On 12/4/2020 12:15 PM, Marcin Wojdyr wrote:
> On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote:
>> learn the sequence you have to go to the mmCIF records that define the
>> connectivity between residues. It is entirely possible that "3" comes
>> before "1" because these indexes don't contain any
On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote:
>
> Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
> exactly the problem.
It's not about "creating meaning" but about consistent naming. For humans.
> "chain names" ( or "entity identifiers" if I
> recall the mmCIF
I agree that the user experience is very important, but that is not
the purpose of a data base design. The data scheme is designed for the
storage and manipulation of data by software in a clear and unambiguous
way. The presentation of the data to a user is the job of the
application
Ah yes, polymer connectivity depends on the order of appearance not the
numbering. On top of that, the connectivity is implicit. There are structures
where some chains are numbered in reverse order, especially in double helices.
How convenient is it that each base pair has residues of the same
No - they're changing the auth_asym_id. See
https://www.wwpdb.org/documentation/carbohydrate-remediation:
Oligosaccharide molecules are classified as a new entity type, branched,
assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF category
introduced to define the type of
Hi Luca,
Your point remains completely valid and I agree that residues that can belong
to a longer chain should be treated as such. The same problem is with peptide
ligands (at least in PDB times), if they consist of three residues they would
their own chains, with 2 residues they would not.
OK, I understand your point more clearly now - but I'm not sure I fully agree,
for the simple reason that people aren't computers. You're right that for the
purposes of software validation tools the chain IDs are essentially arbitrary -
as long as they're unique, nothing else really matters.
Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
exactly the problem. "chain names" ( or "entity identifiers" if I
recall the mmCIF terminology correctly) are simply database "indexes".
The values of indices are meaningless in themselves, they are just
unique values that can
Hi Tristan,
I fully subscribe to your idea! I was quite surprised to see our model revised
with different glycan chain IDs upon PDB annotation. I imagine there must have
been some "administrative" reasoning behind this decision, but it's just a
nightmare for subsequent visualisation. And, to me
This suggestion violates a basic principle of data base theory. A
single data item cannot encode two pieces of information.
I'm sorry if I was unclear, but I don't believe I was suggesting anything of
the sort. Hopefully this example should make it more clear - I'm just
suggesting a slight
Dear Dale and Robbie,
I agree with your comments! But may I stir back the discussion to the original
issue, which is that one-residue N-glycans are now treated differently from
multi-residue N-glycans (although they are both covalently linked to a protein
chain)? This inconsistency is
Michel
Yes, a good point. relevant to the difference between AlphaGo and AlphaFold2.
My understanding is that Alpha Go did begin with information about previous
games but after this, it played against itself and became significantly better.
AlphaFold2 relied perhaps completely on knowledge of
Hi Jack, was the dewar shipped on 1st April and just arrived? You can
buy the CX100 also as CXR100 and there you can replace the adsorbent
material. Looks like this.
Dear Dale,Yes, good point. Let's stop bending over backwards to come up with faux PDB compatibility and focus on making mmCIF better.There are struct_conn records that describe the linkages. This is enough to reconstruct the connectivity. There is an ongoing debate on how to capture the restraints
We use aquarium gravel for this purpose. It does not have the fine
dust-like particles that normal construction gravel might.
On 12/4/20 11:42 AM, Nukri Sanishvili wrote:
Hi John,
I think I know what might have happened:
Many of the MX beamlines at the APS use some sort of filler in the
hey jack,
our experience with these "logistics" people is that you'll probably need to
buy a new dewar ;-)
cheers
jon
Von: CCP4 bulletin board Im Auftrag von Tanner, John J.
Gesendet: Freitag, 4. Dezember 2020 17:04
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Tiny rocks on my CX100 shipping
This suggestion violates a basic principle of data base theory. A
single data item cannot encode two pieces of information. The whole
structure of CIF falls apart if this is done.
Does the new PDB convention contain a CIF record of the link that
bridges between the protein chain and
The Joyce Laboratory, Henry M. Jackson Foundation supporting the Emerging
Infectious Diseases Branch, Walter Reed Army Institute of Research have
openings for two postdoctoral positions and a Lab Manager position in
Structural Biology of Emerging Infectious Diseases. One postdoctoral position
Interesting observation. In our home X-ray lab, we constructed a liquid
nitrogen dumping station from a large garbage can filled with sand to about 12
inches. To keep the sand out of the dewars we topped the sand with a large wad
of screen-door netting. All items can easily be purchased from a
Run it for more cycles. Doesn't take long to drift far enough for it to
not find its way back when you turn x-ray back on.
This isn't just a problem in refmac, or phenix, or x-plor, or even MD
programs like AMBER. The problem is that in order to make a structure
fit into density you have to
Hi John,
I think I know what might have happened:
Many of the MX beamlines at the APS use some sort of filler in the
containers where the LN2 is dumped. If I remember correctly, one of the
beamlines is using fine gravel for this purpose. Also, it is required that
before shipping, the dewars are
It does not look like absorbent material and why should it be outside
the dewar and not all over the pucks?
I concur with Jürgen - it does look like gravel.
Às 16:18 de 04/12/2020, Jurgen Bosch escreveu:
That looks like gravel from the driveway where the dewar was tossed
around
Jürgen
On
We’ve had issues with the adsorbent material inside a dewar peeling out as
small particles but they were white in color. Not sure it’s the same.
If the dewar is defective the stuff will ultimately find its way to and gum up
the goniohead motors, so it’s important to address this.
Thierry
Hi John,
These look like real pebbles. If so, they would not word as an absorbent.
It looks more like a bad joke. Was the FedEx driver expecting some kind of
Thanksgiving gift from you? Wait till Christmas time then to see the real
surprises...
Best,
Nukri
On Fri, Dec 4, 2020 at 10:05 AM Tanner,
That looks like gravel from the driveway where the dewar was tossed around
Jürgen
> On Dec 4, 2020, at 11:04 AM, Tanner, John J. wrote:
>
> When we opened our CX100 shipping dewar returned from APS via FedEx this
> week, we observed what appears to be tiny rocks on the rim below the foam
>
When we opened our CX100 shipping dewar returned from APS via FedEx this week,
we observed what appears to be tiny rocks on the rim below the foam neck core:
https://www.dropbox.com/s/ky09a1vbm9t0mrl/CX100withrocks.png?dl=0
Has anyone seen this before? Is this perhaps the absorbent material
On Fri, 4 Dec 2020 at 09:21, Luca Jovine wrote:
>
> Yes Tristan, that would be even better - also because such an Ag1, Ag2,…
> system could conveniently fall back on a single-character chain A, when
> generating legacy PDB format files from the mmCIF ones.
mmCIF already has two sets of
I think the results from AlphaFold2, although exciting and a breakthrough are
being exaggerated just a bit. We know that all the information required for
the 3D structure is in the sequence. The protein folding problem is simply how
to go from a sequence to the 3D structure. This is not a
Dear all,
for those still interested in experimentally determined structures (maybe to
complement predictions? ;-)
we have a post-doctoral researcher position to join the Klaholz group at the
Centre for Integrative Biology, IGBMC, Illkirch, France:
The subject line for Isabel's email is very good.
I do have a question (more a request) for the more computer scientist oriented
people. I think it is relevant for where this technology will be going. It
comes from trying to understand whether problems addressed by Alpha are NP, NP
hard, NP
Hi all,
Can someone point me to cases of glycoprotein structures in the PDB for which the old (traditional?) system of naming N or O linked chain was found inadequate? Thanks.
Stay safe,
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer
Hi Frank,
Yes, until CASP7 (back in 2006), I used to like saying that there are many more
ways to make a homology model worse than the starting template than to make it
better, and that homology modelling programs were very good at finding them!
After seeing that at least some models (e.g.
Dear all,
on behalf of the organisers, I would like to draw your attention to a
workshop on electron crystallography, taking place December 17th
2020. Its purpose is to update of developers and users in the field
with the current state of their research.
You find more information and a link to
Hi Tristan and all,
I totally agree that randomly naming the glycan chains is going to give users
headaches. But using more than 2 letters would make the entry incompatible
with the PDB format, which I wish will remain as a download option for as long
as possible.
How about restricting the
I guess that also means that AlphaFold has learnt the
crystal-structure-ness that older homology methods never achieved -
which is why (anecdotally?) a "better" homology model tended to give
worse MR performance than the "worse" template?
(Or something like that, I'm parrotting what I
I thought I might be able to add a little to this conversation as I performed
some MR runs as part of the CASP14 High Accuracy analysis. There were 30
targets with reflection data. Of these, AlphaFold2 models could be used to
directly solve 24 structures after converting
RMS error predictions
In defence of experimental science, may I also suggest that the models
AlphaFold2 and other predictors worked on were derived from sequences for which
they knew a well-defined structure is possible. Much of the work we do is
exactly on taking unwieldy sequences with disordered elements,
Hi James,
One really interesting (and to me surprising) aspect of how well AlphaFold2
does is that it does really well without actually understanding chemistry and
physics. (John Jumper from DeepMind talked about choices of deep learning
model types and how they affect the “inductive bias”
AlphaFold2 and its performance are indeed a true breakthrough of
potentially seismic proportion - and will accelerate much of what we are
trying to achieve.
But I feel it is also important to point out that the method principally
relies on experimental data: lots of protein sequences that
Just thinking out loud and following up Tom's post - Could prediction be a
guide to sample preparation for detailed binding studies?
Andy
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Luca Pellegrini
[lp...@cam.ac.uk]
Envoyé : vendredi 4
Exciting times, indeed. I haven’t looked through the results myself, but it
does look like an extraordinary advance. I wonder though how this advance
correlates with ‘understanding’ how proteins folds. Can these outstanding
results be distilled in a set of improved principles for how proteins
Dear all,
We are looking for a highly motivated structural biologist to join the
Crystallography and Protein Engineering Unit at the Spanish National Cancer
Research Centre (CNIO), as a postdoctoral fellow, with a 20 months contract.
The work will be focused on developing a therapeutic molecules
Dear Boaz,
The archimboldo model gives Rot z-score: 8.1, Trans Z-score 13.8
Not sure this matters, as it lacks a few loops that even good old arp/warp can
fill up in ten minutes ;-)
A.
On Dec 4, 2020, at 0:40, Boaz Shaanan
mailto:bshaa...@bgu.ac.il>> wrote:
Just curious, how does the result
Yes Tristan, that would be even better - also because such an Ag1, Ag2,… system
could conveniently fall back on a single-character chain A, when generating
legacy PDB format files from the mmCIF ones.
Exactly for the reason that you pointed out, personally I do not understand the
logic of
btw, if anyone has any leverage to the people making the CASP#14 pages, having
info in acronyms (e.g. GDT) accessible by a simple “mouse over” instead of
re-directing to the explanation page would be handy.
In any case, the Casp web-pages in general, leave quite a bit to be desired for
the
To go one step further: in large, heavily glycosylated multi-chain complexes
the assignment of a random new chain ID to each glycan will lead to headaches
for people building visualisations using existing viewers, because it loses the
easy name-based association of glycan to parent protein
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