Dear Vito
I looked at the examples of I3C in 3e3d, 3e3s and 3e3t and certainly the latter
two show clear 2Fo-Fc for several I3Cs at a range of occupancies. So my mention
of the different difference maps’ effectiveness does not apply.
Hermann and Eleanor suggestions hopefully will explain your
Dear Michael
The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to
me.
Were the diffraction images underexposed?
Best wishes
John
Emeritus Professor of Chemistry John R Helliwell DSc_Physics
> On 3 Nov 2019, at 23:19, Michael Jarva wrote:
>
>
> Hi CCP4BB,
>
>
Dear Kevin
You could try reindexing into P1, then run Phaser and with its solution as
input to Zanuda determine the space group.
Best wishes,
John
Emeritus Professor of Chemistry John R Helliwell DSc_Physics
> On 31 May 2019, at 21:09, Kevin Jude wrote:
>
> Hello community, I wonder if
Dear Colleagues
The UK Open Research Data Task Force Final Report is here:-
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/775006/Realising-the-potential-ORDTF-July-2018.pdf
This will be of general interest. As well as contributing to this report
Hello Harry
I used SRS 7.2 and 9.6 at a wide variety of monochromatic wavelengths for
resonant scattering (AD) studies. But I can imagine high intensity application
PX measurements were made at those specific wavelengths which you mention.
Greetings from Novosibirsk,
John
Emeritus Professor of
Dear Colleagues,
I prepared this overview of our crystallographic science in Biosciences Reports
at the invitation of the Biochemical Society, which I imagine you would be
interested in:-
http://www.bioscirep.org/content/37/4/BSR20170204
It is open access.
All best wishes,
John
Emeritus
Dear Bert
That is a limitation, I agree.
Suffice to say the clarity of details seen, or not seen, will not get better in
the 'real' situation.
The resolution 'limit' based on CC 1/2 also now needs to be considered (in
addition to I/sigI criterion).
John
On 17 Apr 2015, at 17:59, Bert
Good morning Pavel,
That's interesting.
In our study 'ghosts' of waters in our truncated maps did not occur.
Waters and hydrogens behave differently as ghost objects presumably?
Greetings,
John
On 17 Apr 2015, at 20:10, Pavel Afonine pafon...@gmail.com wrote:
Hello,
John, the
Dear Colleagues,
Stimulated by Bernhard's posting, and whilst certainly beyond his sense of
bewilderment, I recalled that there were studies on this issue. These are
neatly summarised in the Topical review :-
http://dx.doi.org/10.1107/S01087681269X
By Frank Herbstein in Acta Cryst B
I
Dear George
My student class would not find that IUCr dictionary definition helpful. What
they do find helpful is to state that they cannot contain an inversion or a
mirror.
To honour Sohnke is one thing but is it really necessary as a label? You're
from Huddersfield I am from Wakefield ie
think belongs to
them? Maybe students would not be as refractory to the idea as might first
be thought.
With best wishes,
Gerard.
--
On Fri, May 02, 2014 at 05:42:34PM +0100, Jrh Gmail wrote:
Dear George
My student class would not find that IUCr dictionary definition
Dear Dean,
I appreciate you might not be able to reveal further details but 'disappearing
during data collection' sounds interesting as does 'metals' plural (are
they expected to be close together?).
Best wishes,
John
Prof John R Helliwell DSc
On 30 Apr 2014, at 11:33, Dean Derbyshire
Dear Dean
An example, albeit not a metal, can be found here:-
http://journals.iucr.org/s/issues/2007/01/00/xh5011/xh5011.pdf
Such specific damage has a long history:-
http://www.sciencedirect.com/science/article/pii/0022024888903223
An X-ray sensitive metals centre is the Mn5Ca OEC of PS II and
Dear Faisal,
When scrutinising such distances do be aware of the possibility of false
precision in the estimates; see eg http://dx.doi.org/10.1107/S2052252513031485
Best wishes,
John
Prof John R Helliwell DSc
On 17 Apr 2014, at 21:13, Faisal Tarique faisaltari...@gmail.com wrote:
Dear
Dear Colleagues,
We wish to let you know that the Triennial report for 2011 to 2014 on
diffraction data deposition matters, prepared by the IUCr Diffraction Data
Deposition Working Group (DDD WG) is now available at:-
http://forums.iucr.org/viewtopic.php?f=21t=343
Best wishes,
John, Brian and
Dear Jacob,
Measurement of the reciprocal space maps at reflections with triple axis
diffractometry allows experimental separation of mosaicity and strain
(variation in unit cell parameter) effects. See eg Boggon et al 2000 Acta Cryst
D56, 868-880 http://dx.doi.org/10.1107/S090744495837 for
Dear Jacob
For a review of this topic see
http://www.tandfonline.com/doi/full/10.1080/08893110310001643551#.UyCVLikgGc0
I also refer you to the more recent OUP IUCr book Chayen, Helliwell and Snell
ie which includes these topics:-
Dear Jacob,
An example where special efforts were made to investigate biocatalysis and the
role of ions, harnessing both softer X-rays and ion substitutions and a WASP
analysis to be sure as possible of their identity, can be found here:-
http://www.ncbi.nlm.nih.gov/pubmed/20099851
The review
Dear Jacob,
Ah yes, I see.
Your wording is perfectly clear.
Sorry for my misunderstanding.
Best wishes,
John
Prof John R Helliwell DSc
On 7 Mar 2014, at 15:18, Keller, Jacob kell...@janelia.hhmi.org wrote:
You indicate that oxygen anomalous scattering could be used; whilst this is
Dear Jacob,
6 phosphogluconate dehydrogenase :-
See Chen et al 2010 J Struct Biol 169,25-35
and for which enzyme there has been a longstanding interest in the protein
dynamics and studies linking with diffuse X-ray scattering: see Biochem Soc
Trans (1986) 14, 653-655.
Best wishes,
John
Prof
Dear Bert,
In my own review:-
http://www.tandfonline.com/doi/abs/10.1080/08893110802360925?journalCode=gcry20#.UulGyGtYCSM
molecular replacement emerged in my mind as the most robust option for
structure determination in such a case, apart from finding an untwinned crystal
form of course.
Best
Dear Ed,
I imagine this reference:-
http://dx.doi.org/10.1021/ja908703c
Will be of interest.
Best wishes,
John
Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
Dear Alastair,
This reference:-
http://dx.doi.org/10.1107/S0907444903004219
seems related to your email input below.
I would be grateful though to be guided with a couple of references from you on
the topics you raise.
Thankyou in anticipation,
Best wishes,
John
Prof John R Helliwell DSc FInstP
Dear Tobias,
Take a look at http://dx.doi.org/10.1107/S0108767389012912
The ribonuclease crystal I used to measure the speed of sound, using laser
generated ultrasound, was of volume 129 mm3 ie 7.7x6.2x2.7 mm . David Moss of
Birkbeck College provided it.
Best wishes,
John
Prof John R Helliwell
Dear Tobias,
There is also this one :- http://dx.doi.org/10.1107/S0021889801007245
In this study we had to use a smaller crystal than the largest ones available
of 125mm3. They were a lovely rhombic dodecahedral crystal habit. Nb we only
published details of the size of the one used. These
, as does
cryo-EM.
Cheers,
Axel
On Oct 10, 2013, at 11:05 AM, Jrh jrhelliw...@gmail.com wrote:
Dear Sacha, Dear Colleagues,
I also offer my congratulations to the Chemistry Nobellists of yesterday. A
very exciting and significant event, which I enjoyed. I recall when my PhD
student
Dear Sacha, Dear Colleagues,
I also offer my congratulations to the Chemistry Nobellists of yesterday. A
very exciting and significant event, which I enjoyed. I recall when my PhD
student, Gail Bradbrook, spoke about our harnessing these exciting methods in
our crystallographic and structural
Dear Frank,
I would only add to Randy's excellent suggestions a commendation of Max
Perutz's book
Is Science necessary
http://www.amazon.com/Is-Science-Necessary-Essays-Scientists/dp/0192861182
It includes global longevity and food production issues and improvements. Of
course these are wider
I prepared this on Sunday, here it is now:-
Well, I was 'shaken but not stirred' to see a program 'fake_Fobs'. However
James' posting on the Rfactor gap in MX is a more respectable, Sunday morning,
topic. I tried to find the previous threads on this via google and couldn't. So
apologies to all
Dear Edward,
Re your em colleagues:-
We are indeed happy to understand their diffraction to 5th order, by which we
mean the d/5 reflection (1st order) because the two are simply different
viewpoints.
Just one loose end:-
The remarkable thing is that the diffraction from a crystal is largely
Dear Pietro,
The n in Bragg's Law is indeed most interesting for teachers and a most
delicate matter for those enquiring about it.
The diffraction grating equation, from which W L Bragg got the idea, a 'cheap
accolade' he said to have it named after him in his Scientific American
article, has
Dear Tom,
I find this suggestion of using the full images an excellent and visionary one.
So, how to implement it?
We are part way along the path with James Holton's reverse Mosflm.
The computer memory challenge could be ameliorated by simple pixel averaging at
least initially.
The diffuse
the thread based sorting of
my emails is soon going to exceed the width of my screem for the
original one.
On 06/24/2013 08:13 AM, Jrh wrote:
Dear Tom, I find this suggestion of using the full images an
excellent and visionary one. So, how to implement it? We are part
way along the path with James
if you convolute all this with the whole diffraction
experiment parameters through using images in refinement that will be big
fun, I'm sure.
Pavel
On Sun, Jun 23, 2013 at 11:13 PM, Jrh jrhelliw...@gmail.com wrote:
Dear Tom,
I find this suggestion of using the full images an excellent
Dear Colleagues,
If we may combine Ethan's quote from Stout and Jensen with Tim's meter:-
With film the estimating of a spot's blackness by eye is not a meter, it
originally was a person's eye aided by a reference strip of blackened graduated
spot exposures.
With measuring devices the
Dear Ed,
Thankyou for this.
Indeed I have not pushed into the domain of I/sigI as low as 0.4 or CC1/2 as
low as 0.012.
So, I do not have an answer to your query at these extremes.
But I concede I am duly corrected by your example and indeed my email did not
tabulate specifically how far one
Dear Gerard,
Many thanks for these useful clarifications.I see your points clearly.
Just to mention that one remark in James's posting regarding photon counting
versus read noise caught my attention. I will follow up on this ASAP , which
like fine phi slicing gets to the heart of the
Good morning Colin (from this side of the pond),
I never liked the word redundancy. Multiplicity is a however a good word for
multiple measurements. So, Ethan, what does someone in the USA say when made
redundant ie out of a job? Surely not that they are now a useful surplus for
the US economy
Dear Zbyszek,
I am concerned that the unmerged data would be bypassed and not preserved in
your recommendation. I also find it counter intuitive that the merged data
would then be unmerged into a lower symmetry and be better than the unmerged
data; there is I imagine some useful reference or
Dear James,
I agree with your chronology of the first full new protein structures by SR
MAD.
The 1975 two wavelength Hoppe and Jakubowksi study of erythrocruorin with Ni
and Co Kalpha Xray tubes is a classic piece of work of in effect MAD phasing .
See the IUCr Anomalous Scattering Conference
Dear Dr Zhu,
I hope the following might make things easier to grasp. The 3.0Angstrom
diffraction resolution is basically required to resolve a protein polypeptide
chain whether your protein is in an 80% solvent content unit cell or a 50%
solvent content unit cell. You will have more
Dear Colleagues,
The paper
http://dx.doi.org/10.1107/S0108768185002233
in work led by Howard Einspahr undertaken at SRS 7.2 is a protein structural
specific result from synchrotron radiation.
The MAD method of course yielded totally specific to SR protein crystal
structures. The
Jacob, I recall Dorothy Hodgkin or Guy Dodson showing a slide (mid to late
1970s) with insulin crystals having grown in the Islets of Langerhans. As you
say, quite remarkable. John
Prof John R Helliwell DSc
On 15 Feb 2013, at 19:44, Jacob Keller j-kell...@fsm.northwestern.edu wrote:
Dear Colleagues,
This paper on the early days of crystallographic computing will be of
relevance:-
http://garfield.library.upenn.edu/classics1980/A1980JR2291.pdf
Greetings,
John
Prof John R Helliwell DSc
On 20 Jan 2013, at 06:38, Edward A. Berry ber...@upstate.edu wrote:
Edward A.
Dear Pavel,
Also worth mentioning the obvious that the mathematical functional form of an
occupancy and a B factor in its -ve exponential is very different BUT at lower
resolutions they behave similarly. Thus higher resolution refinement allows an
'easier' determination of each parameter.
Nomenclature hazard warning:-
Ian, Thankyou for drawing attention to the nomenclature school:-
Partial occupancy disorder
Which I prefer to refer to as
Partial occupancy order.
Outside our MX field static disorder refers to what we call split occupancy
order. I like the latter and dislike the
with the Me group randomly occupied
with half occupancy. The disordered Me was certainly visible in the map,
just with reduced density compared with the other C atoms.
-- Ian
On 20 November 2012 17:58, Jrh jrhelliw...@gmail.com wrote:
Nomenclature hazard warning:-
Ian, Thankyou for drawing
Dear Andrew,
Re cryocooled.
Cooled?
It reminds me of James Bond where Martinis should be shaken but not stirred.
Ie Cooling sounds awfully gentle, a sort of enjoying a cool sea breeze in the
Caribbean heat. (Ian Fleming wrote his Bond novels there.)
Shock frozen is more what we are doing to
software is also hopefully of interest.
Greetings from Taipei,
John
Prof John R Helliwell DSc
On 31 Oct 2012, at 10:37, Ethan Merritt merr...@u.washington.edu wrote:
On Tuesday, 30 October 2012, Jrh wrote:
This paper describes use of data either side of the calcium edge:-
http://dx.doi.org
Dear Colleagues,
A different type of, post publication, fraud is the case of the discovery of
streptomycin. See :-
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext
I am just returned from the ICSTI Conference on Science, Law and Ethics in
Washington DC
...@gmail.com wrote:
On Fri, Oct 19, 2012 at 2:20 PM, Jrh jrhelliw...@gmail.com wrote:
Dear Colleagues,
A different type of, post publication, fraud is the case of the discovery of
streptomycin. See :-
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61202-1/fulltext
I can't resist
Dear Qixu Cai,
The following paper should be informative for your query:-
http://dx.doi.org/10.1107/S0909049595013288
Best wishes,
John
Prof John R Helliwell DSc
On 29 May 2012, at 10:11, Qixu Cai caiq...@gmail.com wrote:
Dear all,
Sorry for the question from MAD beginner.
When we
Dear Anna,
Very interesting diffraction pattern.
Any chance of measuring to higher resolution?
Ie to try and capture the higher order rings, which presumably are there.
Also interesting that these rings seem quite weak ie the ferritin perhaps not
fully loaded?
Best wishes,
John
Prof John R
On 26 Apr 2012, at 12:02, Jrh wrote:
Dear Colleagues,
I have followed this thread with great interest. It reminds me of the Open
Commission Meeting of the Biological Macromolecules Commission in Geneva in
2002 at the IUCr Congress. Ie at which it was concluded that protein
coordinates
Dear Colleagues,
I have followed this thread with great interest. It reminds me of the Open
Commission Meeting of the Biological Macromolecules Commission in Geneva in
2002 at the IUCr Congress. Ie at which it was concluded that protein
coordinates and diffraction data would not be provided to
Dear Ron,
Quite so, and who cannot laugh at the Yes Minister perfect hospital ward
operating theatre sketch ( Thankyou James W).
Anyway:-
Let's not get too hung up on one detail of your point 3. Your various points,
including point 3, added several missing elements in this CCp4bb thread.
Dear Herbert,
Category 4, in Manchester, we find is tricky, for want of a better word.
Needless to say that we have collaborators on our Crystallography Research
Service who request data sets from eg ten years ago, that are now urgent for
publication writing up. So we are keeping everything,
Dear Roger,
At the recent ICSTI Workshop on Delivering Data in science the NSF presenter,
when I asked about monitoring, replied that the PIs' annual reports should
include data management aspects.
See http://www.icsti.org/spip.php?rubrique42
Best wishes,
John
Prof John R Helliwell DSc FInstP
Dear Colleagues,
The real issue is the 'anomalous' word introduced as an X-ray scattering theory
correction, which was not anomalous but the actual physical situation of
resonance scattering. Thus the most recent of the Anomalous Scattering
conferences was correctly called REXS2011. Ie
Jrh correction:- in the last sentence the final statistical test must involve
the comparison of each of the two different dictionary distance values in turn
(essentially assumed to be exactly known for simplicity) versus the
experimentally derived distance and its DPI derived sigma (L
Dear Gerard K,
Many thanks indeed for this.
Like Gerard Bricogne you also indicate that the location option being the
decentralised one is 'quite simple and very cheap in terms of centralised
cost'. The SR Facilities worldwide I hope can surely follow the lead taken by
Diamond Light Source and
to
greatly lower the impact of that data loss rate and allow us to go
forward with greater confidence.
Regards,
Herbert
At 7:53 AM +0100 10/29/11, Jrh wrote:
Dear Gerard K,
Many thanks indeed for this.
Like Gerard Bricogne you also indicate that the location option being the
decentralised
Dear James,
This is technically ingenious stuff.
Perhaps it could be applied to help the 'full archive challenge' ie containing
many data sets that will never lead to publication/ database deposition?
However for the latter,publication/deposition, subset you would surely not
'tamper' with the
Dear Rex,
These issues of energy overlaps are addressed in theory, for either diffraction
probe, in Cruickshank, Helliwell and Moffat 1987 Acta Cryst, and also by the
same authors in 1991 Acta Cryst for spatial overlaps, and in practice in eg
Ren et al JSR 1999 and Nieh et al JSR 1999.
That is neat and tidy!
I don't suppose you know if Windows 7 might have such a facility?
Anyway it's a good tip and I will start looking in that direction,
Thanks,
John
Prof John R Helliwell DSc
On 19 Aug 2011, at 09:05, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
With OSX 10.6 Snow Leopard,
Dear Colleagues,
Thankyou for your detailed, and prompt, helpful advice on this issue, which I
much appreciate.
I see that I have overestimated my anxieties but should probably still move a
little cautiously.
Thus I will first suggest to my IT encryptors' taskforce, for want of a better
term,
Dear Colleagues,
My institution is introducing concerted measures for improved security via
encryption of files. A laudable plan in case of loss or theft of a computer
with official files eg exams or student records type of information stored on
it.
Files, folders or a whole disk drive can be
Dear Jacob,
Ahmed Zewail's papers are worth consulting on this, although not protein/bio.
See also the book by Zewail and Thomas, recently published, easily findable on
amazon etc, as a handy overview.
Best wishes,
John
Prof John R Helliwell DSc
On 14 Apr 2011, at 14:38, Jacob Keller
Dear Ed,
Thankyou for this and apologies for late reply.
If one has chemical evidence for the presence of residues but these residues
are disordered I find the delete atoms option disagreeable. Such a static
disorder situation should be described by a high atomic displacement parameter,
in my
Dear Colleagues,
Agreed! There is a wider point though which is that the 3D structure and data
can form a potential for further analysis and thus the data and the structure
can ideally be more than the current paper's contents. Obviously artificially
high I/ sig I cut offs are both
Dear Alex
I take it this density effect is in each of the four molecules?
I wonder if the crescent is a series termination effect, although relatively
rare in our field. If so what might have caused it? Do you have (radial) gaps
in your data set eg due to heavy ice rings?
Best wishes,
John
Dear Andre
For a continuum wavelength band source this unit is needed. A monochromator of
a given type then extracts it's rocking curves worth of bandpass. Or in Laue
diffraction a wide band is selected with eg a mirror cut off at short
wavelengths and a filter or transmission mirror at long
Dear Rex,
A very informative and careful analysis to help your question be answered can
be found
In Jiang and Sweet JSR 2004, 11, 319-327.
Greetings,
John
Prof John R Helliwell DSc
On 15 Jan 2011, at 20:28, REX PALMER rex.pal...@btinternet.com wrote:
Does anyone know of a statistical
Dear Gerard
I will do a scan of fig 8.1b asap, probably Monday.
Greetings,
John
Sent from my iPad
On 29 Oct 2010, at 18:44, Gerard Bricogne g...@globalphasing.com wrote:
Dear John,
Would it be possible to know more about what you are referring to
without having to buy (or steal) your
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