and 
mixing up old & new terminology would be a disaster waiting to happen!  Also it 
won't end there: someone will always find terminology that they disagree with: 
I can think of plenty cans of worms that we could open, but I think one is 
already one too many!

By the way, "measurements per reflection" won't float, because some 
measurements will be rejected as outliers (that's why we need redundancy! - as 
opposed to simply measuring intensities for longer).  What I call redundancy is 
"the count of _contributing_ measurements per reflection" (CCMPR, sigh).  
Personally I think that adding one more term is going to confuse things even 
more since if I'm right most people will continue to use the old terms in 
parallel anyway.

IMO we should all be free to use the terminology we are most comfortable with, 
and it's up to the receivers of the information to perform the translation.  
That's how it always has been, and IMO always will be.  Of course it behoves 
(behooves?) the sender to point to or make available any necessary translation 
tools, such as a dictionary or glossary, but once that is done it is the 
responsibility of the receiver to make use of those tools.  Even better if you 
can point to formally-published information (i.e. book or peer-reviewed paper), 
since information on the web is so ephemeral.  As a receiver of information 
myself that's what my brain is doing constantly, i.e. converting others' 
terminology into concepts my brain can process.  If I'm forced to write code 
using a different set of terms it's inevitable that I will unconsciously lapse 
into my old bad ways and I'll end up with a dog's breakfast!  If I'm constantly 
having to convert my terminology into some standardised (standardized?) 
terminology before committing it to code, I'm going to use up what little 
brainpower I have left!

The absolutely critical thing surely is to DEFINE all terms that might be 
unfamiliar or ambiguous (yes Bernhard, I abhor a definitional vacuum for this 
very reason!).  That way the developers feel comfortable and the users can 
understand what's going on.  I'm very happy to put my head on the chopping 
block and add redundancy, multiplicity and whatever other terms people find 
unfamiliar or ambiguous in my outputs or documentation to my 
Glossary.  
Note that this covers only terms used on the STARANISO server; it is by no 
means intended as a replacement for the IUCr's Online Dictionary of 
Crystallography (or any other dictionary for that matter).

By the way, James, you left out my favourite (favorite?): "I could/couldn't 
care less", the positive one of which I always find illogical (if one could 
care less that means the amount of caring must be strictly positive since a 
negative amount is meaningless, whereas if one couldn't care less the amount of 
caring must already be exactly zero, which is surely what the expression is 
meant to convey).  I'm not suggesting at all that I don't care, quite the 
opposite: I think it's vital that terminology is universally understood 
("define your terms, Sir, or we'll never agree").

So my 2p's worth is: carry on as we are, but please, please, please DEFINE (and 
only argue about the definitions!).

https://www.brainyquote.com/quotes/dylan_moran_557269?src=t_please_everyone

Cheers

-- Ian


On Thu, 2 Jul 2020 at 11:11, Harry Powell - CCP4BB 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear all

I’ve been persuaded that MPR is a useful name 

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

[David Waterman]

Hi Herman,

I like the idea of MPR, but I continue to worry about the term
"measurement". The intensity associated with a particular reflection is a
fit based on a scaling model, and ultimately, depending on your integration
software, may be linked to a weighted sum of two raw measurements: the
summation and profile-fitted intensities. I think *these* are the
measurements, not the intensity derived during the scaling procedure. Sure,
anyone who wants to be even more pedantic than me will point out that these
"raw measurements" are also the result of fitting procedures. However, to
my eyes, the difference is that we don't consider the profile and summation
integrated intensities to change as a result of the procedure that
ultimately determines the statistic (MPR) of interest. During that
procedure they are independent, not dependent variables.

Maybe I am worrying about nothing. It agree it is *fairly clear* what you
mean by MPR. I just wanted to explore if there was any opportunity for
further reducing ambiguity.

Cheers
-- David


On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear Ian,
>
>
>
> Since some very advanced countries still use miles, Fahrenheit and inches,
> I did not expect anything to change. It was an escalating discussion in
> this thread on data completeness(!) on the use of multiplicity vs
> redundancy that made me suggest a different term. Except for an occasional
> discussion in the BB, there is nothing against people using the term they
> are most comfortable with.
>
>
>
> However, I insist that trying to impose a different definition of
> “measurement” for MPR vs the definition used for the calculation of
> redundancy/multiplicity is not a valid argument against MPR.
>
>
>
> Cheers,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Ian
> Tickle
> *Gesendet:* Donnerstag, 2. Juli 2020 22:06
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to
> get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
>
>
> Well I very much doubt that many software developers are going to trawl
> through all their code, comments, output statements & documentation to
> change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
> agreed on (assuming of course we do manage to come to an agreement, which I
> doubt).  And good luck with persuading wwPDB to change 'redundancy' in
> their mmCIF dictionary!  That would be not only pointless but also a lot of
> work, partly because terms get abbreviated in code and in outputs (e.g. to
> 'redund' in mine, or 'mult').  And don't say I can keep the code & comments
> the same and only change the outputs and documentation: that will really
> tax my brain!  Also don't say this need only apply to new code: no code is
> ever completely new, and mixing up old & new terminology would be a
> disaster waiting to happen!  Also it won't end there: someone will always
> find terminology that they disagree with: I can think of plenty cans of
> worms that we could open, but I think one is already one too many!
>
>
>
> By the way, "measurements per reflection" won't float, because some
> measurements will be rejected as outliers (that's why we need redundancy! -
> as opposed to simply measuring intensities for longer).  What I call
> redundancy is "the count of _contributing_ measurements per reflection"
> (CCMPR, sigh).  Personally I think that adding one more term is going to
> confuse things even more since if I'm right most people will continue to
> use the old terms in parallel anyway.
>
>
>
> IMO we should all be free to use the terminology we are most comfortable
> with, and it's up to the receivers of the information to perform the
> translation.  That's how it always has been, and IMO always will be.  Of
> course it behoves (behooves?) the sender to point to or make available any
> necessary translation tools, such as a dictionary or glossary, but once
> that is done it is the responsibility of the receiver to make use of those
> tools.  Even better if you can point to formally-published information
> (i.e. book or peer-reviewed paper), since information on the web is so
> ephemeral.  As a receiver of information myself that's what my brain is
> doing constantly, i.e. converting others' terminology into concepts my
> brain can process.  If I'm forced to write code using a different set of
> terms it's inevitable that I will unconsciously lapse into my old bad ways
> and I'll end up with a dog's breakfast!  If I'm constantly having to
> convert my terminology into some standardised (standardized?) terminology
> before committing it to code, I'm going to use up what little brainpower I
> have left!
>
>
>
> The absolutely critical thing surely is to DEFINE all terms that might be
> unfamiliar or ambiguous (yes Bernhard, I abhor a definitional vacuum for
> this very reason!).  That way the developers feel 

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

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

Hi James,

At your offline suggestion I tried this myself and observe the same fit 
inducing flashing - however when I shared the desktop (which had a full-screen 
NX session running) it worked fine

The performance seems good enough to be able to follow along with data 
collection at the very least

Best wishes Graeme

> On 3 Jul 2020, at 09:44, Sandy, James (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> Hi all,
> 
> I have had problems trying to share my screen using Teams when using the NX 
> client. I have experienced the screen flashing in a manner which may induce 
> fits! This may be related to sharing a window rather than the whole desktop 
> but something to be aware of. I have taken to using Zoom if I want to work 
> with others sharing an NX session.
> 
> Cheers,
> 
> James
> 
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Winter, Graeme 
> (DLSLtd,RAL,LSCI)
> Sent: 03 July 2020 09:33
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Relaying a remote data collection on using moodle 
> collaborate or Microsoft Teams
> 
> Hi Nick
> 
> I’ll offer a vote in favour of teams, as it is possible with the desktop 
> application to hand over control as well for a shared window (e.g. NX) so 
> your student could perform the collection themselves under your supervision 
> rather than just watching.
> 
> I’ve not tried teams + NX as a combination but I can see no reason why this 
> would not work, it’s not like the network load will be much different to 
> watching a room full of happy faces… you could also try this out in advance, 
> connecting to nx.diamond for e.g. processing and confirming that the screen 
> share works so you lose no time on data collection day. 
> 
> FWIW I prefer zoom for meetings as it’s got better sound & copes better with 
> large groups (IMHO) however for small groups / 1:1 teams has worked quite 
> well in my experience, and I was particularly impressed with the screen 
> sharing. 
> 
> Best wishes Graeme
> 
> 
> 
>> On 3 Jul 2020, at 09:18, Nicholas Keep  wrote:
>> 
>> We are going to be doing a data collection for an MRes student at Diamond in 
>> the next couple of weeks.  These are his first crystals.  It would be good 
>> if he could be involved in watching it.
>> 
>> I was wondering if anyone had tried sharing screen and voice via moodle 
>> collaborate or Microsoft Teams while doing a data collection?  Zoom is 
>> deprecated by our institution but if anyone had succeeded on zoom that would 
>> also be interesting.
>> 
>> I am on Virgin media 100 MB broadband which is pretty much achieving that 
>> (upload is only around 9 MB though).
>> 
>> Alternatively we can try and set him up to connect via nx and watch, but 
>> that would lose the sound connection unless I have a phone tucked under my 
>> chin.
>> 
>> We could just record my screen and sound and he could watch later.
>> 
>> Any tips?
>> 
>> Best wishes
>> 
>> Nick
>> 
>> 
>> 
>> --
>> Prof Nicholas H. Keep
>> Executive Dean of School of Science
>> Professor of Biomolecular Science
>> Crystallography, Institute for Structural and Molecular Biology, 
>> Department of Biological Sciences Birkbeck,  University of London, 
>> Malet Street, Bloomsbury LONDON WC1E 7HX
>> 
>> Dean Email;  scid...@bbk.ac.uk
>> Dept email n.k...@mail.cryst.bbk.ac.uk
>> Telephone 020-7631-6852  (Room G54a Office)
>> 020-7631-6800  (Department Office)
>> Fax   020-7631-6803
>> If you want to access me in person you have to come to the 
>> crystallography entrance and ring me or the department office from the 
>> internal phone by the door
>> 
>> ##
>> ##
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
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> Wales with its registered office at Diamond House, Harwell Science and 
> Innovation Campus, 

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

[David Waterman]

I should say I also saw flashing during screen share in a Zoom call. This
might also be because only a single window was shared, and this window
overlaid another on the speaker's desktop. I saw flickering glimpses of the
Word document underneath the window the speaker was trying to share.

-- David


On Fri, 3 Jul 2020 at 09:56, Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi James,
>
> At your offline suggestion I tried this myself and observe the same fit
> inducing flashing - however when I shared the desktop (which had a
> full-screen NX session running) it worked fine
>
> The performance seems good enough to be able to follow along with data
> collection at the very least
>
> Best wishes Graeme
>
> > On 3 Jul 2020, at 09:44, Sandy, James (DLSLtd,RAL,LSCI) <
> james.sa...@diamond.ac.uk> wrote:
> >
> > Hi all,
> >
> > I have had problems trying to share my screen using Teams when using the
> NX client. I have experienced the screen flashing in a manner which may
> induce fits! This may be related to sharing a window rather than the whole
> desktop but something to be aware of. I have taken to using Zoom if I want
> to work with others sharing an NX session.
> >
> > Cheers,
> >
> > James
> >
> >
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Winter,
> Graeme (DLSLtd,RAL,LSCI)
> > Sent: 03 July 2020 09:33
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Relaying a remote data collection on using moodle
> collaborate or Microsoft Teams
> >
> > Hi Nick
> >
> > I’ll offer a vote in favour of teams, as it is possible with the desktop
> application to hand over control as well for a shared window (e.g. NX) so
> your student could perform the collection themselves under your supervision
> rather than just watching.
> >
> > I’ve not tried teams + NX as a combination but I can see no reason why
> this would not work, it’s not like the network load will be much different
> to watching a room full of happy faces… you could also try this out in
> advance, connecting to nx.diamond for e.g. processing and confirming that
> the screen share works so you lose no time on data collection day.
> >
> > FWIW I prefer zoom for meetings as it’s got better sound & copes better
> with large groups (IMHO) however for small groups / 1:1 teams has worked
> quite well in my experience, and I was particularly impressed with the
> screen sharing.
> >
> > Best wishes Graeme
> >
> >
> >
> >> On 3 Jul 2020, at 09:18, Nicholas Keep 
> wrote:
> >>
> >> We are going to be doing a data collection for an MRes student at
> Diamond in the next couple of weeks.  These are his first crystals.  It
> would be good if he could be involved in watching it.
> >>
> >> I was wondering if anyone had tried sharing screen and voice via moodle
> collaborate or Microsoft Teams while doing a data collection?  Zoom is
> deprecated by our institution but if anyone had succeeded on zoom that
> would also be interesting.
> >>
> >> I am on Virgin media 100 MB broadband which is pretty much achieving
> that (upload is only around 9 MB though).
> >>
> >> Alternatively we can try and set him up to connect via nx and watch,
> but that would lose the sound connection unless I have a phone tucked under
> my chin.
> >>
> >> We could just record my screen and sound and he could watch later.
> >>
> >> Any tips?
> >>
> >> Best wishes
> >>
> >> Nick
> >>
> >>
> >>
> >> --
> >> Prof Nicholas H. Keep
> >> Executive Dean of School of Science
> >> Professor of Biomolecular Science
> >> Crystallography, Institute for Structural and Molecular Biology,
> >> Department of Biological Sciences Birkbeck,  University of London,
> >> Malet Street, Bloomsbury LONDON WC1E 7HX
> >>
> >> Dean Email;  scid...@bbk.ac.uk
> >> Dept email n.k...@mail.cryst.bbk.ac.uk
> >> Telephone 020-7631-6852  (Room G54a Office)
> >> 020-7631-6800  (Department Office)
> >> Fax   020-7631-6803
> >> If you want to access me in person you have to come to the
> >> crystallography entrance and ring me or the department office from the
> >> internal phone by the door
> >>
> >> ##
> >> ##
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright and
> or privileged material, and are for the use of the intended addressee only.
> If you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> > Any opinions expressed within 

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

[Schreuder, Herman /DE]

Dear David,

Thank you for your reaction. It has become clear to me that although most 
people understand what I intended with “measurement”, in practice it is very 
much in the eye of the beholder. It was suggested in the BB to use observation 
instead, but I am fairly sure that some people will also have issues with that.

The advantage of multiplicity/redundancy is that it does not mention what is 
multiple or redundant and that one can refer to the program documentation for 
an exact definition. Since most people are happy with the 
multiplicity/redundancy they grew up with, that is the way it will stay.

Best regards,
Herman




Von: David Waterman 
Gesendet: Freitag, 3. Juli 2020 10:49
An: Schreuder, Herman /DE 
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames 
to get a full dataset?


EXTERNAL : Real sender is dgwater...@gmail.com

Hi Herman,

I like the idea of MPR, but I continue to worry about the term "measurement". 
The intensity associated with a particular reflection is a fit based on a 
scaling model, and ultimately, depending on your integration software, may be 
linked to a weighted sum of two raw measurements: the summation and 
profile-fitted intensities. I think these are the measurements, not the 
intensity derived during the scaling procedure. Sure, anyone who wants to be 
even more pedantic than me will point out that these "raw measurements" are 
also the result of fitting procedures. However, to my eyes, the difference is 
that we don't consider the profile and summation integrated intensities to 
change as a result of the procedure that ultimately determines the statistic 
(MPR) of interest. During that procedure they are independent, not dependent 
variables.

Maybe I am worrying about nothing. It agree it is fairly clear what you mean by 
MPR. I just wanted to explore if there was any opportunity for further reducing 
ambiguity.

Cheers
-- David


On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Ian,

Since some very advanced countries still use miles, Fahrenheit and inches, I 
did not expect anything to change. It was an escalating discussion in this 
thread on data completeness(!) on the use of multiplicity vs redundancy that 
made me suggest a different term. Except for an occasional discussion in the 
BB, there is nothing against people using the term they are most comfortable 
with.

However, I insist that trying to impose a different definition of “measurement” 
for MPR vs the definition used for the calculation of redundancy/multiplicity 
is not a valid argument against MPR.

Cheers,
Herman




Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Ian Tickle
Gesendet: Donnerstag, 2. Juli 2020 22:06
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a 
full dataset?


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


Well I very much doubt that many software developers are going to trawl through 
all their code, comments, output statements & documentation to change 
'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is agreed on 
(assuming of course we do manage to come to an agreement, which I doubt).  And 
good luck with persuading wwPDB to change 'redundancy' in their mmCIF 
dictionary!  That would be not only pointless but also a lot of work, partly 
because terms get abbreviated in code and in outputs (e.g. to 'redund' in mine, 
or 'mult').  And don't say I can keep the code & comments the same and only 
change the outputs and documentation: that will really tax my brain!  Also 
don't say this need only apply to new code: no code is ever completely new, and 
mixing up old & new terminology would be a disaster waiting to happen!  Also it 
won't end there: someone will always find terminology that they disagree with: 
I can think of plenty cans of worms that we could open, but I think one is 
already one too many!

By the way, "measurements per reflection" won't float, because some 
measurements will be rejected as outliers (that's why we need redundancy! - as 
opposed to simply measuring intensities for longer).  What I call redundancy is 
"the count of _contributing_ measurements per reflection" (CCMPR, sigh).  
Personally I think that adding one more term is going to confuse things even 
more since if I'm right most people will continue to use the old terms in 
parallel anyway.

IMO we should all be free to use the terminology we are most comfortable with, 
and it's up to the receivers of the information to perform the translation.  
That's how it always has been, and IMO always will be.  Of course it behoves 
(behooves?) the sender to point to or make available any necessary translation 
tools, such as a dictionary or glossary, but once that is done it is the 
responsibility of 

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

[David Waterman]

Hi Herman,

I started googling and ended up completely lost down a rabbit hole (have a
look here if you want to see what I mean:
https://plato.stanford.edu/entries/measurement-science/). As a result I'm
no longer sure I know what the word "measurement" means! I tried to
simplify things with a practical example. Let's say I take a set of clearly
real world measurements (temperature values over time, say). I can take the
mean of subsets of these values and maybe that is a "measurement" too -
especially for readings taken in quick succession, expressly done to reduce
measurement error. But what if I fit a line to a series of values, is the
gradient of the line also a "measurement"? Maybe?

Anyway, for MPR it probably doesn't matter if the measurement is of a
response variable, rather than something "raw". That's because MPR isn't
actually affected by the values themselves (ignoring the thorny issue of
outlier rejection), it is just a count of them.

Cheers
-- David


On Fri, 3 Jul 2020 at 11:22, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> Dear David,
>
>
>
> Thank you for your reaction. It has become clear to me that although most
> people understand what I intended with “measurement”, in practice it is
> very much in the eye of the beholder. It was suggested in the BB to use
> observation instead, but I am fairly sure that some people will also have
> issues with that.
>
>
>
> The advantage of multiplicity/redundancy is that it does not mention what
> is multiple or redundant and that one can refer to the program
> documentation for an exact definition. Since most people are happy with the
> multiplicity/redundancy they grew up with, that is the way it will stay.
>
>
>
> Best regards,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* David Waterman 
> *Gesendet:* Freitag, 3. Juli 2020 10:49
> *An:* Schreuder, Herman /DE 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Betreff:* Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number
> of frames to get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is dgwater...@gmail.com
>
>
>
> Hi Herman,
>
>
>
> I like the idea of MPR, but I continue to worry about the term
> "measurement". The intensity associated with a particular reflection is a
> fit based on a scaling model, and ultimately, depending on your integration
> software, may be linked to a weighted sum of two raw measurements: the
> summation and profile-fitted intensities. I think *these* are the
> measurements, not the intensity derived during the scaling procedure. Sure,
> anyone who wants to be even more pedantic than me will point out that these
> "raw measurements" are also the result of fitting procedures. However, to
> my eyes, the difference is that we don't consider the profile and summation
> integrated intensities to change as a result of the procedure that
> ultimately determines the statistic (MPR) of interest. During that
> procedure they are independent, not dependent variables.
>
>
>
> Maybe I am worrying about nothing. It agree it is *fairly clear* what you
> mean by MPR. I just wanted to explore if there was any opportunity for
> further reducing ambiguity.
>
>
>
> Cheers
>
> -- David
>
>
>
>
>
> On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
>
> Dear Ian,
>
>
>
> Since some very advanced countries still use miles, Fahrenheit and inches,
> I did not expect anything to change. It was an escalating discussion in
> this thread on data completeness(!) on the use of multiplicity vs
> redundancy that made me suggest a different term. Except for an occasional
> discussion in the BB, there is nothing against people using the term they
> are most comfortable with.
>
>
>
> However, I insist that trying to impose a different definition of
> “measurement” for MPR vs the definition used for the calculation of
> redundancy/multiplicity is not a valid argument against MPR.
>
>
>
> Cheers,
>
> Herman
>
>
>
>
>
>
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Ian
> Tickle
> *Gesendet:* Donnerstag, 2. Juli 2020 22:06
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to
> get a full dataset?
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
>
>
> Well I very much doubt that many software developers are going to trawl
> through all their code, comments, output statements & documentation to
> change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is
> agreed on (assuming of course we do manage to come to an agreement, which I
> doubt).  And good luck with persuading wwPDB to change 'redundancy' in
> their mmCIF dictionary!  That would be not only pointless but also a lot of
> work, partly because terms get abbreviated in code and in outputs (e.g. to
> 'redund' in mine, or 'mult').  And don't say I can keep the code & comments
> the same and only change the outputs and documentation: that will really
> tax my brain!  Also don't say this need only apply to new code: no code is

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

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

Hi Nick

I’ll offer a vote in favour of teams, as it is possible with the desktop 
application to hand over control as well for a shared window (e.g. NX) so your 
student could perform the collection themselves under your supervision rather 
than just watching.

I’ve not tried teams + NX as a combination but I can see no reason why this 
would not work, it’s not like the network load will be much different to 
watching a room full of happy faces… you could also try this out in advance, 
connecting to nx.diamond for e.g. processing and confirming that the screen 
share works so you lose no time on data collection day. 

FWIW I prefer zoom for meetings as it’s got better sound & copes better with 
large groups (IMHO) however for small groups / 1:1 teams has worked quite well 
in my experience, and I was particularly impressed with the screen sharing. 

Best wishes Graeme



> On 3 Jul 2020, at 09:18, Nicholas Keep  wrote:
> 
> We are going to be doing a data collection for an MRes student at Diamond in 
> the next couple of weeks.  These are his first crystals.  It would be good if 
> he could be involved in watching it.
> 
> I was wondering if anyone had tried sharing screen and voice via moodle 
> collaborate or Microsoft Teams while doing a data collection?  Zoom is 
> deprecated by our institution but if anyone had succeeded on zoom that would 
> also be interesting.
> 
> I am on Virgin media 100 MB broadband which is pretty much achieving that 
> (upload is only around 9 MB though).
> 
> Alternatively we can try and set him up to connect via nx and watch, but that 
> would lose the sound connection unless I have a phone tucked under my chin.
> 
> We could just record my screen and sound and he could watch later.
> 
> Any tips?
> 
> Best wishes
> 
> Nick
> 
> 
> 
> -- 
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck,  University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
> 
> Dean Email;   scid...@bbk.ac.uk
> Dept email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-7631-6852  (Room G54a Office)
>  020-7631-6800  (Department Office)
> Fax   020-7631-6803
> If you want to access me in person you have to come to the crystallography 
> entrance
> and ring me or the department office from the internal phone by the door
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] flow rate for cooling stream?

[Elspeth Garman]

Yes, if you don’t match the inner and outer stream rates you get turbulent flow 
at the boundary between them and ice build up on the sample.
Best wishes
Elspeth

From: CCP4 bulletin board  On Behalf Of Marcus Winter
Sent: 03 July 2020 09:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] flow rate for cooling stream?




Dear Patrick, Herman,



Regarding the Cryostream, then referring to the Cryostream 800 brochure 
indicates that the N2 (gas) flow rates employed are in the range of 5 - 10 
litres / minute, … and, I guess, therefore something similar for the outer dry 
air 'shield' stream.   Obviously, it’s best to check directly with the 
manufacturers (Oxford Cryosystems) directly on the details.



All The Best,



Marcus Winter

(Rigaku)





 -Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Schreuder, Herman /DE
Sent: Friday, July 03, 2020 7:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [EXTERNAL] [ccp4bb] flow rate for cooling stream?



Dear Patrick,

if I recall correctly, our systems run at 10-15 ml/min (gas). I will check on 
Monday when I am back in the lab.

The original cryostreams would run for several day's on a tank of liquid 
nitrogen. However, they had significant hardware to dry the nitrogen and to 
ensure a constant flow.



Best, Herman



-Ursprüngliche Nachricht-

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Patrick Loll

Gesendet: Donnerstag, 2. Juli 2020 22:03

An: CCP4BB@JISCMAIL.AC.UK

Betreff: [EXTERNAL] [ccp4bb] flow rate for cooling stream?



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







Sorry, way off topic:



Does anyone have an estimate for the flow rate one would typically use for the 
cold nitrogen stream passing over a protein crystal in a standard data 
collection?



Background: Our nitrogen “generator” has gone belly-up and the vendor no longer 
services it, so I’m testing the feasibility of using the boil-off from a liquid 
nitrogen tank to provide the gas to support a short data collection (this 
nitrogen gas would serve as the feedstock into our helium cryostat). But I 
don’t know the flow rate required, so I can’t calculate if one tank has enough 
nitrogen to support a day or so of data collection. There are flow meters for 
the warm and cold stream on the nitrogen generator, but these flow meters have 
no apparent units anywhere on them, so I have no idea of the rate at which the 
gas would be consumed.



Thanks for any useful tidbits.



And for those of you in the US, best wishes for a happy “Holy crap, even MORE 
fireworks?!?!!” Day



Pat





---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology Drexel University College of 
Medicine Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA  19102  USA



(215) 762-7706

pjl...@gmail.com

pj...@drexel.edu





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To 

Re: [ccp4bb] flow rate for cooling stream?

[James Holton]

To add: I think what Dr. Garman means by "match" is not necessarily to 
set the two flow rates to the same value.  The optimal settings will 
depend on the size, shape, and even orientation of your nozzle.  You 
need to fiddle with the outer stream flow rate to find the one that 
minimizes the turbulence.


Mounting up a large, long-necked nylon loop with a big drop of liquid in 
it makes an excellent vibrometer.  You can often see the loop vibration 
under the video microscope if your frame rate is high enough.  And, of 
course, the most systematic, sensitive and relevant assay is to put a 
crystal in it and collect some data:

https://doi.org/10.1107/S0021889808032536

-James Holton
MAD Scientist

On 7/3/2020 3:09 AM, Elspeth Garman wrote:


Yes, if you don’t match the inner and outer stream rates you get 
turbulent flow at the boundary between them and ice build up on the 
sample.


Best wishes

Elspeth

*From:*CCP4 bulletin board  *On Behalf Of 
*Marcus Winter

*Sent:* 03 July 2020 09:29
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] flow rate for cooling stream?

Dear Patrick, Herman,

Regarding the Cryostream, then referring to the Cryostream 800 
brochure indicates that the N2 (gas) flow rates employed are in the 
range of 5 - 10 */litres/* / minute, … and, I guess, therefore 
something similar for the outer dry air 'shield' stream.   Obviously, 
it’s best to check directly with the manufacturers (Oxford 
Cryosystems) directly on the details.


All The Best,

Marcus Winter

(Rigaku)

 -Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Schreuder, Herman /DE

Sent: Friday, July 03, 2020 7:44 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] AW: [EXTERNAL] [ccp4bb] flow rate for cooling stream?

Dear Patrick,

if I recall correctly, our systems run at 10-15 ml/min (gas). I will 
check on Monday when I am back in the lab.


The original cryostreams would run for several day's on a tank of 
liquid nitrogen. However, they had significant hardware to dry the 
nitrogen and to ensure a constant flow.


Best, Herman

-Ursprüngliche Nachricht-

Von: CCP4 bulletin board > Im Auftrag von Patrick Loll


Gesendet: Donnerstag, 2. Juli 2020 22:03

An: CCP4BB@JISCMAIL.AC.UK 

Betreff: [EXTERNAL] [ccp4bb] flow rate for cooling stream?

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



Sorry, way off topic:

Does anyone have an estimate for the flow rate one would typically use 
for the cold nitrogen stream passing over a protein crystal in a 
standard data collection?


Background: Our nitrogen “generator” has gone belly-up and the vendor 
no longer services it, so I’m testing the feasibility of using the 
boil-off from a liquid nitrogen tank to provide the gas to support a 
short data collection (this nitrogen gas would serve as the feedstock 
into our helium cryostat). But I don’t know the flow rate required, so 
I can’t calculate if one tank has enough nitrogen to support a day or 
so of data collection. There are flow meters for the warm and cold 
stream on the nitrogen generator, but these flow meters have no 
apparent units anywhere on them, so I have no idea of the rate at 
which the gas would be consumed.


Thanks for any useful tidbits.

And for those of you in the US, best wishes for a happy “Holy crap, 
even MORE fireworks?!?!!” Day


Pat

---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology Drexel University 
College of Medicine Room 10-102 New College Building


245 N. 15th St., Mailstop 497

Philadelphia, PA 19102  USA

(215) 762-7706

pjl...@gmail.com 

pj...@drexel.edu 



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

[Gerard Bricogne]

Dear Herman and David,

 This thread seems inexhaustible :-) .

 On the matter of "measurement" vs. "observation", we seem again to be
in a situation described by the British idiom "half of one and half-a-dozen"
of the other, i.e. distinct but synonymous terms between which a choice is
quite indifferent.

 In the work on STARANISO and the documentation of that work, a
distinction had to be made between the two terms, for which readers are
referred to Ian's carefully crafted material at 

http://staraniso.globalphasing.org/anisotropy_about.html

and 

http://staraniso.globalphasing.org/staraniso_glossary.html

Here, a measurement is a number plucked out of examining the raw data,
namely an integrated intensity obtained by considering the pixel values
around the position in 3D reciprocal space predicted from an indexing
solution. The next step is to determine whether this qualifies as an
observation, in the sense of containing information that a structural model
would be expected to comply with. This determination is carried out by
computing a local average of I/sig(I) through reciprocal space and applying
a cut-off criterion based on a threshold value for that local average. Other
criteria can be considered, and are indeed offered by the program as
alternatives. Measurements complying with this selection criterion are then
called "observations". In this picture, an observation is defined as a
significant measurement. This basic distinction of vocabulary is then
extended to talking about "unmeasured" reflections (for which there weren't
any detector pixels to catch any photons at their predicted position - e.g.
in gaps between detector modules) and "unobserved" reflections (that are
unmeasured but for which the analysis of the I/sig(I) distribution predicts
that they would have been significant, had they been measured - e.g. in
cusps or missing angular ranges, as well as in module gaps etc.). The
display of the latter as blue dots in the STARANISO Reciprocal Lattice
Viewer then gives a vivid picture of the inadequacies of the experimental
protocol used, in failing to catch all the significant diffraction from the
sample.

 This being said, things could very well had been done the other way,
saying that the blindly integrated intensity was an observation, and that
the subsequent analysis was intended to determine whether you had really
measured something significant (i.e. a useful integrated intensity) by
making that observation. We were aware of this ambivalence, but felt that we
had to comply with the boundary condition that what we ended up with, after
conversion to an amplitude, had to be denoted "Fobs" ;-) . If the early
crystallographers had used the notation "Fmeas" for what they considered as
their experimental data, the choice of terminology would definitely have
gone the other way.

 As Graeme said, use the terminology you want, but document exactly what
you mean by it. The two URLs quoted above (especially the second) show that
this suggestion was conscientiously followed by the STARANISO developers.


 With best wishes,

  Gerard,

--
On Fri, Jul 03, 2020 at 10:22:43AM +, Schreuder, Herman /DE wrote:
> Dear David,
> 
> Thank you for your reaction. It has become clear to me that although most 
> people understand what I intended with “measurement”, in practice it is very 
> much in the eye of the beholder. It was suggested in the BB to use 
> observation instead, but I am fairly sure that some people will also have 
> issues with that.
> 
> The advantage of multiplicity/redundancy is that it does not mention what is 
> multiple or redundant and that one can refer to the program documentation for 
> an exact definition. Since most people are happy with the 
> multiplicity/redundancy they grew up with, that is the way it will stay.
> 
> Best regards,
> Herman
> 
> 
> 
> 
> Von: David Waterman 
> Gesendet: Freitag, 3. Juli 2020 10:49
> An: Schreuder, Herman /DE 
> Cc: CCP4BB@jiscmail.ac.uk
> Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of 
> frames to get a full dataset?
> 
> 
> EXTERNAL : Real sender is dgwater...@gmail.com
> 
> Hi Herman,
> 
> I like the idea of MPR, but I continue to worry about the term "measurement". 
> The intensity associated with a particular reflection is a fit based on a 
> scaling model, and ultimately, depending on your integration software, may be 
> linked to a weighted sum of two raw measurements: the summation and 
> profile-fitted intensities. I think these are the measurements, not the 
> intensity derived during the scaling procedure. Sure, anyone who wants to be 
> even more pedantic than me will point out that these "raw measurements" are 
> also the result of fitting procedures. However, to my eyes, the difference is 
> that we don't consider the profile and summation integrated intensities to 
> change as a result of the procedure that ultimately determines 

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

[John R Helliwell]

Dear Colleagues,
Now that Herman has announced a quietude I thought you might enjoy this quite 
short report on a synchrotron radiation issue that came up some years back via 
the JSR Main Editors into the IUCr Nomenclature Committee, chaired by Andre 
Authier, Past President of the IUCr:-
https://journals.iucr.org/s/issues/2005/03/00/es0344/es0344.pdf
Have a great weekend,
John 
Emeritus Professor John R Helliwell DSc




> On 3 Jul 2020, at 11:22, Schreuder, Herman /DE  
> wrote:
> 
> 
> Dear David,
>  
> Thank you for your reaction. It has become clear to me that although most 
> people understand what I intended with “measurement”, in practice it is very 
> much in the eye of the beholder. It was suggested in the BB to use 
> observation instead, but I am fairly sure that some people will also have 
> issues with that.
>  
> The advantage of multiplicity/redundancy is that it does not mention what is 
> multiple or redundant and that one can refer to the program documentation for 
> an exact definition. Since most people are happy with the 
> multiplicity/redundancy they grew up with, that is the way it will stay.
>  
> Best regards,
> Herman
>  
>  
>  
>  
> Von: David Waterman  
> Gesendet: Freitag, 3. Juli 2020 10:49
> An: Schreuder, Herman /DE 
> Cc: CCP4BB@jiscmail.ac.uk
> Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of 
> frames to get a full dataset?
>  
> EXTERNAL : Real sender is dgwater...@gmail.com
> 
>  
> 
> Hi Herman,
>  
> I like the idea of MPR, but I continue to worry about the term "measurement". 
> The intensity associated with a particular reflection is a fit based on a 
> scaling model, and ultimately, depending on your integration software, may be 
> linked to a weighted sum of two raw measurements: the summation and 
> profile-fitted intensities. I think these are the measurements, not the 
> intensity derived during the scaling procedure. Sure, anyone who wants to be 
> even more pedantic than me will point out that these "raw measurements" are 
> also the result of fitting procedures. However, to my eyes, the difference is 
> that we don't consider the profile and summation integrated intensities to 
> change as a result of the procedure that ultimately determines the statistic 
> (MPR) of interest. During that procedure they are independent, not dependent 
> variables.
>  
> Maybe I am worrying about nothing. It agree it is fairly clear what you mean 
> by MPR. I just wanted to explore if there was any opportunity for further 
> reducing ambiguity.
>  
> Cheers
> -- David
>  
>  
> On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE 
>  wrote:
> Dear Ian,
>  
> Since some very advanced countries still use miles, Fahrenheit and inches, I 
> did not expect anything to change. It was an escalating discussion in this 
> thread on data completeness(!) on the use of multiplicity vs redundancy that 
> made me suggest a different term. Except for an occasional discussion in the 
> BB, there is nothing against people using the term they are most comfortable 
> with.
>  
> However, I insist that trying to impose a different definition of 
> “measurement” for MPR vs the definition used for the calculation of 
> redundancy/multiplicity is not a valid argument against MPR.
>  
> Cheers,
> Herman
>  
>  
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von Ian Tickle
> Gesendet: Donnerstag, 2. Juli 2020 22:06
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a 
> full dataset?
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> 
>  
> 
>  
> Well I very much doubt that many software developers are going to trawl 
> through all their code, comments, output statements & documentation to change 
> 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is agreed on 
> (assuming of course we do manage to come to an agreement, which I doubt).  
> And good luck with persuading wwPDB to change 'redundancy' in their mmCIF 
> dictionary!  That would be not only pointless but also a lot of work, partly 
> because terms get abbreviated in code and in outputs (e.g. to 'redund' in 
> mine, or 'mult').  And don't say I can keep the code & comments the same and 
> only change the outputs and documentation: that will really tax my brain!  
> Also don't say this need only apply to new code: no code is ever completely 
> new, and mixing up old & new terminology would be a disaster waiting to 
> happen!  Also it won't end there: someone will always find terminology that 
> they disagree with: I can think of plenty cans of worms that we could open, 
> but I think one is already one too many!
>  
> By the way, "measurements per reflection" won't float, because some 
> measurements will be rejected as outliers (that's why we need redundancy! - 
> as opposed to simply measuring intensities for longer).  What I call 
> redundancy is "the count of _contributing_ measurements per reflection" 
> (CCMPR, sigh).  Personally 

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

[Schreuder, Herman /DE]

Hi David,

you are right, the M in MPR is just a count of “whatever” is averaged to get 
the final intensities.
However, from this “inexhaustible thread” it is also clear that there will be 
no agreement on what to call this “whatever” 

Best, Herman

Von: David Waterman 
Gesendet: Freitag, 3. Juli 2020 13:11
An: Schreuder, Herman /DE 
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames 
to get a full dataset?


EXTERNAL : Real sender is dgwater...@gmail.com

Hi Herman,

I started googling and ended up completely lost down a rabbit hole (have a look 
here if you want to see what I mean: 
https://plato.stanford.edu/entries/measurement-science/).
 As a result I'm no longer sure I know what the word "measurement" means! I 
tried to simplify things with a practical example. Let's say I take a set of 
clearly real world measurements (temperature values over time, say). I can take 
the mean of subsets of these values and maybe that is a "measurement" too - 
especially for readings taken in quick succession, expressly done to reduce 
measurement error. But what if I fit a line to a series of values, is the 
gradient of the line also a "measurement"? Maybe?

Anyway, for MPR it probably doesn't matter if the measurement is of a response 
variable, rather than something "raw". That's because MPR isn't actually 
affected by the values themselves (ignoring the thorny issue of outlier 
rejection), it is just a count of them.

Cheers
-- David


On Fri, 3 Jul 2020 at 11:22, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear David,

Thank you for your reaction. It has become clear to me that although most 
people understand what I intended with “measurement”, in practice it is very 
much in the eye of the beholder. It was suggested in the BB to use observation 
instead, but I am fairly sure that some people will also have issues with that.

The advantage of multiplicity/redundancy is that it does not mention what is 
multiple or redundant and that one can refer to the program documentation for 
an exact definition. Since most people are happy with the 
multiplicity/redundancy they grew up with, that is the way it will stay.

Best regards,
Herman




Von: David Waterman mailto:dgwater...@gmail.com>>
Gesendet: Freitag, 3. Juli 2020 10:49
An: Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>>
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames 
to get a full dataset?


EXTERNAL : Real sender is dgwater...@gmail.com

Hi Herman,

I like the idea of MPR, but I continue to worry about the term "measurement". 
The intensity associated with a particular reflection is a fit based on a 
scaling model, and ultimately, depending on your integration software, may be 
linked to a weighted sum of two raw measurements: the summation and 
profile-fitted intensities. I think these are the measurements, not the 
intensity derived during the scaling procedure. Sure, anyone who wants to be 
even more pedantic than me will point out that these "raw measurements" are 
also the result of fitting procedures. However, to my eyes, the difference is 
that we don't consider the profile and summation integrated intensities to 
change as a result of the procedure that ultimately determines the statistic 
(MPR) of interest. During that procedure they are independent, not dependent 
variables.

Maybe I am worrying about nothing. It agree it is fairly clear what you mean by 
MPR. I just wanted to explore if there was any opportunity for further reducing 
ambiguity.

Cheers
-- David


On Fri, 3 Jul 2020 at 08:12, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Ian,

Since some very advanced countries still use miles, Fahrenheit and inches, I 
did not expect anything to change. It was an escalating discussion in this 
thread on data completeness(!) on the use of multiplicity vs redundancy that 
made me suggest a different term. Except for an occasional discussion in the 
BB, there is nothing against people using the term they are most comfortable 
with.

However, I insist that trying to impose a different definition of “measurement” 
for MPR vs the definition used for the calculation of redundancy/multiplicity 
is not a valid argument against MPR.

Cheers,
Herman




Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Ian Tickle
Gesendet: Donnerstag, 2. Juli 2020 22:06
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a 
full 

Re: [ccp4bb] Relaying a remote data collection on using moodle collaborate or Microsoft Teams

[David Schuller]

We routinely use NoMachine NX or X2Go to share the desktop for remote 
data collection. And recently I have personally collected data using 
such while simultaneously running a Zoom window for communication. 
Internet speed to my home is about 100 Mbps download, 11 Mbps upload. A 
few notes:


If the remote desktop is full access rather than view-only, there is the 
fun game of fighting for control of the mouse. A voice channel is useful 
for establishing who gets the wheel.


If limited bandwidth and latency are issues, limit use of streaming 
video. Our video windows allow reduction of the frame rate for precisely 
that reason.


In Zoom, and I presume in equivalent applications, you can turn the 
video off and use it for sound sharing only. If the desktop is being 
shared via NX there is no need to share it again with a second app.


The data collection and the Zoom or equivalent do not necessarily need 
to be running on the same machine. Our data collection workstations tend 
not to have cameras and microphones.


I have no experience with Teams nor anything else that is geared to 
Microsoft/Windows.


Cheers,


On 2020-07-03 04:18, Nicholas Keep wrote:
We are going to be doing a data collection for an MRes student at 
Diamond in the next couple of weeks.  These are his first crystals.  
It would be good if he could be involved in watching it.


I was wondering if anyone had tried sharing screen and voice via 
moodle collaborate or Microsoft Teams while doing a data collection?  
Zoom is deprecated by our institution but if anyone had succeeded on 
zoom that would also be interesting.


I am on Virgin media 100 MB broadband which is pretty much achieving 
that (upload is only around 9 MB though).


Alternatively we can try and set him up to connect via nx and watch, 
but that would lose the sound connection unless I have a phone tucked 
under my chin.


We could just record my screen and sound and he could watch later.

Any tips?

Best wishes

Nick





--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu



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