Dear James,
let's spin the thought a bit further. What if there is a new program
(Phaser-II) some day,
for which the coordinates in your "new crystal form" are all of a sudden
within the
radius of convergence again? Does this bring your "new crystal form"
back to the old
crystal form again?
I'd
Hmmm…interesting James!. I don’t usually make a habit of trying to form a
class, or losing face because of a point, -or even making a group in space..
But..
Id say it is neither different form nor different habit. -since these are
centuries old terms -and still valuable, - from mineralogy
I have a semantics question, and I know how much this forum loves
discussing semantics.
We've all experienced non-isomorphism, where two crystals, perhaps even
grown from the same drop, yield different data. Different enough so that
merging them makes your overall data quality worse. I'd say
Dear all;
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Hi Joseph,
It is a very beautiful crystal with neat diffraction patterns and
background, which may suggest a good cryoprotection. Here is my observation
from your images.
1. From your image taken at 30 degrees (first page), I believe it is a
protein crystal with a larger unit cell length on one
Dear PDB Data Users:
Thank you for providing feedback on the results of an archival-level
carbohydrate remediation project that led to the re-release of over
14,000 PDB structures in July 2020. This update includes diverse
oligosaccharides: glycosylation; metabolites such as maltose, sucrose,
The first is a very interesting pattern! - It would be good to know more about
exactly how the patterns were taken, camera length and dimensions to determine
the spacings. - The first patterns look very strongly like Bessel functions of
a helical diffraction pattern that is then sampled by a
Hi Joseph
Great diffraction patterns. As Jon has just said, it could be zinc acetate.
There are some very strong spots which would be consistent with a single
crystal of this. However, something else seems to be present.
Could it instead be PEG crystals with some superlattice repeat? For unit
Hello, the first of those diffraction patterns is very beautiful. What was the
concentration of zinc acetate? Also, did you keep the crystal? It might be
worth prodding it with a needle and if holds together well or if you hear a
loud crack it's probably salt. The second image shows a salt-like
... and of course I meant "between model and target".
From: Tristan Croll
Sent: 08 December 2020 16:35
To: CCP4BB@JISCMAIL.AC.UK ; Marko Hyvonen
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
An example: this is
Hi Ian,
The data on Alphafold2 target RMSDs seems to be correct, but that
"resolution around 2.5Å", makes no sense, I agree - had not
noticed that before. I can see that this has been raised in the
Twitter feed comments to his post too.
I
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
Dear John,
Your article touches all the important points about this breakthrough and its
caveats.
I would just like to add that the ligand problem is of a different order: it is
fundamentally not about whether, where and how a ligand is predicted to bind,
but rather about whether it indeed
Hi Marko
I hope he hasn't confused resolution with RMSD error:
"Just keep in mind that (1) a lower RMSD represents a better predicted
structure, and that (2) most experimental structures have a resolution
around 2.5 Å. Taking this into consideration, about a third (36%) of Group
427’s submitted
Here is another take on this topic, by Carlos
Quteiral (@c_outeiral), from a non-crystallographer's point of
view, covering many of the points discussed
in this thread (incl. an example
of the model guiding correction of the experimental structure).
Hi Tristan,
Point taken: unobserved parts of the structure have a very large (if not
undefined) experimental error!
I'd be interested to see how that average 1.6 Ang. error is distributed in
space: presumably that data is in the CASP analysis somewhere.
Cheers
-- Ian
On Tue, 8 Dec 2020 at
Well that is sad, and true, and also very common. I have personally
experienced dozens of cases where methods from literature do not reproduce
because (and this is important) the authors "just slap some generic
boilerplate" instead of the actual methods. My favorite is always to read
stuff like
scientific research requires that experimental results must be testable, so you
have to publish your methods too. if the alphafold2 people don't make their
code accessible, they are playing a game with different rules. maybe it's
called capitalism: i gather they're a private company
best
This is a number that needs to be interpreted with some care. 2 Å crystal
structures in general achieve an RMSD of 0.2 Å on the portion of the crystal
that's resolved, including loops that are often only in well-resolved
conformations due to physiologically-irrelevant crystal packing
Since I didn’t actually read the press release (but “attended" the CASP event
instead where the results were discussed in a little more detail…) this is news
to me, but I’d agree that there is some hyperbole there.
Alphafold2 (it’s probably important to distinguish it from AlphaFold since it’s
Dear Isabel,
My article in the IUCr Newsletter on DeepMind and CASP14 is released today and
can be found here:-
https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14
Best wishes,
John
Emeritus Professor John R Helliwell DSc
> On 3 Dec 2020, at 11:17, Isabel Garcia-Saez
There was a little bit of press-release hype: the release stated "a score
of around 90 GDT is informally considered to be competitive with results
obtained from experimental methods" and "our latest AlphaFold system
achieves a median score of 92.4 GDT overall across all targets. This means
that
Hi
It’s a bit more than science by press release - they took part in CASP14 where
they were given sequences but no other experimental data, and did significantly
better than the other homology modellers (who had access to the same data) when
judge by independent analysis. There were things
My impression is that they haven’t published the code, and it is science by
press-release. If one of us tried it, we would - rightly - get hounded out of
time.
Adrian
On 4 Dec 2020, at 15:57, Michel Fodje
mailto:michel.fo...@lightsource.ca>> wrote:
I think the results from AlphaFold2,
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