Dear colleagues,
As a community of structural molecular (and, increasingly, cellular) biologists
we are fortunate to have a large collection of well-established, well-managed
and open data resources at our disposal. (Physicists are often impressed when
they learn that a protein structure depos
Hi all,
Following up on this: some time ago, Martyn Winn was kind enough to put the
source of a bunch of old Uppsala Software Factory programs in GitHub:
https://github.com/martynwinn/Uppsala-Software-Factory
It's all unsupported now (I haven't compiled anything in 12 years...) but free
t
Dear all,
Cross-posting this on behalf of Julia Mahamid.
--Gerard
---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk
-- Forwarded message --
Date: Mon, 28 Se
631-286-1339FAX: 1-631-286-1999
=========
On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
There was a case a few years ago (not too many though) where a 1.6 ?
structure had been solved using an incorrect value for the wavelength (~5%
too low, leading to a c
were part of them? Did you wear a Dutch hat?
E
On Thu, 16 Jul 2020 at 12:07, Gerard DVD Kleywegt
wrote:
Hi Eleanor,
Yes, I remember those meetings, when the UK was still an EU member and
Sweden
not yet (so Uppsala couldn't be formally involved) :-)
Did Victor look into this too? I remember
There was a case a few years ago (not too many though) where a 1.6 Å structure
had been solved using an incorrect value for the wavelength (~5% too low,
leading to a cell that was slightly too small for its contents to be
comfortable). It was later corrected so we could compare their validation
Hi Eleanor,
Yes, I remember those meetings, when the UK was still an EU member and Sweden
not yet (so Uppsala couldn't be formally involved) :-)
Did Victor look into this too? I remember Gert doing it. And maybe Tom
Oldfield?
Best wishes,
--Gerard
On Thu, 16 Jul 2020, Eleanor Dodson wro
8-430-8565
email jeffrey.bona...@einsteinmed.org
-Original Message-
From: CCP4 bulletin board On Behalf Of Gerard DVD
Kleywegt
Sent: Wednesday, July 15, 2020 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Quote source inquiry
Well, I've had this in my CSHL X-ray Course tal
Sorry to have taken this matter up in such a visible manner: I noticed
this very wrong formula in someone's paper, and that person then told me
where he had found it. Having landed on that page, I didn't know where to go
For the students:
"someone" = systematic absence of information = 0
If this is the case, why can't we use model B factors to validate our
structure? I know some people are skeptical about this approach because B
factors are refinable parameters.
Rangana
It is not clear to me exactly what you are asking.
B factors _should_ be validated, precisely because they
Dear colleagues,
We are developing a new validation method that takes EM maps and models into
account. In order to understand the potential, the applicability and the
limitations of the method we are looking for good test cases, which turn out
to be surprisingly hard to find.
What we are loo
"Structural biology: it's a vision thing" (inspired by George H.W. Bush)
Two of these were rejected by Comms (for reasons you may not believe) so the
surprising winner is... nr 2! Thanks Nigel!
Thanks again for all your good-humoured contributions!
--Gerard
On Fri, 16 A
Thu, 15 Aug 2019 13:42:10 +0200
From:Gerard DVD Kleywegt
Subject: [OT] Structure-related pun needed urgently
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
sentence/statement/claim/expression to p
ial Science and Engineering
343 Royal Parade
Parkville. VIC. 3052
Australia
Tel +613 9662 7326
Email janet.new...@csiro.au
From: CCP4 bulletin board on behalf of Gerard DVD Kleywegt
Sent: Thursday, August 15, 2019 9:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subjec
42, Gerard DVD Kleywegt wrote:
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
sentence/statement/claim/expression to put in a speech bubble attached
to a life-size bobblehead version of yours truly (don&
r, but
maybe it's a starting point.
-Daniel
On Thu, Aug 15, 2019 at 7:42 AM Gerard DVD Kleywegt
mailto:ger...@xray.bmc.uu.se>> wrote:
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
senten
volve nucleic acids? I’m afraid protein structure puns might
be a bit outside my domain.
— Bill
On Aug 15, 2019, at 4:42 AM, Gerard DVD Kleywegt wrote:
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-rela
Dear CCP4BB-ers,
Once again I turn to you in my hour of need. I *urgently* need a
side-splittingly funny, and ideally punny, structure-related
sentence/statement/claim/expression to put in a speech bubble attached to a
life-size bobblehead version of yours truly (don't ask)!
I know there are
If you have a copy of MOLEMAN2 lying around, you can use the XYz DIstort
command to do exactly this: http://xray.bmc.uu.se/usf/moleman2_man.html#S77
--Gerard
On Mon, 12 Mar 2018, Franck Coste wrote:
Hi all,
I'd like to apply an improper rotation matrix to PDB files but it seems it's
not al
Dear colleagues,
EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand
usage of its resources (there are several dozen, including UniProt, Ensembl,
ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you
to forward this request within your departmen
The main issue is that carboxyls seem to be invisible and Coot tries to fit
them as though the map had them there
Well, if the atoms are part of the model, then Coot will try to fit them to
the "data." I routinely chop off GLU and ASP side-chain when modelling into
cryo-EM maps (that's what th
Hi all,
We are seeking to recruit a Team Leader for the Cellular Structure & 3D
Bioimaging team at the European Bioinformatics Institute (EMBL-EBI) located at
the Wellcome Trust Genome Campus near Cambridge in the UK. EMBL-EBI is a
world-leader in archival and dissemination of 3D biomacromolec
Hi all,
After tirelessly serving the scientific community with (mostly) beautiful maps
for two decades, the Uppsala Electron Density Server (EDS;
http://eds.bmc.uu.se/) is now reaching the end of its life (in fact, it has
been living on borrowed time for several years already). Some time in 20
Hi all,
Applications are invited for a course on Structural Bioinformatics that is
being organised by EMBL-EBI and that will be held from 12-16 October 2015.
This course will explore bioinformatics data resources and tools that are
available for the interpretation and exploitation of biomacrom
It works again now. Sorry for the inconvenience.
--Gerard
On Tue, 9 Jun 2015, Xiao Lei wrote:
Hi All,
I am trying to get electron density map of some pdb structures, I know
there is a database called "Electron density server" (EDS
http://eds.bmc.uu.se/eds). But somehow these days I can not c
Dear CCP4BB-ers,
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is urgently seeking
to recruit an experienced scientific programmer to develop and maintain
validation and analysis tools for biomacromolecular structure data. Applicants
should ideally be established structural biologis
Hi all,
We have an opening for a scientific programmer to work (1) on the
incorporation of small-angle scattering (SAS) data into the wwPDB Deposition
and Annotation system and (2) on presentation and dissemination of SAS data
through the PDBe website. The project (which will last for 18 month
Hi all,
We are looking to recruit an expert structural biologist (with experience in
structure determination) to join the Protein Data Bank in Europe curation team
(PDBe: pdbe.org) at the European Bioinformatics Institute (EMBL-EBI,
Cambridge, UK) as a Scientific Database Curator. The work inv
Hi all,
We are looking to recruit an experienced and motivated "Scientific Programmer
Bioimaging & EMPIAR" to join the Protein Data Bank in Europe (PDBe) team at
the European Bioinformatics Institute (EBI) located on the Wellcome Trust
Genome Campus near Cambridge in the UK.
PDBe has recentl
Hi all,
This is just a quick reminder that the application period for our 3 vacancies
is closing this Friday at midnight. We are seeking to recruit:
- two curators (PDB/EMDB) -
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=53264&aid=15470
- one web front-end developer -
http://ig1
Hi all,
We are looking to recruit *TWO* expert structural biologists to join the
Protein Data Bank in Europe curation team (PDBe: pdbe.org) at the European
Bioinformatics Institute (EMBL-EBI, Cambridge, UK) as Scientific Database
Curators. The work involves annotating preliminary PDB and Elect
Hi all,
We are looking to recruit an experienced Web Front-End Developer with an
interest in biological data to work within the Protein Data Bank in Europe
team (PDBe; pdbe.org) at the European Bioinformatics Institute (EMBL-EBI) in
Cambridge (UK).
For more information, please surf to:
h
Dear all,
The EMDB team at the Protein Data Bank in Europe (PDBe; http://pdbe.org) has
two vacancies for scientific programmers to work on an exciting new MRC and
BBSRC funded project to help bridge the worlds of cellular and molecular
structural biology. The project aims to develop:
1) a we
What you want is a test for how well each model agrees with its own map. It
is fair to argue that the model that is more self-consistent (agrees better
with its own map) is the better model. But you won't learn that by
comparing model A to map B.
However, conversely, if your modified model fi
MAPMAN contains several related options, e.g. CEll, SPacegroup, TRanslate and
GTranslate, PAste (see the manual for caveats -
http://xray.bmc.uu.se/usf/mapman_man.html ). Saving as an ASCII file and
editing may also work, if you know what you are doing.
--Gerard
On Tue, 20 May 2014, Edwar
:33 PM, Gerard DVD Kleywegt wrote:
See: http://www.wwpdb.org/news/news_2014.html#06-May-2014
Even if you don't deposit anything, we'll reach the 100,000-entry
milestone with next Wednesday's release :-)
--Gerard
On Fri, 9 May 2014, mesters wrote:
Great, just a few more struct
See: http://www.wwpdb.org/news/news_2014.html#06-May-2014
Even if you don't deposit anything, we'll reach the 100,000-entry milestone
with next Wednesday's release :-)
--Gerard
On Fri, 9 May 2014, mesters wrote:
Great, just a few more structures to deposit and then 100.000 structures to
c
Hi all,
I don't know why my posting about validation reports re-appeared several
times. The mail headers show that all 4 came through the domain ouhsc.edu but
why they would be resent to ccp4bb is not clear, nor why this only happened
with my posting.
--Gerard
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFM
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFM
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFM
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see https://urldefense.proofpoint.com/v1/url?u=http://www.wwpdb.org/news/news_2014.html%2318-March-2014&k=7DHVT22D9IhC0F3WohFM
es.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Gerard DVD Kleywegt
? : CCP4BB@JISCMAIL.AC.UK
Envoy? le : Mercredi 16 avril 2014 19h01
Hi all,
You may not have noticed, but 19 March 2014 was VR Day - the day that new
style wwPDB validation reports for all X-ray structures were made publicly
available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014
The validation-related files for individual X-ray PDB entries can
Dear colleagues,
The wwPDB partners are pleased to announce that X-ray structure validation
reports can now be generated on demand by macromolecular crystallographers by
using the new stand-alone wwPDB validation server.
For the full scoop, see: http://wwpdb.org/news/news_2013.html#27-Novembe
The server has been rebooted and appears to be working again.
--Gerard
On Fri, 25 Oct 2013, Rojan Shrestha wrote:
Hello,
Is EDS (electron density server) dead? In the absence of EDS, how can be mtz
file directly downloaded?
Regards,
Rojan
Best wishes,
--Gerard
**
a bit like having your cake and NOT eating it.
It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.
++Martyn
On 16/09/2013 14:03, Gerard
Dear all,
At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data model
will be required (at the moment, hkl must be unique within the reflection
data, which is logical for merged data but precludes handling o
On Thu, 22 Aug 2013, Gloria Borgstahl wrote:
We have a protein sequence that probably contains OB folds. What is the
best way to search for the top structural homologs to this sequence in the
pdb? G
Hi Gloria,
If you expect decent sequence simnilarity to one or more proteins in the PDB,
an
wwPDB Workshop on mmCIF/PDBx for Programmers
What, why and how?
--
The world of the PDB will be changing rapidly and profoundly over the next few
years. A major change will involve the transition from PDB to mmCIF/PDBx as
the principa
As for Gerard's follow up, I remind him of the immortal wisdom of Jack
Handey:
"Maybe in order to understand mankind, we have to look at the word itself.
Basically, it's made up of two separate words ? "mank" and "ind." What do
these words mean? It's a mystery, and that's why so is mankind."
do, I believe has to do with smell,
and kilometer is hyphenated kilo-meter, no kil-ometer, so the origin
of that word is nothing to do with 'ometer'. Remembering stuff from
your school days help a great deal understanding the world around you ;-)
Best,
Tim
On 06/20/2013 01:14 AM, Gerard DVD
Wait, so a geometer measures ges, an odometer measures ods, and a kilometer
measures kils?
--dvd
On Thu, 20 Jun 2013, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Ed,
to me, an '-ometer' is a device that measures whatever you put in
front of the 'o', so in case of a
Dear colleagues,
I would like to draw your attention to a notification from the wwPDB partners
about "Deposition and Release of PDB Entries Containing Large Structures" -
see:
http://www.wwpdb.org/news/news_2013.html#22-May-2013
There are major changes afoot in the way large struct
LSQMAN aligns just about anything, incl. DNA and RNA -
http://xray.bmc.uu.se/usf/lsqman_man.html
There's a ready-to-use macro that will do all the hard work for you -
ftp://xray.bmc.uu.se/pub/gerard/omac/align_rna.lsqmac - there's one line that
may need editing, it defines the name of the nomi
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit a
junior structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
in some area of structural biology or structural chemistry
If you have an old copy of MOLEMAN (not MOLEMAN2!) lying around, this can be
done very easily (ever since it was programmed on Valentine's Day 1993, in
fact - I even remember who my Valentine was :-) - see:
http://xray.bmc.uu.se/usf/moleman_man.html#S13
- READ your original model (PDB fi
This sounds like a job for SPASM. We used it to find instances of left-handed
helices in the PDB. See:
- SPASM: http://www.ncbi.nlm.nih.gov/pubmed/9917419
- Left-handed helices: http://www.ncbi.nlm.nih.gov/pubmed/15740737
The database for SPASM hasn't been updated for a few years, but it may g
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an
expert structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
in some area of structural biology or structural chemistry
Dear all,
The EDS server was unfortunately down for a number of days. However, as of
yesterday it is up and running again. Apologies for the inconvenience.
http://eds.bmc.uu.se/
--Gerard
**
Hi all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases
new, improved and updated versions of its tools and resources. Below is a
brief description of new features and services that have been released this
summer (or what passes as summer in the UK). As always, t
Hi all,
Plants suffer from DNA damage caused by ultraviolet light in the same way that
humans do. Unlike us though, they cant put on a sunhat (or move to England) to
avoid the suns rays. Read more about how plants sense UV-B light and turn on a
suite of genes to protect their DNA against its d
Because I want all the structures of a particular protein itself, not it's
homologues. I just went through several cycles of reducing E-value down to
If you know the UniProt accession code of your protein, then UniPDB is your
friend - pdbe.org/unipdb
If not, try pdbe.org/fasta where you can
Hi all,
In the past couple of years, Mark Harris in Uppsala has developed a bunch of
programs and servers that are useful for crystallographers, structural
biologists and structural bioinformaticians. Some of his programs are listed
here:
http://xray.bmc.uu.se/markh/programs.html
M
Hi all,
E3 ubiquitin ligase is responsible for flagging proteins for degradation by
transferring ubiquitin from a donor protein onto the molecule to be degraded.
It is activated by phosphorylation of a tyrosine which promotes a huge
conformational change, swinging its RING domain 180 degrees t
A good tool should leave "b" as is: it is ASX (the standard ambiguity
code for ASP or ASN). "j", "o" and "u" are a different matter :-)
http://www.uniprot.org/manual/non_std
"Selenocyteine [sic!] and pyrrolysine are represented in the sequence using
the one-letter codes U for selenocysteine an
Hi Paul,
You saw the wwPDB/CCDC JPG in my PPT at GSK :-)
Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means,
amongst a number of other things, that wwPDB will be allowed to use Mogul in
its validation pipeline and that wwPDB will be allowed to incorporate and
redistribute
Are you an aspiring science communicator who has a wonderful way with words?
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an
enthusiastic 'jack of all trades', to coordinate its outreach activities. We
are looking for someone who will raise the profile of PDBe through
[Cross-posted from the 3DEM mailing list.]
--Gerard
-- Forwarded message --
Date: Wed, 4 Apr 2012 16:34:39 +0100
From: Helen Saibil
To: 3DEM Mailing List <3...@ncmir.ucsd.edu>
Subject: [3dem] CCP-EM positions now available
Dear Colleagues,
We have been awarded a Partnership gr
ure:
http://en.wikipedia.org/wiki/German_humor
Andreas
(still living on Sunday time)
On 02/04/2012 4:03, Gerard DVD Kleywegt wrote:
Dear Manfred,
Outside Germany, such excursions are called "humour". If you are
interested, here is the Wikipedia page for it:
http://en.wikipedia.or
Dear Manfred,
Outside Germany, such excursions are called "humour". If you are interested,
here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour
--Gerard
PS: It was on a Sunday so all levity was perpetrated in people's own time.
Today we'll all be serious again and frown and
http://trololololololololololo.com/
Trollus, Trollum, Trolli, Trollo, Trolli, Trollos, Trollorum, Trollis.
David C. Briggs PhD
Father, Structural Biologist and Sceptic
University of Manchester E-mail:
david.c.bri...@manchester.ac.uk
==
Is it to late to refer to data as if there were more than one of them?
Is it too late to explain the difference between "to" and "too"?
--A much mellowed CD
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has
launched a number of PDB archive browsers in the past two years. These allow
users to explore and analyse what is in the PDB based on concepts and
classifications they are familiar with, such as the EC syste
MOLEMAN2 is your friend.
Stats: http://xray.bmc.uu.se/usf/moleman2_man.html#S50
Plots: http://xray.bmc.uu.se/usf/moleman2_man.html#S57
--dvd
Will you please tell me a server of software which can draw a curve for the
B factor of the atoms in a protein PDB file from the first residue to the
Hi all,
In April we will once again organise the EMBO practical course on
"Computational structural biology - from data to structure to function". The
application deadline is only a week away - 24 February.
For more information about the course and how to apply, surf to:
http://www.e
Hi all,
As many of you know by now, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) regularly produces Quips, short interactive stories about
QUite Interesting Pdb Structures (http://pdbe.org/quips). Quips articles
address biologically interesting aspects of one or more PDB entries fro
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved
and updated versions of its tools and resources twice a year. Now it's time
for the winter update. Below is a brief description of new features and
services. As always, the URL http://pdbe.org will take you
There can be many different reasons why EDS calculates an R-value that is
different from the one reported by the authors - some of these are listed
here: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS
Back in the "dark ages" (actually, the late 90s) we arbitrarily decided to use
a tolerance o
Due to an as yet unspecified "explosion in a network duct in London", the EBI
in Hinxton (where all PDBe services, including deposition, are hosted) is
currently cut-off from its London data centres (through which all EBI web and
ftp traffic is routed). At present, it looks like normal PDBe serv
Hi all,
If you should suffer from Christmas Disease, and you were to cut yourself
while carving the turkey, you could be in trouble! Find out why in the last
episode for 2011 of Quips, PDBe's collection of interactive stories about
QUite Interesting Pdb Structures.
To access this Quips episo
Hi all,
This is to inform PDB/EMDB depositors (note: at PDBe only) and users of PDBe
services (http://pdbe.org/) that we will be operating with a reduced level of
service in the holiday season:
- this week, we will do our best to process entries that are deposited before
Friday, but cannot g
Hi all,
Someone pointed me to this:
http://cdn3.spiegel.de/images/image-287176-galleryV9-qokb.jpg
Apparently, it is a page from this book:
http://www.amazon.co.uk/Science-Ink-Tattoos-Obsessed/dp/1402783604
Personally, if I had to get a tramp stamp, it would obviously be of 1cbs
(http://pdb
Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?
You mean to produce something like this?
http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif
That can be done with LSQMAN - http://xray.b
Hi all,
As you may know, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly
produces Quips, short stories about QUite Interesting Pdb Structures
(pdbe.org/quips). Quips address biologically interesting aspects of one or
more PDB entries, coupled with animated and interactive graphics v
iting before I hit ^X , obviously.
--Gerard
On Tue, 15 Nov 2011, Gerard DVD Kleywegt wrote:
Hi all,
I came across this YouTube clip the other day that is well worth 3 1/2
minutes of your time:
http://www.youtube.com/watch?v=Dhs1YO5nqXA
It was made by Tommy Christensen and shows how he
Hi all,
I came across this YouTube clip the other day that is well worth 3 1/2 minutes
of your time:
http://www.youtube.com/watch?v=Dhs1YO5nqXA
It was made by Tommy Christensen and shows how he built a model of DNA out of
LEGO bricks (of PDB entry 2DAU, to be precise) to celebrate th
Relevant to the discussion about archiving image data:
http://federalregister.gov/a/2011-28621
--Gerard
**
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
*
Hi all,
The UniProt (uniprot.org) team at the EBI (www.ebi.ac.uk) currently has a
vacancy for a structural biology curator. From the job description:
"The curator will be mainly involved with the collection, organisation and
dissemination of data on biological macromolecular structures. (S)he
On Friday, October 28, 2011 02:02:46 pm Gerard DVD Kleywegt wrote:
I'm a tad disappointed to be only in fourth place, Colin!
What has the Pope ever done for crystallography?
http://covers.openlibrary.org/b/id/5923051-L.jpg
Fock'n'Pope! Great find, Ethan! So maybe he deserv
nt to come back
as the bond market. You can intimidate everyone.
--James Carville, Clinton campaign strategist"
Thanks for the comprehensive reply
Regards
Colin
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard
DVD Kleywegt
Sent: 28 Oc
Hi all,
It appears that during my time here at Cold Spring Harbor, I have missed a
small debate on CCP4BB (in which my name has been used in vain to boot).
I have not yet had time to read all the contributions, but would like to make
a few points that hopefully contribute to the discussion an
Dear PDBe users and depositors,
Due to essential maintenance of the computers in the campus data centre this
coming weekend, all web, ftp and e-mail services of the Protein Data Bank in
Europe (PDBe; pdbe.org), as well as most other EBI services, will be
unavailable from Friday 21 October 11 a
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) regularly produces Quips,
short stories about QUite Interesting Pdb Structures (pdbe.org/quips). Quips
address biologically interesting aspects of one or more PDB entries, coupled
with interactive graphics views and often a mini-tutorial
(Posted on behalf of wwPDB)
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is pleased to direct PDB
depositors and users to the recommendations of the wwPDB X-ray Validation Task
Force (VTF) that were published in the journal Structure this week (2011, vol.
19: 1395-1412; http://www.cell.c
Hi all,
The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an
expert structural biologist to join the PDBe curation team at the EBI near
Cambridge, UK. Applicants should be computer-literate and possess a recent PhD
in some area of structural biology or structural chemistry
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; pdbe.org) regularly
produces Quips, short stories about QUite Interesting Pdb Structures
(pdbe.org/quips). Quips address biologically interesting aspects of one or
more PDB entries, coupled with interactive graphics views and of
Hi all,
Just a quick reminder that the deadline for applications for this EMBO
practical course is 30 September. See:
http://www.ebi.ac.uk/training/handson/course_110912_structures.html#registration
--Gerard
-- Forwarded message --
Hi all,
From 14-18 November, an EMBO Pract
Hi all,
Unfortunately, I am no longer able to support or maintain (let alone develop
or port to new OS versions) any of my old USF programs. For this reason, Mark
Harris (http://xray.bmc.uu.se/markh/email.html) has made a distribution kit
with source code (yes, Fortran77...) and compilation sc
Hi all,
Simple question, is there a way I can upload my own data into the EDS
server? I see only place for it to take from data already published in the
PDB.
First of all, if you deposit at PDBe, EDS will be run on your deposition and
you can access the results after annotation. Second, RCSB
1 - 100 of 230 matches
Mail list logo
