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 pafon...@gmail.com wrote:
What about structures that are obviously wrong based on inspection of the
density, but no one has bothered to challenge yet? The
16-May-2014
Dear Patrick,
Proteopedia [http://proteopedia.org] uses exactly the same style for
referencing published material.
Proteopedia allows for the easy insertion of Pubmed and DOI references by only
requesting from the user to enter the Pubmed or DOI ids. We have extended the
same
Hi Joel and Jaime - very nice to hear from you. I hope everything is going
well in Rehovot.
Proteopedia is the natural place to put comments etc. However it might
look more natural if there was more info there in the first place - ie if
people gave more explanation about the significance of
...@york.ac.uk
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 14:28
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
249GB? That's a whole lot of DVDs!
On 14 May 2014 14:08, MARTYN SYMMONS
martainn_oshioma...@btinternet.commailto:martainn_oshioma
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
the coefficients,
we can work out when the PDB takes over the present universe. This would be
time to retire.
Can anyone do this?
Thanks
Colin
From: James Holton [mailto:jmhol...@lbl.gov]
Sent: 14 May 2014 16:19
To: ccp4bb
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
. Perhaps this is the
sort of thing that could work for structural data?
cheers
Martyn
From: Ethan A Merritt merr...@u.washington.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's just a Technical Comments section - an obvious concern
would be the signal/noise in the comments themselves. I'm sure PDB
would
that could work
for structural data?
cheers Martyn
From: Ethan A Merritt merr...@u.washington.edu To:
CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's
for discussing the literature, is currently
under testing. Perhaps this is the sort of thing that could work
for structural data?
cheers Martyn
From: Ethan A Merritt merr...@u.washington.edu To:
CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes
A Merritt
merr...@u.washington.edumailto:merr...@u.washington.edu
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's just
biological community.
all the best
Martyn
From: Zachary Wood z...@bmb.uga.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 15 May 2014, 14:47
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
Adding to Tim’s comment, I would not expect a tremendous
:22
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's just a Technical Comments section - an obvious concern
would be the signal/noise in the comments themselves. I'm sure PDB
would not relish having to moderate
@JISCMAIL.AC.UK] On Behalf Of Joel
Sussman
Sent: Donnerstag, 15. Mai 2014 16:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
15-May-2014
Dear Martyn
Proteopedia's (http://proteopedia.org) goal goes well beyond just
education - it is aimed at Structural Biology
A Merritt merr...@u.washington.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's just a Technical Comments section - an obvious concern
would
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
15-May-2014
Dear Martyn
Proteopedia's (*http://proteopedia.org http://proteopedia.org*) goal
goes well beyond just education - it is aimed at Structural Biology and non
Structural Biology Community
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart patr...@douglas.co.uk
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.
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
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
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
of the feedback by the rest of the community
would sort all problems out, provided there is enough participation.
Jose
-Original Message-
From: CCP4 bulletin board on behalf of Zachary Wood
Sent: Thu 5/15/2014 7:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000
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
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 and
;)
*From:* Jon Agirre jon.agi...@york.ac.uk
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 14 May 2014, 14:28
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
249GB? That's a whole lot of DVDs!
On 14 May 2014 14:08, MARTYN SYMMONS martainn_oshioma...@btinternet.com
@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to=CCP4BB@JISCMAIL.AC.UK]
*On Behalf Of *mesters
*Sent:* Mittwoch, 14. Mai 2014 14:42
*To:*
CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure
=1to=CCP4BB@JISCMAIL.AC.UK]
*On Behalf Of *mesters
*Sent:* Mittwoch, 14. Mai 2014 14:42
*To:*
CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to
=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure
2014 14:42
*To:*
CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to
=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure ended up as number 100.000?
- J. -
Am 14.05.14 10:42, schrieb battle
:* Mittwoch, 14. Mai 2014 14:42
*To:*
CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to
=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure ended up as number 100.000?
- J. -
Am 14.05.14 10:42
@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1;
to
=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure ended up as number 100.000?
- J. -
Am 14.05.14 10:42, schrieb battle:
The Worldwide Protein Data Bank
be clearly marked.
Debasish
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark
Wilson
Sent: Wednesday, May 14, 2014 12:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone
Hi Tim,
Getting to Eric's point
@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure ended up as number 100.000?
- J. -
Am 14.05.14 10:42, schrieb battle:
The Worldwide Protein Data Bank (wwPDB) organization is proud to
announce
that the Protein Data
://mail.google.com/mail/?view=cmfs=1tf=1to
=CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
Amazing, great!
And, which structure ended up as number 100.000?
- J. -
Am 14.05.14 10:42, schrieb battle:
The Worldwide Protein Data Bank (wwPDB) organization
On Wed, May 14, 2014 at 10:26 AM, Mark Wilson mwilso...@unl.edu wrote:
Getting to Eric's point about an impasse, if the PDB will not claim the
authority to safeguard the integrity of their holdings (as per their
quoted statement in Bernhard's message below), then who can?
I think this may in
As long as it's just a Technical Comments section - an obvious concern
would be the signal/noise in the comments themselves. I'm sure PDB
would not relish having to moderate that lot.
Alternatively PDB can overtly link to papers that discuss technical
issues that reference the particular
Hi Nat,
I agree that journals should be doing the heavy lifting here, for the
reasons that you note. I also want to be clear that I believe the PDB is a
crowning achievement of transparency and open access in the sciences,
which is one reason that I am so concerned about this issue. I am in no
On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
As long as it's just a Technical Comments section - an obvious concern
would be the signal/noise in the comments themselves. I'm sure PDB
would not relish having to moderate that lot.
Alternatively PDB can overtly link to papers that
;)
*From:* Jon Agirre jon.agi...@york.ac.uk
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 14 May 2014, 14:28
*Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
249GB? That's a whole lot of DVDs!
On 14 May 2014 14:08, MARTYN SYMMONS
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
The policy doesn't say you can supersede someone else's entry.
It says you can deposit your own version, if you have a publication.
Then there will be two bogus structures instead of one. Pretty soon
the PDB will start to look like one of the
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