Following up what Kay Diederichs recently wrote, each page of Proteopedia that
contains user added comments have a visible banner on the top,
e.g. see: https://proteopedia.org/w/2bs2
n.b. these user added comments are all signed, i.e. they are NOT anonymous, so
it is a good location to consider u
We faced a similar situation recently where our molecular replacement
suggested 2 molecules in the asymmetric unit but the B factors of the
second chain were twice as large as the first protien chain. At a
resolution of 1.8 Å2 you could see the electron density for both chains. We
performed ARP/wAR
What about AI doing our job in the future?
https://www.nature.com/articles/d41586-019-01357-6?utm_source=Nature+Briefing&utm_campaign=4c1d57fdf3-briefing-dy-20190722&utm_medium=email&utm_term=0_c9dfd39373-4c1d57fdf3-44201949
Best Regards
Nishant
On Mon, 22 Jul 2019 at 11:30 PM,
Dear Harry
We will be shortly making it mandatory for depositors to provide a value for at
least one of the merging statistics (Rmerge, Rpim, CC1/2 etc..). Most
depositors do, but we want to ensure that all depositors do provide at least
one value for a merging metric.
We would welcome
I'd like to point out that the MAchine Recognition of Crystallization Outcomes
(MARCO) makes a start to 'deep learning applied to crystallization outcomes',
at least in terms of being able to classify drop images efficiently.
There is obviously more work to be done to correlate these data with
> What about 'deep learning' applied to crystallization outcomes? Can it guide
> individual trials better than intuition? Can it find previously unknown
> promising combinations on a larger scale?
I think several people were well aware of this need for some sort of sound
machine learning alread
> Could there be two versions of each model: a "robustly-observed" and a
"most-likely" version?
We tried/suggested something in this spirit once. Not sure how it was
received
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
Best, BR
++
This is the old question of what a structural model represents. One perspective
is that it represents the things one is certain about above some threshold,
from the crystallographic data and maps alone. The other perspective is that it
represents the most likely guess of what is actually there.
Isnt it most likely that this chain is partially occupied?
Eleanor
On Mon, 22 Jul 2019 at 12:32, wrote:
> Dear Peer,
>
> I did not check, but I expect that atoms with B-factors exceeding 200 Å2
> will not contribute much to the F's at 2.3 Å. A good test might be to
> calculate Rfree's at 4 or 4
Good morning,
We have two relevant job postingings that I would like to share.
Thank you for your attention :)
Artem
https://careers.massbio.org/job/sr-scientistprincipal-scientist-computational-chemistry/49455467/
and
https://careers.massbio.org/job/scientist-enzymology-protein-chemistry/4
Well it is also on the webpage of the entry but I suppose not all eight authors
listed in this field did the crystallography. Since the pdb has not come up
with a set of “contribution” fields to be filled in yet (maybe that would
actually be useful!) the person in charge of the actual submission
On 7/22/19 3:40 AM, Bärbel Blaum wrote:
"As I said, the lead author may not actually be the crystallographer here"
Bärbel
No need to wonder, that info should be in the PDB file header. The
author of the coordinates is not necessarily the same as the author of
the primary reference.
--
===
Dear Peer,
I did not check, but I expect that atoms with B-factors exceeding 200 Å2 will
not contribute much to the F's at 2.3 Å. A good test might be to calculate
Rfree's at 4 or 4.5 Å (no refinement!) to see if the missing protein chain
contributes at low resolution. If it does, I would keep
Proteopedia has this - see
https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures
Kay
On Fri, 19 Jul 2019 17:42:33 +, Bonsor, Daniel
wrote:
>Would it be possible to add a public annotations section to the PDB, to allow
>us to potentially flag/warn whoever dow
Hi John
These are great, but the things that make me suspicious are the values of
overall R(merge); these are tucked away in the full reports, rather than
highlighted with all the other structural metrics in the validation sliders. It
would be wonderful to be able to see at a glance where overa
Dear Colleagues,
We are working on a structure where the density for a whole protein
chain (>200 aa) is questionable, since the B-factors exceed 200 Å2 (2.3
Ang resolution). However, the initial difference density map and the
feature enhanced map (normal 2fo-fc map to a minor extend) support t
Dear Daniel
The issues you mentioned are highlighted in the wwPDB validation report
http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf
and global issues with the entry are highlighted in the validation sliders
http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0
The validation sliders ar
You are absolutely right of course, Jacob! I just did that “just for fun”. As I
said, the lead author may not actually be the crystallographer here and if that
is the case it is possible that he would actually appreciate some feedback from
this list. Despite the bad experiences some of us had wi
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