Forgot to credit the Nobel Prize website :The Nobel Prize in Chemistry 1946nobelprize.org-BWL
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The Nobel Prize in Chemistry 1946
James Batcheller Sumner
“for his discovery that enzymes can be crystallized”
Prize share: 1/2
John Howard Northrop and Wendell Meredith Stanley "for their preparation of
enzymes and virus proteins in a pure form"
Prize share 1/2 jointly
Thought it might be w
The idea of "Global Sustainability" can be found in the documents for the noted
projects, so the United Nations "Sustainable Development Goals" appear to be
worth reviewing as background - even though it appears the UN or UNESCO (below)
is irrelevant to them :
“Transformation is the red thread
Adding to that literature list a bit outside :
Merchant, A., Batzner, S., Schoenholz, S.S. et al.
Quote:
"... we show that graph networks trained at scale can reach unprecedented
levels of generalization, improving the efficiency of materials discovery by an
order of magnitude. "
Scaling dee
A quote comes to mind (I cannot resist) :
"Now, my own suspicion is that the universe is not only queerer than we
suppose, but queerer than we can suppose [...]"
-J. B. S. Haldane
"Possible Worlds"
in Possible Worlds and Other Essays (1927), p. 286
###
" Is there a canned consensus paragraph that one can add with references to
grants "
How about:
“In general we look for a new law by the following process. First we guess it.
Then we compute the consequences of the guess to see what would be implied if
this law that we guessed is right. Then w
These magnetically-linking atomically accurate single-atom models look interesting - but I understand they might be too detailed or might shift around inadvertently :Snatoms Online Store - Magnetic Molecular Models for Educationsnatoms.comI also cannot say I used them (but I am always looking for a
And of course,"... all models are approximations. Essentially, all models are wrong, but some are useful. However, the approximate nature of the model must always be borne in mind"Box, G. E. P.; Draper, N. R. (1987)Empirical Model-Building and Response SurfacesJohn Wiley & Sons"Since all models
[ emphasis/bold font is mine]:
“In general we look for a new law by the following process. First we guess it.
Then we compute the consequences of the guess to see what would be implied if
this law that we guessed is right. Then we compare the result of the
computation to nature, with experiment
Thank you very much for this delightful applet!
-Bryan W. Lepore
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This message was issued to me
Greetings
This enzyme meets none of the stipulations, but I will point out as it is
somewhat unusual to find in a grocery store :
A food product called Just Egg contains “transglutaminase” as an ingredient.
Make of that what you will.
-Bryan W. Lepore
(No affiliation with Just Egg or anything
Greetings - one assumption of this proposal seems to be that only H. sapiens
will spread and harbor (?) the one specifically designed virus.
I apologize if this is naive, but what is the basis for a virus staying only in
one species?
Or, if the specifically designed virus only does nice good he
> On Dec 11, 2020, at 07:42, Phil Evans wrote:
>
> But I’ve always thought the more interesting question is “this is the
> structure, what does it do?”
It sounds compelling though, that methods of the sort implemented in the CASP
work are perfectly poised to make progress on the question:
“ho
> On Dec 9, 2020, at 07:45, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> ... GDT_TS (Global Distance Test - Total Score - you can look it up on
> Wikipedia
Thanks, this is helpful.
Wikipedia:
“The primary GDT assessment uses only the alpha carbon atoms.”
On Dec 9, 2020, at 07:16, Harry Powell wrote:
>
> ...the important thing is [...] they’ve done something that no-one else has
> managed to do as well in spite of years of trying.
What, precisely, is the “something”?
Exactly how much better than second place?
Was the scoring the same across al
Greetings — I am interested to know more about the following points to
understand the results :
[1] How was the “C-alpha-IDDT” (Mariani et. al., Bioinformatics, 29(21),
2722-2728, 2013) used, as - if I understand, the unprecedented and exceptional
prediction capabilities of AlphaFold2 - as com
Greetings - an important recent article from Science, I thought would be good
to include as background reading:
“NIH’s new cluster hiring program aims to help schools attract diverse faculty”
“The National Institutes of Health (NIH) is hoping universities will use a
controversial—and largely un
Greetings - I just learned about a nifty representation of the Fourier
series using epicycles, perhaps the CCP4 readers would be interested in -
there's an animated gif here :
https://twitter.com/johncarlosbaez/status/1094671748501405696?lang=en
This longer video shows more detail of this approac
On Jan 28, 2017, at 06:32, Bryan Lepore wrote:
>
> can I get a little help? For instance, what is the reference?
The reference is:
Acta Cryst D71 1799
Free to download - thank you to all who helped.
-Bryan
>
> On Jan 27, 2017, at 11:05, Tim Gruene wrote:
> [...], and a
> pointer to your article with its explanation
> http://dx.doi.org/10.1107/S1399004715011803:
> [...]
Apologies, but the above link was not pointing to an article - and I tried so
many times I think I'm being blocked now - can I
[ example structures with disordered crystal contacts ]
Yes and they all have a good bulk solvent correction.
-Bryan
> On Nov 28, 2014, at 00:22, Gregg Crichlow wrote:
...
> The paper now has been published,
...
> PDB ID 4K9G.
... The "primary citation" in the PDB summary is (2014) INT J ONCOL. 45:
1457-1468
... unless any others are worth mentioning here...
-Bryan
FYI
Kevin Cowtan has a web page that discusses using color diagrams with respect to
the color blind interpretation.
http://www.ysbl.york.ac.uk/~cowtan/colour/colour.html
-Bryan
Coming next :
Negative Absolute Temperature for Motional Degrees of Freedom
http://m.sciencemag.org/content/339/6115/52
On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey wrote:
> I don't think that anybody has shown a significant performance difference
> on Apple memory vs a reasonable 3rd party supplier. Apple may potentially
> have better quality controls but places like Crucial essentially have
> lifetime warrantie
On Jan 22, 2013, at 13:08, Nat Echols wrote:
> On Tue, Jan 22, 2013 at 9:59 .
>
> I would definitely recommend maxing out the memory, but don't buy it
> from Apple - we were able to get 16GB from CDW for less than $100.
I think it is just that Apple only offers the highest end memory - CL and a
B-factor needs to be weighted by occupancy, I think.
I think Moleman does it.
-Bryan
warning - tangential:
Steven Pinker's talk/promo on his new-new book "The Sense of Style :
Scientific Communication for the 21st Century" :
*
*
http://video.mit.edu/watch/communicating-science-and-technology-in-the-21st-century-steven-pinker-12644/
-Bryan
On Fri, Nov 9, 2012 at 7:26 AM, Frank von Delft wrote
> Anybody know
> a) how hazardous is cacodylate?
> b) does it really matter for crystallization screens?
[...]
>
(We're being subjected to a safety review.)
I know you are in the UK but this wouldn't have anything to do with this:
On Fri, Oct 19, 2012 at 2:20 PM, Jrh 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 posting this quite interes
wondering if aimless performs anisotropic scaling or "elliptical"
rejections lately.
I ask because:
[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala
... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimle
> On Tue, Apr 24, 2012 at 10:20 AM, David Gallagher
> wrote:
>> I've been using a Belle technologies anaerobic glovebox with in built
>> microscope and liquid nitrogen dewar port [...]
>> plunging loops straight into vials preloaded into an ESRF puck
why, why, why, and why?
>> [...] This requir
On Thu, Apr 19, 2012 at 4:28 PM, wtempel wrote:
> I went ahead and explicitly applied that +0.5*a translation. [...] It turns
> out that after the origin
> shift, some distances between equivalent atoms of the two structures
> exceeded 3A
I'd be interested to know if cphasematch would reach the
On Tue, Apr 3, 2012 at 5:16 PM, Dale Tronrud wrote:
> I'm not sure how encryption can solve a problem of "truth or falsity".
AFAIU any given checksum will tell you if a file is corrupted or not.
My brain decided to interpret that as true or false. and
> A person can use their private key t
On the topic of MX fraud : could not an encryption algorithm be
applied to answer the question of truth or falsity of a pdb/wwpdb/pdbe
entry? has anyone proposed such an idea before?
for example (admittedly this is a mess):
* a detector parameter - perhaps the serial number - is used as a
public
On Sat, Mar 31, 2012 at 6:08 PM, Kevin Jin wrote:
> I have seen several stories like this. Here is an open letter to Nature.
>
> http://www.jinkai.org/AAD/AAD_letter_2_nature.html
>
I'd like to understand this better : please explain precisely, on this
forum, the connection being made between th
On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller
wrote:
> What's the harm?
have you seen usenet/Google groups?
-Bryan
On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin wrote:
> Here is way I have used for [...]
I hate to be a curmudgeon, but can a list member please explain why
this is not specifically blogspam or spam - or whatever it is exactly?
-Bryan
not sure I follow this thread, but this table might be interesting :
http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf
from:
Detection and correction of underassigned rotational symmetry prior to
structure deposition
B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Saut
On Tue, Oct 18, 2011 at 5:01 PM, Jacob Keller
wrote:
> references studying variation in cell params
> systematically as a function of temperature, with many points on the
> curve (not just RT and 100K?)
a well cited article, from 1992:
Effects of temperature on protein structure and dynamics: x-
It would be important to recall the most famous null result : the
Michelson-Morley experiment, published in The American Journal of Science,
explained 18 years later.
it seems that shift-double-clicking on a buccaneer+refmac job in ccp4i
and rerunning it with everything the same (except output name) will
produce results (c-alphas built, Rfree, etc.) that are non-identical
after a few cycles. apparently this is holds for Intel mac osx 10.5 or
10.6 only, not Linux
I seem to have noticed that (i)mosflm can index on one image, or two
images that are not related by 90 degrees. also, cell refinement
sometimes splits up a set of frames into maybe 3 or four segments of
e.g. a few degrees each. and of course, I can set it based on frames
90 degrees apart.
reason I
can preferences go in .mosflm/.profile?
or - is there a place to put global preferences e.g. something like
the .mos appears to be crystal-specific.
-Bryan
p.s: thanks DW AL HP JH for the interesting 'gain' comments.
wondering if mosflm can automatically estimate the gain.
i.e. i gather it is still estimated the usual way.
-Bryan
can mosflm handle a dataset defined by images with correct but unequal
oscillation angles in the image headers?
-Bryan
if anyone knows of a cornercorrect file I might be able to use in
scala, perhaps for an adsc q[any], please let me know off-list if you
don't mind.
-Bryan
On Tue, Feb 8, 2011 at 7:17 AM, Simon Kolstoe wrote:
> XDS [...] signal/noise >= -3.0.
i'd be interested to know if there is an equivalent in scala...
perhaps 'REJECT 6 ALL -8'
-Bryan
On Fri, Jan 28, 2011 at 9:35 AM, wrote:
> [...] due to the 3-dimensional profile fitting.
what is the specific difference between 3-d profile fitting and using
a sliding window of more than one image?
-Bryan
On Jan 28, 2011, at 8:45, "Bosch, Juergen" wrote:
> Mark Robien and I did a "systematic" study on about 30 data sets while we
> were at SGPP.
can you name the detector(s)?
-Bryan
On Wed, Dec 15, 2010 at 6:10 AM, Kevin Cowtan wrote:
> Looks like you're missing
> -colin-fo '/*/*/[F,SIGF]'
that did it.
i gather the input is much like buccaneer then.
also - is 0.2 the latest version - and the only command line options
in v0.2 (15/04/05) that i see listed are:
Usage: cmake
does cmakereference v0.2 in ccp4 6.1.13 require 'project', 'dataset'
or 'crystal' to be in the .mtz? because i thought by default, these
were eponymous
e.g my .mtz - that has labels F and sigF - :
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 project
On Thu, Dec 2, 2010 at 12:17 PM, wrote:
> get values for chosen torsion angles of ligand ...
moleman with a script.
-Bryan
> I want to do the sequence alignment of these two proteins from all
> species in such a way that the structure based sequence remain constant
> while extending the sequence only at the c-terminus.
IIUC :
profile 1 = *structure-based* sequence alignment i.e. from STAMP (THESEUS?)
profile 2 = a hu
[ scala 3.3.16 ]
in scala's "final table", there's "Mean((I)/sd(I))". i could be wrong,
but the error of this measurement seems to me to exist, considering
the uncertainty of sigma = 1 / sqrt( 2 (N-1) ) ... but its not clear
where the logfile has the values of I or sigma and N that correspond
to
[ mosflm 7.0.6 ]
[ imosflm 1.0.4 ]
wondering if users can define a mask to associate with specific frames.
e.g. if theres something weird on one region of frame 23, make a mask
to block that part out only, and for all other frames, use the default
mask for beamstop shadow.
AFAIK the only way to
On Fri, Oct 29, 2010 at 4:25 PM, Ethan Merritt wrote:
> You may laugh, but the Google finds hits on the topic here:
>
> http://atlas-conferences.com/cgi-bin/abstract/cauu-47
anyone who made complete sense of that abstract is invited to go here :
http://snarxiv.org/vs-arxiv/
and if you do, ple
On Thu, Oct 21, 2010 at 11:42 AM, Ian Tickle wrote:
> There are a number of things that don't look right here, both with the
> Refmac and the Phenix runs: [...]
interesting, thanks for these comments.
> S should not have been symmetrized
to actually display the principal axes in molscript, i me
> documentation
then i conclude the TLS protocol in refmac is markedly different from
phenix (i know this is not strictly a ccp4 question). cf. :
refmac:
TLS
RANGE 'A 245.' 'A 252.' ALL
ORIGIN14.019 -10.476 -35.068
T 0.4974 0.0372 0.3453 0.0674 0.2984 0.0431
L 21.5463
[ ccp4 6.1.3 ]
i have some phenix TLS tensors i'd like to evaluate in tlsanl [*].
are there specific conversions/transformations to be wary of when
setting up the job or interpreting the output?
-bryan
[*] originally posted on phenix BB with some gory details.
btw, buckyballs have measurable wave properties. i think they are trying virus
particles now.
On Mon, 19 Feb 2007, Patrick Loll wrote:
Matlab
octave is the free software answer to Matlab:
www.octave.org
i heard it can take matlab scripts.
-bryan
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