I think it is quite an interesting question in principle for Laue crystallography (now probably only relevant in the neutron world?) since, for example, if one had a crystal in the 432 point group, you could collect an essentially complete dataset with one 'image'. Given that each image can take se
Dear Ed,
Concerning your remark that "use of terms redundancy and multiplicity
to describe the same concept is by itself redundant", one could perhaps say
that redundancy is an abstract property of a dataset, while multiplicity is
a numerical attribute. Redundancy is desirable because if some
Hello JohnDoes the IUCr dictionary list 'degeneracy'?Jon CooperOn 30 Jun 2020 17:11, Gerard Bricogne wrote:Dear Bernhard,
That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones (
Dear Bernhard,
That is true, and the discrepancies between repeated measurements of
the same hkl would have to be parametrised differently from those between
symmetry-related ones (e.g. in terms of radiation damage only, while the
others would also involve absorption effects). However I am no
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Gerard, fantastic proposal - let's call it "abundancy"!!!
Which developer will be the first to change their logfile?
On 30/06/2020 16:38, Gerard Bricogne wrote:
Dear Phil,
I would like to make an attempt to not let this question get mired in
exchanges of well-researched linguistic argum
.…but there is a difference whether I measure the same identical hkl over again
or ‘preferably in more than one symmetry-equivalent position’, to quote the
IUCr. So do we have a MPSR for the same reflection and a MPRR for the related
reflections?
Cacophonically yours,
BR
From: CCP4 b
Dear Phil,
I would like to make an attempt to not let this question get mired in
exchanges of well-researched linguistic arguments at risk of being drowned
in a cacophony of sound bites :-) .
You refer to the days of SCALA, at which time data were collected on
CCD detectors, whose lengt
Dear Herman,
I think that MPR is a very neat and tidy, excellent, proposal.
Moreover it uses the word “measurements”, and we are an experimental based
science.
I support it.
Great.
Greetings,
John
Emeritus Professor John R Helliwell DSc
> On 30 Jun 2020, at 15:10, Schreuder, Herman /DE
> w
Replicate is a good option with its own problems as it can be seen as
referring to exact copy which multiple measurements clearly aren't. It does
have an advantage of being the word used by non-crystallographers though.
As a lame attempt at joke, use of terms redundancy and multiplicity to
describ
Dear BB,
Since there does not seem a generally accepted term for the subject of this
discussions, and since even the IUCR scriptures do not give any guidance, I
would propose to introduce a completely new term:
Measurements per reflection or MPR
This term is politically neutral, should adequat
On 30/06/2020 10:51, Daniele Veggi wrote:
Dear CCP4bb,
I'm trying to insert an Acetone molecule between two cysteine residues
in coot or modifying the pdb. I'm working on this modified molecule
where the disulfide bridge was chemichally opened and inserted an
acetone molecule between the two
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
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 m
By all means, if you still have "disks" you should get rid of them, and
replace them with some modern storage.
On 2020-06-29 21:17, Edward A. Berry wrote:
Now can we get rid of all the superfluous disks in our RAID? Or at
least not replace them when they fail?
On 06/29/2020 06:24 PM, Andrea
Dear Colleagues,
In an effort to break this naming deadlock, and with Massimo and Ian not
showing up as yet, I checked the IUCr Dictionary.
“Redundancy“ and “Multiplicity“ are not listed.
The more generic term “Statistical Descriptors“ is though and even offers
Recommendations:-
http://ww1.iucr.o
The people that already use multiplicity are going to find reasons why
it's the superior naming scheme - although the underlying reason has a
lot to do with negative associations with 'redundant', perhaps hightened
in the current environment. And conversely redundant works for many
others - Gr
To verify the presence of a non protein ligand, you need to come at this
from an unbiased perspective.
1. Remove what you think is not there (e.g. disulfide bond) by truncating
the Cys residues
2. Examine the difference density map to see if it conforms to your
expectations of what is proposed to
As also suggested by Dr. Roger you should first see the density then the
next step of molecule addition is suggested. Omit is also a good idea for
further confirmation.
On Tue, Jun 30, 2020 at 4:55 PM Daniele Veggi
wrote:
> Hi Yadav,
> yes, this is only a representation of what I would like to
Hi Yadav,
yes, this is only a representation of what I would like to do. If during
the refinement will continue to appear density, probably I'm on the good
track..but currently my big issue is inserting the ACN
covalently linked to both cys.
many thanks
Daniele Veggi
GSK Vaccines Siena Italy
The first step would be to verify consistent, convincing electron density
for the proposed thioketal adduct. A good way to start might be an "omit"
map of the region by mutating the Cys residues to Ala, truncating them to
the beta-carbon. The resulting difference density may be suggestive of a
thio
Hi Daniele,
Do you see Fo-Fc density near disuphide bond where you are trying to fit
acetone?
On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi
wrote:
> Dear CCP4bb,
>
> I'm trying to insert an Acetone molecule between two cysteine residues in
> coot or modifying the pdb. I'm working on this modifi
Dear CCP4bb,
I'm trying to insert an Acetone molecule between two cysteine residues in
coot or modifying the pdb. I'm working on this modified molecule where the
disulfide bridge was chemichally opened and inserted an acetone molecule
between the two cysteine.
MS data confirm this modification (9
The Multiscale Research Institute for Complex Systems (MRICS) at Fudan
University is located at the Zhangjiang Campus of Fudan University and is
supported by the Shanghai High-level Talents Program. MRICS is strongly
committed to the development of novel and effective multi-scale imaging
techn
Or, we could accept the fact that crystallographers are kinda used to
multiplicity of an individual Miller index being different to multiplicity of
observations, and in Table 1 know which one you mean? 😉 Given that they add new
information (at the very least to the scaling model) they are strict
Ok, the analogy is not great because most reflection data sets have some
"fault tolerance" whereas RAID 0 does not. But the point is that anything
that is not an exact copy and brings actual information should not be
considered "redundant"
On Tue, 30 Jun 2020, 09:00 David Waterman, wrote:
> Refl
Reflections are as "redundant" as the disks in a RAID 0 array
On Tue, 30 Jun 2020, 02:49 James Holton, wrote:
> What could possibly go wrong?
>
> -James Holton
> MAD Scientist
>
> On 6/29/2020 6:17 PM, Edward A. Berry wrote:
> > Now can we get rid of all the superfluous disks in our RAID? Or at
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