On 12/08/2011 00:30, David Schuller wrote:
link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
Ferric C. Fang Arturo Casadevall
Retracted Science and the Retraction Index
Infec. Immun. doi:10.1128/IAI.05661-11
Abstract: Articles may be retracted when their findings are no longer
considered
PIR is fairly similar to Fasta, from addled memory the format is...
protein name;
empty line
MPREIL...rest of amino acid sequence with an optional asterisk to mark the
sequence end.
Tony
Sent from my iPhone
On 12 Aug 2011, at 09:14, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Can
That's what I had
protein
GSP etc
...
SEN*
On 12 Aug 2011, at 09:19, Antony Oliver wrote:
PIR is fairly similar to Fasta, from addled memory the format is...
protein name;
empty line
MPREIL...rest of amino acid sequence with an optional asterisk to mark the
sequence end.
I was missing the semicolon, but it still fails
On 12 Aug 2011, at 10:12, Antony Oliver wrote:
Interesting iPhone formatting things going on... Let's try again...
First line is greater than symbol followed by some text about your
protein then closed with a semicolon. The next line is
NBRF/PIR Format:
A sequence in PIR format consists of:
1. One line starting with
1. a ** (greater-than) sign, followed by
2. a two-letter code describing the sequence type (P1, F1, DL, DC, RL,
RC, or XX), followed by
3. a semicolon, followed by
4. the sequence
Thanks Suku - forgot about the P1, F1 stuff.
Still don't understand why you just can't use the simpler FASTA format with all
these programs, or even just a plain text file!
Tony.
Sent from my iPhone
On 12 Aug 2011, at 10:18, sukanta mondal
Dear Phil,
I remember one case where reading a sequence file in PIR format failed,
although I did my best to have the right format. It turned out, that the
error message about the wrong PIR format was misleading - the real
cause was a non-standard amino acid letter, in this case a X. Maybe,
A few words on obsoleted entries and validation reports:
OBSOLETE ENTRIES
Obsolete entries remain available to the public through the PDB ftp archive at
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/.
For example, for entry 1F83, you can access the coordinate file at
I think you'll find it works better if you use Fasta format:
http://en.wikipedia.org/wiki/FASTA_format
Chris
From:
Phil Evans p...@mrc-lmb.cam.ac.uk
To:
CCP4BB@JISCMAIL.AC.UK
Date:
08/12/2011 01:16 AM
Subject:
Re: [ccp4bb] Another paper structure retracted
Sent by:
CCP4 bulletin board CCP4BB
.
__
From: Phil Evans p...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Date:
08/12/2011
01:16 AM Subject: Re: [ccp4bb] Another paper structure retracted Sent
by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK
--
Can anyone get this server to work
Phil,
The sever was developed by Chris. Currently, Abhinav is taking care of it.
If you have any questions, you may contact Abhinav Kumar at JCSG.
Kevin
On Fri, Aug 12, 2011 at 1:14 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Can anyone get this server to work? For me it keeps complaining
The server has always been available to everyone.
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 08/12/2011 11:10 AM, Kevin Jin wrote:
I seriously think this sever should be available to folks. It is very
helpful for most students.
Kevin
To make my idea a little bit clearer, the reviewers first make the
acceptance decision just based on the paper itself, on the condition the
coordinate matches the description of the paper. Then the editor promises
the publication date and the pdb can be subjected to final quick review,
either by
On 11/08/11 09:13, Nian Huang wrote:
To make my idea a little bit clearer, the reviewers first make the
acceptance decision just based on the paper itself, on the condition the
coordinate matches the description of the paper. Then the editor
promises the publication date and the pdb can be
What about going on a different route ? If the author name will be
confident as well it may cause the community to judge the scientific
part by itself without relating identities and locations. In that case
you may even allow the release of coordinates.
Another problem that may rise from
Any structure deposited at the PDB should be peer-reviewed by a
crystallographer before acceptance by the PDB and his name should be
asociated to the pdb. This job cannot be done by the pdb team but a
crystallographer, not working in the field of the depositor to avoid
conflict, could detect
Perhaps paper and structure should be peer-reviewed independently, and only
when both have been given the green-light should both be released,
simultaneously.
I don't see why we should be especially precious about reviewing structural
data - we gladly hand functional data, protocols, etc to
Surely in this ''modern age data could be uploaded to review server whereby
a reviewer could be given privileged access - to be able to see the model and
maps, via something like AstexViewer, to gauge the quality and reliability of
modelling - without actually getting the PDB coordinates or
Dear all
Does anybody have the list (pdb as well as structure factors) of all retracted
structures?
regards
Garib
On 10 Aug 2011, at 22:01, David Schuller wrote:
Time to fuel up the gossip engines for the approaching weekend:
2011/8/11 Antony Oliver antony.oli...@sussex.ac.uk
Surely in this ''modern age data could be uploaded to review server
whereby a reviewer could be given privileged access - to be able to see the
model and maps, via something like AstexViewer, to gauge the quality and
reliability of modelling
Message below...
Dear Nat,
I think this has actually been implemented, at least on the European side of
things. I've recently uploaded some structures to the PDB, via the EBI's
deposition service, and was given a link to the ePDB, with this very useful
information. Admittedly, I should have
It is my understanding that there is no retracted category in the
wwPDB. Models are obsoleted, usually with a replacement but sometimes
without. I don't know of a way to distinguish between those models obsoleted
for gross error and those simply replaced by one of higher quality. Surely
this
And there's yet another one in today's Nature -- the paper hasn't been
retracted completely but the structural conclusions have:
http://www.nature.com/nature/journal/v476/n7359/full/nature10281.html
Corrigendum: Migrastatin analogues target fascin to block tumour metastasis
Again, the PDB
that nobody cited the structural aspect of
the paper.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Dale Tronrud
Sent: Thursday, August 11, 2011 18:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another paper structure
A quick glance at the header of the PDB file shows that there is one glaring
discrepancy between it and the table in the paper that hasn't been mentioned
yet in this forum. The data completeness (for data collection) reported in the
paper is 95.7%, but in the header of the PDB file (actually,
On Thu, Aug 11, 2011 at 9:40 AM, Diana Tomchick
diana.tomch...@utsouthwestern.edu wrote:
A quick glance at the header of the PDB file shows that there is one
glaring discrepancy between it and the table in the paper that hasn't been
mentioned yet in this forum. The data completeness (for data
On 11 Aug 2011, at 17:40, Diana Tomchick wrote:
A quick glance at the header of the PDB file shows that there is one glaring
discrepancy between it and the table in the paper that hasn't been mentioned
yet in this forum. The data completeness (for data collection) reported in
the paper is
I agree with Prof. Tomchick: if the point of your paper is your crystal
structure of
the binding of a ligand to a protein you should include a figure with the omit
map
(displayed without a cover radius) that convinced you that binding took
place. I
prefer that map over some simulated,
Dale, This is exactly the conversation I just had with my student Jason,
right on!
The paper we are writing just now, this is figure 1.
But I always get rejected by Nature, so go figure.
On Thu, Aug 11, 2011 at 1:25 PM, Dale Tronrud det...@uoxray.uoregon.eduwrote:
I agree with Prof. Tomchick:
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria Borgstahl
[gborgst...@gmail.com]
Sent: 11 August 2011 19:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another paper structure retracted
Dale, This is exactly the conversation I just
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another paper structure retracted
Dale, This is exactly the conversation I just had with my student Jason, right
on!
The paper we are writing just now, this is figure 1.
But I always get rejected by Nature, so go figure.
On Thu, Aug 11, 2011 at 1:25 PM
of the Erdos number calculation. How many publications
are each of us away from this. Is anyone safe.
Colin :(
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David
Schuller
Sent: 10 August 2011 22:01
To: ccp4bb
Subject: [ccp4bb] Another paper structure retracted
Time to fuel up
process.
J
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria
Borgstahl [gborgst...@gmail.com]
Sent: 11 August 2011 19:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another paper structure retracted
Dale, This is exactly
@JISCMAIL.AC.UK] On Behalf Of Gloria
Borgstahl [gborgst...@gmail.com]
Sent: 11 August 2011 19:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another paper structure retracted
Dale, This is exactly the conversation I just had with my student
Jason, right on!
The paper we are writing just now
publications
are each of us away from this. Is anyone safe.
Colin :(
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David
Schuller
Sent: 10 August 2011 22:01
To: ccp4bb
Subject: [ccp4bb] Another paper structure retracted
Time to fuel up the gossip engines
Aug 2011 16:42:34 -0500
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Jacob Keller
j-kell...@fsm.northwestern.edu)
Subject: Re: [ccp4bb] Another paper structure retracted
To: CCP4BB@JISCMAIL.AC.UK
Do reviewers ever get taken to task for these things? Don't they share
link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
Ferric C. Fang Arturo Casadevall
Retracted Science and the Retraction Index
Infec. Immun. doi:10.1128/IAI.05661-11
Abstract: Articles may be retracted when their findings are no longer
considered trustworthy due to scientific misconduct or
I think they fudged the data in this paper...
JPK
On Thu, Aug 11, 2011 at 6:30 PM, David Schuller dj...@cornell.edu wrote:
link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
Ferric C. Fang Arturo Casadevall
Retracted Science and the Retraction Index
Infec. Immun. doi:10.1128/IAI.05661-11
Time to fuel up the gossip engines for the approaching weekend:
http://www.sciencedirect.com/science/article/pii/S096921260800186X
RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus
Bound to the G-Protein Dimer G?_1 ?_2
Structure, Volume 16, Issue 7
On the surface it doesn't seem as bad as others, i.e., it does not
seem to be a real fake--perhaps just a strong form of wishful thinking
and creative density interpretation. I wonder what would be a good
metric in which to establish a cutoff for present/not present in
density. CC, maybe?
Jacob
CC alone wouldn't be totally sufficient. CC is scale independent. For
example, if you compare two very weak densities, say visible at below 0.1
sigma, and If these densities are similar enough then you will still get
good CC.
Therefore it's good to use CC and map values together. This is exactly
For some ideas on this see my presentation to the last CCP4 study weekend
(with some further ideas in Acta D, to be published):
http://www.cse.scitech.ac.uk/events/CCP4_2011/talks/tickle.pdf
Cheers
-- Ian
On Wed, Aug 10, 2011 at 10:35 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Just another example of where it would have been good for the reviewers to
get access to the data during the review process... and where at least one
of the reviewers *should* be a protein crystallographer...
Filip Van Petegem
On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu
I've made a quick look at the model and the paper - and it doesn't
need more than a quick look. The description of the model in
the paper sounds great. The problems in the model are clear. My
favorite is the quote Trp-477 of PTH1R makes several van der Waals
contacts with Trp-339 and Lys-337
Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable
but not quite as bad.
Sorry,
Dale Tronrud
On 08/10/11 15:45, Dale Tronrud wrote:
I've made a quick look at the model and the paper - and it doesn't
need more than a quick look. The description of the model in
the
The paper with this structure was published in the year 2008, following
which, the PI and coPIs who co-authored the paper would have submitted
grants using this information as preliminary data. It is possible some
of these grant applications may even have got funded at the expense of
other
I Agree with the idea of adding crystallographer reviewers. But accessing to
data is not feasible unless there is a good way to protect authors. For
example, the editor should agree to publish the paper swiftly in advance
before the data become accessible to reviewers.
In any case, the flaw of
the editor should agree to publish the paper swiftly in advance before the
data become accessible to reviewers.
This seems to miss the point - how is the reviewer then supposed to judge
the map?
BR
Nian
On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem
filip.vanpete...@gmail.com
On Wednesday, 10 August 2011, Nian Huang wrote:
I Agree with the idea of adding crystallographer reviewers.
But accessing to data is not feasible unless there is a good way
to protect authors.
Disagree.
The data supporting a paper's claims should always be made available
to the reviewers.
The reviewers who wish to get access to raw data should reveal their
identity by signing the report!
-Sankar
On Thu, Aug 11, 2011 at 10:28 AM, Ethan Merritt merr...@u.washington.eduwrote:
On Wednesday, 10 August 2011, Nian Huang wrote:
I Agree with the idea of adding crystallographer
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