oordinates have been modelled carelessly that I would like to avoid!
Obviously, I will discuss this openly in the publication, and
only rely on features that are unambiguous for my conclusions,
but it would be good to know peoples thoughts on what they would
do or expect to see.
ve been modelled carelessly that I
> would like to avoid!
>
> Obviously, I will discuss this openly in the publication, and only rely on
> features that are unambiguous for my conclusions, but it would be good to
> know peoples thoughts on what they would do or expect to see.
>
> Best
>
> Matthew.
>
>
>
d be good to know
peoples thoughts on what they would do or expect to see.
Best
Matthew.
From: Karplus, Andy
Sent: 06 March 2025 01:02
To: Matthew Snee ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IDS in PDB
Hi Matthew.
Your post reminds me of some
From: Karplus, Andy
Sent: 06 March 2025 01:02
To: Matthew Snee ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IDS in PDB
Hi Matthew.
Your post reminds me of some work my student did earlier related to the question of what to consider as “too high a B-factor.” Back in 2003 a refe
AC.UK
Subject: Re: [ccp4bb] IDS in PDB
[This email originated from outside of OSU. Use caution with links and
attachments.]
Thankyou for those links
One of those papers seems to basically say that atoms that accumulate
stratospheric B factors are "speculative", but Im working on an exa
>
>
>
> --------------
> *From:* CCP4 bulletin board on behalf of Italo
> Carugo Oliviero
> *Sent:* 05 March 2025 16:21
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] IDS in PDB
>
>
> Just wanted to thank you for your remarkable contributi
t the B factors
are certainly not describing the relationship between the model and the data in
a useful way!
Best wishes
Matthew.
From: CCP4 bulletin board on behalf of Italo Carugo
Oliviero
Sent: 05 March 2025 16:21
To: CCP4BB@JISCMAIL.AC.UK
Subject:
Just wanted to thank you for your remarkable contributions to this
discussion.
These are a couple of articles that dive into the issue of unusually large
B-factors: BMC Bioinformatics 2018 19 61 (
https://doi.org/10.1186/s12859-018-2083-8) & Zeit. Krist. 2018 234 73-77 (
https://doi.org/10.1515/zk
Interesting...
Has this got onto the radar (or critical path) of the PDB's mmCIF
working group (or whatever it's called?)
I'm assuming that's where this would go to next, if the downstream
developers are ever going to take it seriously.
Frank
On 04/03/2025 12:21, Alexandre Ourjoumtsev wr
Dear all,
Fully relevant to this discussion, you might noted that a couple of years ago,
we (Vladimir Lunin and myself) argued
[ https://journals.iucr.org/m/issues/2022/06/00/tf5001/ |
https://journals.iucr.org/m/issues/2022/06/00/tf5001/ ]
that, when describing an atomic model, each atom s
My personal observation is that people handle the unobserved electron
density sections in three ways - assuming sufficient resolution (i.e.
ignoring ripple effects of truncate Fourier transformations at ~2.9A)
a) Leave it out. Usually a surface loop.
b) Refine B factors - hopefully at suffici
08ec2c4efb208-dmarc-requ...@jiscmail.ac.uk>
Sent: 04 March 2025 09:06
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IDS in PDB
Dear Pavel and Oliverio,
In our group we have had recent discussion about this issue, and I second
Pavel's suggestion to introduce such a confidence measure.
W
I third this idea - it's about 4 decades overdue, but got pressing with
the CryoEM revolution, and is now existential after AlphaFold.
Our use case (large collections of near-identical ligand-bound
structures) also really really needs this - a way to capture confidence
that stems from far more
Dear Pavel and Oliverio,
In our group we have had recent discussion about this issue, and I
second Pavel's suggestion to introduce such a confidence measure.
When interpreting cryo-EM (but also X-ray crystallography) maps with
models, we often face the problem that we have complete models (tha
Greetings,
It's hard to disagree with this! Resolution, occupancies, and B factors
only indirectly suggest what's visible and what isn't — and they can be
especially difficult to interpret correctly for non-specialists. Perhaps a
local confidence measure — similar to pLDDT for predicted models — c
A brief reflection on IDPs
Increasingly, people with a computer science background are analyzing the
data deposited in the Protein Data Bank. In the case of conformation
disorder analyses, they consider residues that are explicitly stated to be
disordered (the old REMAR 465 records). This is not
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