Re: [ccp4bb] flow rate for cooling stream?

[Ian Clifton]

Hello Patrick,

On 02/07/2020 21:03, Patrick Loll wrote:

[...]


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?


[...]

A Cryostream 700 works at 5 litres per minute (gas), I believe. (10 in 
“turbo” mode.)


--
Ian.



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

[Ian Tickle]

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 (and see that there are
> shortcomings with both “multiplicity” and “redundancy") and I agree with
> much of what’s been said most recently in this thread.
>
> BTW, just because the Physics definition of a
> measurement/quantity/whatever is given on wikipedia (or elsewhere, for that
> matter), it doesn’t mean that’s what we (crystallographers, structural
> biologists, etc) should use without question. If you check
>
> https://en.wikipedia.org/wiki/Reflection_(physics)
>
> you will find no mention of diffraction maxima corresponding to
> reflections except a link to a page on diffraction. Or maybe we should
> slavishly follow the Physicists and use another term…
>
> H
>
> > On 2 Jul 2020, at 10:41, 

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

[Ian Tickle]

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 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 

[ccp4bb] flow rate for cooling stream?

[Patrick Loll]

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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[ccp4bb] Post-doctoral position in structural biology - Institut Curie - Paris

[Houdusse-Juille Anne]

Job opening for a structural biologist to join the Structural Motility team at 
the Curie Institute Paris, France.
We are looking for a post-doctoral fellow to join the Structural Motility team 
at the Curie Institute (Paris Center) directed by Anne Houdusse.
The Structural Motility team at the Institut Curie has gathered important 
structural insights on how force generated by molecular motors can power 
cellular processes in human health and disease. We develop chemical biology and 
cell biology approaches to test these insights and understand how molecular 
motors produce force, how their activity is regulated and how they are 
recruited to their cellular targets. One of our goals is to develop specific 
modulators of the force they can produce. Many of these motors are also 
involved in human pathologies and their modulation could lead to new therapies.
We are looking for an expert in biochemical, crystallogenesis and structural 
determination studies. The post-doctoral fellow will also gain expertise in 
functional and cellular studies.
Energy and a strong will to quickly gain autonomy in the lead of exciting 
scientific projects are essential.
Experience in cryo-electron microscopy or cell biology, is a plus. Experience 
in cloning, expression and purification of recombinant proteins, protein 
biophysics and/or biochemical assays are also welcome, and we are ready to 
train a dynamic and motivated candidate.
If you are interested, please send a CV and a letter of motivation as well as 
letters of recommendation of your previous employers.
Contact : Anne Houdusse (anne.houdu...@curie.fr)
https://science.institut-curie.org/research/multiscale-physics-biology-chemistry/umr144-subcellular-structure-and-cellular-dynamics/team-houdusse/
Key publications
Julien Robert-Paganin, Olena Pylypenko, Carlos Kikuti, H Lee Sweeney, Anne 
Houdusse (2019 Nov 6)
Force Generation by Myosin Motors: A Structural Perspective.
Chemical reviews : 5-35 : DOI : 
10.1021/acs.chemrev.9b00264

Julien Robert-Paganin, Daniel Auguin, Anne Houdusse (2018 Oct 3)
Hypertrophic cardiomyopathy disease results from disparate impairments of 
cardiac myosin function and auto-inhibition.
Nature communications : 4019 : DOI : 
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Florian Blanc, Tatiana Isabet, Hannah Benisty, H Lee Sweeney, Marco Cecchini, 
Anne Houdusse (2018 May 31)
An intermediate along the recovery stroke of myosin VI revealed by X-ray 
crystallography and molecular dynamics.
Proceedings of the National Academy of Sciences of the United States of America 
: 6213-6218 : DOI : 
10.1073/pnas.1711512115

Vicente J Planelles-Herrero, James J Hartman, Julien Robert-Paganin, Fady I 
Malik, Anne Houdusse (2017 Aug 5)
Mechanistic and structural basis for activation of cardiac myosin force 
production by omecamtiv mecarbil.
Nature communications : 190 : DOI : 
10.1038/s41467-017-00176-5

I-Mei Yu, Vicente J Planelles-Herrero, Yannick Sourigues, Dihia Moussaoui, 
Helena Sirkia, Carlos Kikuti, David Stroebel, Margaret A Titus, Anne Houdusse 
(2017 Jun 30)
Myosin 7 and its adaptors link cadherins to actin.
Nature communications : 15864 : DOI : 
10.1038/ncomms15864

Sirigu S, Hartman J, Planelles-Herrero VJ, Ropars V, Clancy S, Wang X, Chuang 
G, Qian X, Lu P-P, Barrett E, Rudolph K, Royer C, Morgan B, Stura EA, Malik FI, 
Houdusse A (2016 Nov 4)
Highly selective inhibition of myosin motors provides the basis of potential 
therapeutic application.
Proceedings of the National Academy of Sciences of the United States of America 
: 201609342 : DOI : 
10.1073/pnas.1609342113




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

[Bernhard Rupp]

There is probably some justification for the absence of 'reflection'  (as used 
in crystallography) - in 'purist' Physics. The process
itself is not a 'reflection', despite that it can be macroscopically described 
(in first approximation at least, and good enough for finding diffraction spot 
positions) 
as the 'reflection' (as in mirror) on a lattice plane. The underlying single 
scattering photon process itself  - and the bb discussed this in multiple 
threads - is
inherently quantum mechanical, and the 'reality' of that process is not readily 
visualized in macroscopic, human-brain-derived terms.   

Happy mpring, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Harry Powell - 
CCP4BB
Sent: Thursday, July 2, 2020 03:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames to get a 
full dataset?

Dear all

I’ve been persuaded that MPR is a useful name (and see that there are 
shortcomings with both “multiplicity” and “redundancy") and I agree with much 
of what’s been said most recently in this thread.

BTW, just because the Physics definition of a measurement/quantity/whatever is 
given on wikipedia (or elsewhere, for that matter), it doesn’t mean that’s what 
we (crystallographers, structural biologists, etc) should use without question. 
If you check 

https://en.wikipedia.org/wiki/Reflection_(physics)

you will find no mention of diffraction maxima corresponding to reflections 
except a link to a page on diffraction. Or maybe we should slavishly follow the 
Physicists and use another term…

H

> On 2 Jul 2020, at 10:41, Schreuder, Herman /DE  
> wrote:
> 
> Dear all,
>  
> While following the development of this thread, I am truly amazed how people 
> cling to names for the number of measurements per reflection whose meaning:
>   • Depends on the cultural/engineering/scientific context
>   • Can only be understood by experts
>   • Where the experts, as witnessed by the discussions in this thread, do 
> not agree on which name to use.
>  
> What is wrong with the name “measurements per reflection”? The definition for 
> measurement is the same as is used to calculate the multiplicity/redundancy.
> The only disadvantage I see is that it can be understood by non-experts as 
> well, which reminds me of medical doctors, who invent complicated Latin names 
> for common ailments to prevent patients to understand where they are talking 
> about. 
>  
> Another 2 cents/pennies from my side,
> Herman
>  
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von James 
> Holton
> Gesendet: Mittwoch, 1. Juli 2020 20:52
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> 
>  
> 
> 
> Sorry to take this thread on a detour/diversion: What I was attempting to 
> point out below, perhaps unclearly, is that the different interpretations of 
> the word "redundant" are a cultural difference.  As a student of multiple 
> English languages perhaps I can explain:
> 
> Few US English speakers know that in UK/European/Australian English the word 
> "redundant" has a strong negative connotation. I, for one, was surprised to 
> learn that the phrase "made redundant" is used in the UK to describe loss of 
> employment.  That is, a layoff, firing or perhaps a furlough. So, I think it 
> important to spell out for my fellow US English speakers that the emotional 
> ties to this negative connotation can be strong ones.
> 
> Conversely, many UK English speakers do not know that in US English the word 
> "redundant" has a strong positive connotation.  We never use the phrase "made 
> redundant" to describe a lost job.  Most Americans I think would be confused 
> by such a turn of phrase. If a US English speaker was told their jobs was 
> "made redundant" they would most likely think that a new hire was onboarded 
> to back them up.  This would imply that their job was so important that the 
> company wanted at least two people doing it, just in case you got hit by a 
> bus. This strong positive connotation also has emotional roots.
> 
> Personally, I prefer the positive connotation. Perhaps that is my cultural 
> bias, or perhaps I just generally believe that positivity is better than 
> negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has 
> changed enormously over the last few hundred years, and I don't think we're 
> going to change that any more than we are going to change the meaning of 
> "redundant" in these two major forms of English.
> 
> However, just because a word has slightly different meanings in two slightly 
> different languages does not mean we should abandon it.  Are we going to stop 
> eating "chips" just because we are not sure if our fried potato will come as 
> sliced wedges or thin crispy wafers? If you are unhappy with your meal, is it 
> the fault of the culture you are visiting? or the customer 

Re: [ccp4bb] Question about small molecule crystallography

[Navdeep Sidhu]

Correction: It should read "with the detector almost but not quite
hitting the source."


On 02.07.20 17:13, Navdeep Sidhu wrote:
> Alexander Blake wrote a nice chapter on small-molecule crystallization
> in this book, if you run into problems in the crystallization stage:
> 
> Alexander Blake. Crystal growth and evaluation (Chapter 3). In Clegg,
> William (Ed.) Crystal Structure Analysis: Principles and Practice. 2nd
> Edition. IUCr/Oxford, 2009
> ;
> .
> 
> With the detector almost but not quite hitting the detector, one can
> typically collect all the data one needs on a home Cu source. Overloads
> can often be a problem---as has been pointed out out for
> synchrotrons---even on a home source. But they can usually be dealt with
> easily by modifying exposure, collecting lower- and higher-angle data
> separately, leaving some overlap between the two regions (see "Intensity
> level", Blake, Ch. 6.7.1, p. 88 in book above) and scaling. In extreme
> cases, one may need to lower the generator power.
> 
> The nice thing about the slow pace of data collection on a home source
> is that one can think while doing the collection, thus catching and
> correcting most problems before it's too late. In Ch. 7.6 in the book,
> Blake also discusses some other problem cases. (The whole book's a great
> read.)
> 
> Cheers,
> Navdeep
> 
> 
> 
 ---
 On 01.06.20 23:50, Jiyuan Ke wrote:
 > Hi Everyone,
 >
 > I want to crystallize a small organic molecule. I have
 very limited
 > experience in small molecule crystallography. I found
 that the Crystal
 > Screen HT from the Hampton research is good for both
 small molecule and
 > macromolecule crystallization. Plan to set up a sitting
 drop screen just
 > like setting up protein crystallization. I don’t know
 if this is the
 > proper way to do it. Is the MRC sitting drop 2-well
 plate (HR3-083) used
 > for protein crystallization good for small molecule
 crystallization? Are
 > there any special plates used for small molecule
 crystallization? Is
 > room temperature ok or not? 
 >
 > For data collection, can I use the beamline for protein
 crystals to
 > collect data on small molecule crystals? Larger
 oscillation angle,
 > shorter exposure, reduced beam intensity? 
 >
 > For structure determination, is SHELXL the preferred
 software for
 > solving small molecule structures?
 >
 > If anyone has experience in small molecule
 crystallography, please
 > help.  Thanks!
 >
 > Best Regards,
 >
 > --
 >
 > *Jiyuan Ke, Ph.D.*
 >
 > *
 > *
 >
 > Research Investigator
 >
 > H3 Biomedicine Inc.
 >
 > 300 Technology Square, Floor 5
 >
 > Cambridge, MA 02139
 >
 > Phone: 617-252-3923
 >
 > Email: jiyuan...@h3biomedicine.com
 
 >
 >
 > Website: www.h3biomedicine.com
 
 



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Re: [ccp4bb] Question about small molecule crystallography

[Navdeep Sidhu]

Alexander Blake wrote a nice chapter on small-molecule crystallization
in this book, if you run into problems in the crystallization stage:

Alexander Blake. Crystal growth and evaluation (Chapter 3). In Clegg,
William (Ed.) Crystal Structure Analysis: Principles and Practice. 2nd
Edition. IUCr/Oxford, 2009
;
.

With the detector almost but not quite hitting the detector, one can
typically collect all the data one needs on a home Cu source. Overloads
can often be a problem---as has been pointed out out for
synchrotrons---even on a home source. But they can usually be dealt with
easily by modifying exposure, collecting lower- and higher-angle data
separately, leaving some overlap between the two regions (see "Intensity
level", Blake, Ch. 6.7.1, p. 88 in book above) and scaling. In extreme
cases, one may need to lower the generator power.

The nice thing about the slow pace of data collection on a home source
is that one can think while doing the collection, thus catching and
correcting most problems before it's too late. In Ch. 7.6 in the book,
Blake also discusses some other problem cases. (The whole book's a great
read.)

Cheers,
Navdeep



>>> ---
>>> On 01.06.20 23:50, Jiyuan Ke wrote:
>>> > Hi Everyone,
>>> >
>>> > I want to crystallize a small organic molecule. I have
>>> very limited
>>> > experience in small molecule crystallography. I found
>>> that the Crystal
>>> > Screen HT from the Hampton research is good for both
>>> small molecule and
>>> > macromolecule crystallization. Plan to set up a sitting
>>> drop screen just
>>> > like setting up protein crystallization. I don’t know
>>> if this is the
>>> > proper way to do it. Is the MRC sitting drop 2-well
>>> plate (HR3-083) used
>>> > for protein crystallization good for small molecule
>>> crystallization? Are
>>> > there any special plates used for small molecule
>>> crystallization? Is
>>> > room temperature ok or not? 
>>> >
>>> > For data collection, can I use the beamline for protein
>>> crystals to
>>> > collect data on small molecule crystals? Larger
>>> oscillation angle,
>>> > shorter exposure, reduced beam intensity? 
>>> >
>>> > For structure determination, is SHELXL the preferred
>>> software for
>>> > solving small molecule structures?
>>> >
>>> > If anyone has experience in small molecule
>>> crystallography, please
>>> > help.  Thanks!
>>> >
>>> > Best Regards,
>>> >
>>> > --
>>> >
>>> > *Jiyuan Ke, Ph.D.*
>>> >
>>> > *
>>> > *
>>> >
>>> > Research Investigator
>>> >
>>> > H3 Biomedicine Inc.
>>> >
>>> > 300 Technology Square, Floor 5
>>> >
>>> > Cambridge, MA 02139
>>> >
>>> > Phone: 617-252-3923
>>> >
>>> > Email: jiyuan...@h3biomedicine.com
>>> 
>>> >> >
>>> >
>>> > Website: www.h3biomedicine.com
>>> 
>>> 



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[ccp4bb] Protein-DNA covalent bond refinement

[Cristina Machon]

 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



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[ccp4bb] PhD positions in early stage drug discovery

[Groves, Matthew]

Dear all,

The MepAnti project aims to tackle the antimicrobial resistance problem by
targeting enzymes of the methylerythritol phosphate pathway. The MepAnti
consortium consists of nine academic partners and seven non-academic
partners coordinated by The Helmholtz Institute for Pharmaceutical
Research. The consortium aims to go beyond the state-of-the-art in the
anti-infective field by tackling the attractive and underexplored enzymes
from the 2C-methyl-D-erythritol 4-phosphate (MEP) pathway.

We have a few PhD positions in early-stage drug discovery that I would
appreciate if you could bring to the attention of any interested parties.
There are specifically 3 opportunities for structural biologists  within
the ITN:
http://mepanti.hips-wordpress.helmholtz-hzi.de/

Interested parties can contact me for further information informally, but
the official route for applications can be found on:

https://academicpositions.com/ad/helmholtz-institute-for-pharmaceutical-research-saarland-hips/2020/12-phd-positions-early-stage-researchers-esrs-at-mepanti-consortium/145377

Thanks in advance,

Matthew



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

[Navdeep Sidhu]

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 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 

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

[Harry Powell - CCP4BB]

Dear all

I’ve been persuaded that MPR is a useful name (and see that there are 
shortcomings with both “multiplicity” and “redundancy") and I agree with much 
of what’s been said most recently in this thread.

BTW, just because the Physics definition of a measurement/quantity/whatever is 
given on wikipedia (or elsewhere, for that matter), it doesn’t mean that’s what 
we (crystallographers, structural biologists, etc) should use without question. 
If you check 

https://en.wikipedia.org/wiki/Reflection_(physics)

you will find no mention of diffraction maxima corresponding to reflections 
except a link to a page on diffraction. Or maybe we should slavishly follow the 
Physicists and use another term…

H

> On 2 Jul 2020, at 10:41, Schreuder, Herman /DE  
> wrote:
> 
> Dear all,
>  
> While following the development of this thread, I am truly amazed how people 
> cling to names for the number of measurements per reflection whose meaning:
>   • Depends on the cultural/engineering/scientific context
>   • Can only be understood by experts
>   • Where the experts, as witnessed by the discussions in this thread, do 
> not agree on which name to use.
>  
> What is wrong with the name “measurements per reflection”? The definition for 
> measurement is the same as is used to calculate the multiplicity/redundancy.
> The only disadvantage I see is that it can be understood by non-experts as 
> well, which reminds me of medical doctors, who invent complicated Latin names 
> for common ailments to prevent patients to understand where they are talking 
> about. 
>  
> Another 2 cents/pennies from my side,
> Herman
>  
>  
>  
> Von: CCP4 bulletin board  Im Auftrag von James Holton
> Gesendet: Mittwoch, 1. Juli 2020 20:52
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?
>  
> EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
> 
>  
> 
> 
> Sorry to take this thread on a detour/diversion: What I was attempting to 
> point out below, perhaps unclearly, is that the different interpretations of 
> the word "redundant" are a cultural difference.  As a student of multiple 
> English languages perhaps I can explain:
> 
> Few US English speakers know that in UK/European/Australian English the word 
> "redundant" has a strong negative connotation. I, for one, was surprised to 
> learn that the phrase "made redundant" is used in the UK to describe loss of 
> employment.  That is, a layoff, firing or perhaps a furlough. So, I think it 
> important to spell out for my fellow US English speakers that the emotional 
> ties to this negative connotation can be strong ones.
> 
> Conversely, many UK English speakers do not know that in US English the word 
> "redundant" has a strong positive connotation.  We never use the phrase "made 
> redundant" to describe a lost job.  Most Americans I think would be confused 
> by such a turn of phrase. If a US English speaker was told their jobs was 
> "made redundant" they would most likely think that a new hire was onboarded 
> to back them up.  This would imply that their job was so important that the 
> company wanted at least two people doing it, just in case you got hit by a 
> bus. This strong positive connotation also has emotional roots.
> 
> Personally, I prefer the positive connotation. Perhaps that is my cultural 
> bias, or perhaps I just generally believe that positivity is better than 
> negativity. Maybe I'm just a "nice" guy. The meaning of the word "nice" has 
> changed enormously over the last few hundred years, and I don't think we're 
> going to change that any more than we are going to change the meaning of 
> "redundant" in these two major forms of English.
> 
> However, just because a word has slightly different meanings in two slightly 
> different languages does not mean we should abandon it.  Are we going to stop 
> eating "chips" just because we are not sure if our fried potato will come as 
> sliced wedges or thin crispy wafers? If you are unhappy with your meal, is it 
> the fault of the culture you are visiting? or the customer for forgetting 
> where they are? Context is everything. 
> 
> So, for those unfamiliar with one or more of the major English-speaking 
> cultures, here are a few other important differences to be aware of: 
> "Football" may not be the game you think it is. 
> If you are offered a "biscuit" in the US, do not expect it to be sweet. 
> If you want to leave a building you should take the "lift" to the "ground 
> floor", but if you take an "elevator" get off on the "1st floor". 
> A "dummy" is a pacifier for a baby in the UK/Australia, but in the US it only 
> means an unintelligent person, or a plastic replica of one. 
> "please" and "thank you" are considered baseline politeness in some English 
> cultures, but their excessive use in others, such as the US, can be seen as 
> rude.
> A "tap" in the US dispenses beer, water comes out of a "faucet".
> A "flat" in the US 

Re: [ccp4bb] Commercial source of His-tagged protein

[Tristan Croll]

Thermo Fisher sells His-tagged GFP quite cheaply.
https://www.thermofisher.com/order/catalog/product/A42611#/A42611 


Tristan

On 2020-07-02 10:31, Mark J van Raaij wrote:

Dear All, 

Wondering if anyone knows of an economical commercial source of a soluble His-tagged protein. In principle any His-tagged protein would suffice, because it's for testing coupling to a surface via the His-tag. Asking for an international collaborator, who don't have access/expertise of a molecular biology lab (except us :-).  
We can and will make the His-tagged proteins of interest for them, but if there is an economical and reliable commercial source, it might be worth using that for initial tests. 

Best wishes, 


Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616 
Section Editor Acta Crystallographica F

https://journals.iucr.org/f/

-

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Re: [ccp4bb] unable to launch ccp4 old interface on mac

[David Waterman]

Dear Luca,

Thanks for your email. CCP4i is no longer supported by the CCP4 Core Team.
The main interfaces in CCP4 7.1 are CCP4i2 and the CCP4cloud client.
However, ccp4i is still included with the suite, as you found, and can be
run from the command line if you source the CCP4 environment in a terminal.
On a Mac this will be something like "source
/Applications/ccp4-7.1/bin/ccp4.setup-sh". Please note that not everything
is guaranteed to work in CCP4i.

Best wishes
-- David


On Sun, 28 Jun 2020 at 07:42, Luca Mazzei  wrote:

> Dear CCP4 people,
> Can you help me with this?
> At the end of installation of CCP4 7.1 on Mac with OS Mojave, CCP4 folder
> contains ccp4i2 icon, whereas ccp4 icon is not present. This way I can not
> launch the old interface, neither by clicking on the invisible icon nor
> using the terminal. I just fixed the problem by a copy-and-paste of the
> ccp4 icon coming from another Mac on which CCP4-7.0 is installed and It
> seems to work well (I ran Refmac, Coot and Molrep with success usingthe old
> interface)! Do you have any suggestion on why this occurs and how to
> overcome this problem in a more efficient way?
>
> Thanks in advance,
>
> Luca
>
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology
> University of Bologna
> Viale Giuseppe Fanin, 40 - 40127
> Bologna - Italy
>
> 
>
> 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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>



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

[Schreuder, Herman /DE]

Dear all,

While following the development of this thread, I am truly amazed how people 
cling to names for the number of measurements per reflection whose meaning:

  *   Depends on the cultural/engineering/scientific context
  *   Can only be understood by experts
  *   Where the experts, as witnessed by the discussions in this thread, do not 
agree on which name to use.

What is wrong with the name “measurements per reflection”? The definition for 
measurement is the same as is used to calculate the multiplicity/redundancy.
The only disadvantage I see is that it can be understood by non-experts as 
well, which reminds me of medical doctors, who invent complicated Latin names 
for common ailments to prevent patients to understand where they are talking 
about.

Another 2 cents/pennies from my side,
Herman



Von: CCP4 bulletin board  Im Auftrag von James Holton
Gesendet: Mittwoch, 1. Juli 2020 20:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?


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


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

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

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

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

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

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

Then there are words like "capillary", which means the same thing in both 
languages but the alternate pronunciations never 

Re: [ccp4bb] Commercial source of His-tagged protein

[Beatrice Vallone]

Dear Mark,

  this is a small spin-off company from my Dept. I am not personally
involved, but as they are biochemists they produce biophysics quality
proteins and they have the expertise to discuss your needs.

   All the best,

   Beatrice
--
Prof. Beatrice Vallone, PhD
Director-H2CU International Honors Center of Italian Universities
Dipartimento di Scienze Biochimiche
Università di Roma "La Sapienza"
P.le Aldo Moro, 5
00185 - Roma
Italy
Tel +39 06 49690276
Fax +39 06 4440062
eMail beatrice.vall...@uniroma1.it
https://prometeus-rise.org/ 
https://vallonelab.it/
--


Il giorno gio 2 lug 2020 alle ore 11:31 Mark J van Raaij <
mjvanra...@cnb.csic.es> ha scritto:

> Dear All,
>
> Wondering if anyone knows of an economical commercial source of a soluble
> His-tagged protein. In principle any His-tagged protein would suffice,
> because it's for testing coupling to a surface via the His-tag. Asking for
> an international collaborator, who don't have access/expertise of a
> molecular biology lab (except us :-).
> We can and will make the His-tagged proteins of interest for them, but if
> there is an economical and reliable commercial source, it might be worth
> using that for initial tests.
>
> Best wishes,
>
> Mark
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>

-- 

*Il tuo 5 diventa 1000 - *Fai crescere la tua università - Dona il 5 per 
mille alla Sapienza
Codice fiscale: *80209930587*

https://www.uniroma1.it/it/pagina/fai-crescere-la-tua-universita-con-il-cinque-mille
 



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Re: [ccp4bb] Commercial source of His-tagged protein

[David Briggs]

Hi Mark,

NEB

https://international.neb.com/products/p8112-tev-protease#Product%20Information

And Sigma

https://www.sigmaaldrich.com/catalog/product/sigma/t4455?lang=en=GB

Both sell His-tagged TEV protease.

Maybe suitable?

HTH,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Mark J van Raaij 

Sent: Thursday, July 2, 2020 10:31:37 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Commercial source of His-tagged protein

Dear All,

Wondering if anyone knows of an economical commercial source of a soluble 
His-tagged protein. In principle any His-tagged protein would suffice, because 
it's for testing coupling to a surface via the His-tag. Asking for an 
international collaborator, who don't have access/expertise of a molecular 
biology lab (except us :-).
We can and will make the His-tagged proteins of interest for them, but if there 
is an economical and reliable commercial source, it might be worth using that 
for initial tests.

Best wishes,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/





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The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



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[ccp4bb] Commercial source of His-tagged protein

[Mark J van Raaij]

Dear All,

Wondering if anyone knows of an economical commercial source of a soluble 
His-tagged protein. In principle any His-tagged protein would suffice, because 
it's for testing coupling to a surface via the His-tag. Asking for an 
international collaborator, who don't have access/expertise of a molecular 
biology lab (except us :-). 
We can and will make the His-tagged proteins of interest for them, but if there 
is an economical and reliable commercial source, it might be worth using that 
for initial tests.

Best wishes,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/





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

[David Waterman]

It is hard for us to rise above these cultural differences, so perhaps the
adoption of a third, precisely-defined, and neutral term is indeed
warranted. MPR seems a good start, but it forces us to think about what we
mean by measurement. My feeling is that a diffraction spot can be
measured in many ways: the summation integration and profile-fitted
intensities are separate measurements, are they not? Also, one can measure
the background intensity, the position, spot skewness and an
inexhaustible number of other quantities from a single observed Bragg spot.
So perhaps Observations Per Reflection (OPR) is better, but is there really
a difference between observation and measurement? Perhaps each reflection
is already a separate event, in which case Reflections Per Miller Index
(RPMI) looks better. However, what about the term "reflection" itself, is
that precise enough for us...?

-- David


On Wed, 1 Jul 2020 at 19:52, 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 

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

[John R Helliwell]

Good morning Jose,
The devil is always on the detail:-
You are of course correct that I had presumed, as Ethan pointed out, a sub 10 
fsec pulse. 

Neutrons creating magnetic waves, you are again correct, “spin echo“ does 
occur, but without damage though as neutrons have such gentle energies versus 
Xray photons. 

In re reading my “treading through the terminology carefully” email (hinting at 
“going where Angels fear to tread“) I had substituted d spacing for resolution, 
the latter term able to raise lengthy debates, which I sought to avoid, but 
should have changed low to large to read “large d spacings”. Apologies to all.

So, this lockdown is giving us time for considering such issues
Sam Horrell, Andrea Thorn and Dale Tronrud have been have carefully preparing 
via twitterdebate, and including a written document, their suggested options to 
resolve the issue of what to do in our pdb coordinate files where there is 
insufficient electron density for very mobile side chains. Over to you Sam, 
Andrea and Dale.

Greetings,
John 
Emeritus Professor John R Helliwell DSc




> On 2 Jul 2020, at 02:51, 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).
> 
> 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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