So, a bit like "Fold-it" but with actual data? :-D
Dr David C Briggs PhD
http://about.me/david_briggs
On 16 May 2014 06:19, "Pavel Afonine" wrote:
>
> What about structures that are obviously wrong based on inspection of the
>> density, but no one has bothered to challenge yet? The TWILIGHT dat
> What about structures that are obviously wrong based on inspection of the
> density, but no one has bothered to challenge yet? The TWILIGHT database
> helps some, if that counts, but it doesn't catch everything.
>
How about this utopia.. Imagine PDB has two versions: one is the original
data an
For P212121, I would put money on something divisible by 2 for the total
molecules per asu. Anything from 6-12 might be likely. One of the early
structures I worked on had 6 molecules per asu, which was darn near
impossible to find using momomers (at the time). The way it was
eventually solved
Have you tried fixing the molecule that looks correct and searching for others?
You might have greater than one but less than 9 molecules per ASU.
When you do this, try imposing severe restraints on the packing function. This
worked for me in Phaser with a difficult case. My anecdotal experience
Hello everyone,
I am gonna report the mosaicity of my data set as required by the journal.
I processed the data using HKL2000. So I checked the denzo log file. I
found many different mosaicity values. The first one is default input
(0.3), the rest are corresponding to specific images. I think the
Hello all,
I am working on the structure of a small protein in space group P212121.
The protein is monomeric in solution based on gel filtration analysis.
The Matthews Coefficeint program indicates that 9-10 molecules per
asymmetric unit results in ~50% solvent content, while 1 molecule per
asy
Hi,
The research group of Dr. Reza Khayat at the City College of
New York (www.khayatlab.org) is seeking candidate postdoctoral
fellows to study host pathogen interaction using a combination
of cryo-electron microscopy (cryo-EM), X-ray crystallography,
biophysics and biochemistry. The research
TWILIGHT database, PDBREDO database, ... what else I forgot to name? I
wonder why it should be under different brands and names, and not just be
where it belongs to - the PDB?!
Back in 2005 when I (and colleagues) started re-refining the entire PDB (to
test phenix.refine, mostly) and seeing odditi
If one limits such a comment system to authors of PDB structures then you are
closing the door to a lot of potentially good contributors: anyone involved in
analysing protein structures. For instance that can be anyone in the fields of
structural bioinformatics, molecular dynamics, computational
That is an extraordinary case, and it certainly took a huge amount of
work. What about structures that are obviously wrong based on inspection
of the density, but no one has bothered to challenge yet? The TWILIGHT
database helps some, if that counts, but it doesn't catch everything.
-Nat
On T
I may be missing something here, but I don't think you have to rebut
anything. You simply report that someone else has rebutted it. Along the
lines of
Many scientists regard this published structure as unreliable since a
misconduct investigation by the University of Alabama at Birmingham has
con
I agree with Nat. If you think a structure has a problem area, it is much
easier to point it out to the users than to publish a rebuttal.
Comments are easy. Simply state your observation. If you are wrong in your
assessment, I am sure you will receive a fine education from the more learned
ind
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart wrote:
> It seems to me that the Wikipedia mechanism works wonderfully well. One
> rule is that you can't make assertions yourself, only report pre-existing
> material that is attributable to a "reliable published source".
>
This rule would
It seems to me that the Wikipedia mechanism works wonderfully well. One
rule is that you can't make assertions yourself, only report pre-existing
material that is attributable to a "reliable published source".
It's immediately obvious when something is controversial. Here's the first
para of the
PhD studentships in a collaborative project "Tackling Mycobacterium abscessus
infection in Cystic Fibrosis"
http://www.jobs.cam.ac.uk/job/3954/
(see "Position 3" for the structural biology project)
The Departments of Biochemistry and Medicine, University of Cambridge, are
pleased to offer 3
Dear Jaime and Joel,
Perhaps an easier solution would be to get the PDB to put an obvious link on
each entry directing the user to the Proteopedia site for discussion and
additional details. I would personally prefer a comments/discussion section on
the PDB page, but as long as one is easily
Maybe a prominent link in the summary page of e.g. PDBe 2a01 would help.
So far, you need to go there and expand Links -> pdb_redo -> links ->
Proteopedia to get to the corresponding warning.
http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html#
http://www.cmbi.ru.nl/pdb_redo/a0
As one of the responsible people for the pdbwiki project I feel I should
comment on this one. We went out of business simply for lack of
resources, it was difficult to keep things up-to-date and specially it
was very difficult to combat spam. So in the end we decided to shut down
the project.
Dear Zachary
I once suggested this sort of discussion forum to a PDB PI as a possible
service that could be a ' validation fight-club ' - which suggestion was not
well received ;) But as you say it is down to setting the correct professional
tone.
One thing that would allow a visual discussio
15-May-2014
Dear Martyn
Proteopedia's (http://proteopedia.org) goal goes well beyond just education
- it is aimed at Structural Biology and non Structural Biology Community and it
would be pleased to be a forum for discussion of structures that are
questionable. There are now over 2,600 regis
Adding to Tim’s comment, I would not expect a tremendous amount of spurious
comments about a single PDB out of 100,000 unless there was a problem.
Especially if the Pubmed Commons model was applied, and only depositors could
comment. I would assume this would be very beneficial, given that we a
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Hash: SHA1
Dear all,
isn't the ccp4bb a very good example that spam may not be such an
issue for a discussion platform on structures in the PDB? There is a
great variety of opinions, some to agree with, some to disagree, but
all of them interesting and contribut
I agree with Martyn,
Pubmed Commons could be a great model. I believe you have to be a published
author to obtain an account. It might cut down on some of the spam/noise if the
PDB adopted such a model for depositors.
Best regards,
Z
***
Zachary
Roger
Thanks for this reply. Sometime in the next millennium I guess.
I did get replies from several well wishers implying that it would be a good
idea if I retired as soon as possible.
More usefully, Marjolein Thunnissen reminded me of the article
http://www.uic.edu/labs/caz/downloads/Abad-Zap
Dear CCP4bb,
Does anyone know who (if anyone) supports Crystal Miner (Emerald / Decode).
Kind Regards,
David
David Hargreaves
Associate Principal Scientist
_
AstraZeneca
Discovery Sciences, Structure & Biophysics
Mereside, 50F4
I agree some forum for community annotation and commenting would be a good
thing for users of structural data.
There was an attempt to do that with the pdbwiki project which was a community
resource for the bioinformatics community. Unfortunately pdbwiki has now folded
(see http://pdbwiki.org/)
A logarithmic plot of cumulative entries to the PDB is approximately linear
and shows a growth rate of about 15% per year. That means it doubles in
size about every 5 years at current growth rate.
Roger Rowlett
On May 15, 2014 4:23 AM, "Colin Nave" wrote:
> From James's figure, assuming perfect
Hello,
I also agree that the right order of things would be the journals
taking action (i.e. retracting and commenting on why), then informing
the pdb which structures are associated with a retraction - for the
simple reason that very likely many readers take conclusions in
made-up public
>From James's figure, assuming perfect lossless compression, the information
>content of the PDB is 20GB or about 2X10**11 bits
The information content of the universe has been estimated to be 2**305 bits or
10**92 bits (this might or might not be changing).
The PDB is said to be growing exponent
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