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
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
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
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
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
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
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
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
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
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
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,
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,
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,
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
(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) 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
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,
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
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
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
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
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,
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
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,
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
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,
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
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,
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
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
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
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
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,
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
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,
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
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
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
==
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
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
[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
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
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
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
For an older paper with several examples, see: Acta Cryst. (1993). D49,
505-512 [ doi:10.1107/S0907444993003737 ], Orientation of non-crystallographic
symmetry axes in protein crystals, X. Wang and J. Janin
My favourite example is 1cel: pdbe.org/1cel and pdbe.org/download/1cel (see:
http://www
Following feedback from students, collaborators and other structural
biologists, the Protein Data Bank in Europe (PDBe; pdbe.org) has become aware
of a need for a social networking presence to strengthen the link with current
and potential users of its resources.
So if you would like to be
Hi all,
We have two new openings at the Protein Data Bank in Europe (http://pdbe.org -
part of the European Bioinformatics Institute in Cambridge, UK) to work in the
Databases & Services team:
- Software/Database Engineer
http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=AdmOlRWtGeVHmJjVeb&jobid
Not sure if this helps, but MAPMAN contains options to make 1D and 2D
projections - see http://xray.bmc.uu.se/usf/mapman_man.html#S45
Many moons ago, I also wrote a script to generate general projections (e.g.,
onto the plane of an aromatic ring) using various USF programs - you may want
to tr
This was one of the things that Indonesia was written for (a long time ago, in
a galaxy far, far away), although I'm not sure if it will still run. If you're
desperate, see http://xray.bmc.uu.se/~dennis/
--Gerard
On Fri, 26 Nov 2010, Muhammed bashir Khan wrote:
Dear All;
I have structures
If you have LSQMAN, this is trivial - read your superimposed files and use the
RMsd_calc command - http://xray.bmc.uu.se/usf/lsqman_man.html#S59
--Gerard
On Tue, 23 Nov 2010, Huiying Li wrote:
Another question on RMSD:
I have two structures of the same protein superposed with the LSQ Super
Hi all,
This is to inform PDB/EMDB depositors (at PDBe only) and users of PDBe
services (http://pdbe.org/) that we will be operating with a reduced level of
service in the next few weeks:
- on 23 and 24 December we are operating with a skeleton crew, especially in
the depositon and annotatio
Cross-posted from pdb-l
--Gerard
-- Forwarded message --
Date: Thu, 23 Dec 2010 15:35:10 -0500
From: Christine Zardecki
To: pd...@rcsb.org
Subject: pdb-l: From 7 to 70,000: The PDB Reaches a New Milestone
From 7 to 70,000: The PDB Reaches a New Milestone
As the year 2010 dr
Hi all,
There is an EMBL Inter-disciplinary Post-doc (EIPOD) position available to
work on "Validation of low resolution structural models". For details, see:
http://www.embl.de/training/postdocs/eipod/app2011-1/svergun.pdf
The post-doc will be based at EMBL Hamburg and supervised jointly b
Hi,
SIFTS provides mappings between PDB and UniProt (and a number of other
resources) - see pdbe.org/sifts
This file may contain the info you need:
ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/text/pdb_chain_uniprot.lst
--Gerard
On Mon, 31 Jan 2011, Sridharan, Sudharsan wrote:
Hi all,
Hi all,
In October 2011, the Worldwide Protein Data Bank (wwPDB; wwpdb.org) will host
a scientific symposium in Cold Spring Harbor, celebrating the 40th anniversary
of the inception of the PDB and the many scientific contributions it archives.
The program will showcase the scientific impact m
[Forwarded on behalf of the EMDataBank.org Team]
We are proud to announce that the cryoEM community has reached a significant
milestone: more than 1000 maps representing a wide variety of biological
assemblies are now archived in the EM Data Bank.
In addition, structures from EMDB and PDB wer
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
announced a substantial make-over of its website last summer, including the
release of a number of new features (such as PDBprints -
http://pdbe.org/pdbprints - and a biologist-friendly structure browser -
http
Hi all,
As part of its recent winter update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) released a new widget, called PDBportfolio, that we hope will
find widespread use. It displays a slideshow of images that convey important
information about the entry (or entries). Every image
Hi,
MAPMAN can read and write a number of formats - see:
http://xray.bmc.uu.se/usf/mapman_man.html#H8
While it doesn't write "cube" format, it can produce maps in various ASCII
formats (e.g., NEWEZD, CNS, X-PLOR) that you should be able to convert into
something that suits your needs.
Hi all,
As part of its recent winter update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced a new, chemistry-based module of its PDB archive
browser (a.k.a. PDBeXplore). It can be accessed at:
http://pdbe.org/compounds
As you may (or may not) know, th
Hi all,
As part of its recent winter update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced Quips - "QUite Interesting PDB Structures". Quips
are short stories about one or more interesting or topical structures, coupled
with an interactive viewer and often a tutorial that
People of the disordered sidechains, ave!
-
perhaps the IUCr and/or PDB (Gerard K?) should issue some guidelines along
these lines? And oblige us all to follow them?
(Mark J van Raaij)
-
this discussion has flared up many times in the past, and maybe it's time for
a powerful dictat
Hi all,
As part of its recent winter update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org/) has improved its facility that allows for tandem searches of
PDB and EMDB. It was designed to allow users to carry out many of their
day-to-day searches (without the need to fill out a complex
Hi all,
The following question was posed on the CCP4 bulletin board earlier this week:
I have a question related to protein structure, but not crystallography
per se. Has anyone see a disulfide forming between the two cys of "CXC"
in the middle of a loop, and create a sharp turn, where X is not
In June 1999, staff of the Macromolecular Structure Database (MSD; nowadays
known as the Protein Data Bank in Europe, http://pdbe.org/) at the European
Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk/) began annotating
PDB entries. Now, eleven years later, PDBe has annotated its 10,000t
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org) has vacancies for a
(possibly junior) scientific programmer and for a system
administrator/software engineer. For links to the job descriptions, surf to:
http://pdbe.org/jobs
The deadline for applications is 15
Hi all,
This may be of interest to those methods developers amongst us who are ogling
the rich potential bounties to be reaped by applying low-resolution X-ray
model-building and refinement methods to EM maps...
--Gerard
-- Forwarded message --
Date: Thu, 12 May 2011 07:52:48
Hi all,
A fresh installment of Quips (interactive stories about interesting entries
from the PDB) is now available on the PDBe website. It is called "Getting a
good rate of exchange - the mitochondrial ADP-ATP carrier" and can be found
here: http://www.ebi.ac.uk/pdbe-apps/quips?story=ATPexchan
Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
carried out a substantial make-over of its website last summer, including the
launch of several new features (such as PDBprints - http://pdbe.org/pdbprints
- and a biologist-friendly structure browser - http://p
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is organising a scientific
symposium in Cold Spring Harbor this autumn to celebrate the 40th anniversary
of the inception of the PDB and the many scientific contributions it archives.
The meeting ("PDB40") will kick off with an evening receptio
Hi all,
From 14-18 November, an EMBO Practical Course on "Computational structural
biology - from data to structure to function" will be held at the EBI in
Cambridge (UK). The course is organised by James Watson, Rosemary Wilson,
Gerard Kleywegt, Victor Lamzin, Christine Orengo and Gert Vriend
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) continues to improve
its services to the scientific community. As part of our recent website
update, we have reorganised and simplified the way information about NMR
entries is shown. We have also released Vivaldi (Visualisation
This is correct - see http://xray.bmc.uu.se/usf/dataman_man.html#S27
At the time I wrote this (1993...), I was a recovering NMRtist and The Other
Gerard was doing a sabbatical in Uppsala and in fact in the office next to
mine. He pointed out that I had to do this and also provided code.
--The
Hi all,
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for
graphical display of the coverage in the PDB of any UniProt entry (e.g.,
http://pdbe.org/unipdb?uniprot=P19909). The widget can be used
Hi all,
Just a heads-up - if you upgrade to OSX Lion, your trusty old USF executables
will no longer work.
Help is on its way - in the near future the indefatigable and intrepid
Lion-taming heroes of the USF will release a distribution kit that includes
source code. However, for now you may
Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve
its services to the scientific community. As part of our recent website
update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved.
EMDB (http://emdatabank.org) contains over 1000 maps and is
Hi all,
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced PDBeXpress (http://pdbe.org/express), an umbrella
name for a set of easy-to-use yet powerful PDB analysis tools. The first two
modules can be used to answer questions such as "what r
!Hola!
About 6 years ago I noted a couple of structures I was interested in were
removed from the pdb. I saw in a recent email discussion that it is possible
to access obsolete entries, however unfortunately I do not have the pdb code
of the structure I am interested in - and neither does the
What a funny & pleasant piece of discussion !
Given any physical quantity "Something", having any kind of dimension (even
as awful as inches^2*gallons*pounds^-3)
Would it exist any room for a discussion about the dimension of 2*Something
? And what about 1*Something ?
(1) You can always con
'Allo! 'Allo!
I suspect that you are looking for the CCPN mailing list rather than the CCP4
one. You have just confused thousands of innocent crystallographers!
--dvd
On Fri, 20 Nov 2009, Julien Litt?rature wrote:
Hi,
Since the newest upgrade of analysis, I get this warning message once in
Dear colleagues!
I would like to draw your attention to two new job opportunities that have
opened up at the Protein Data Bank in Europe (PDBe) at the EBI (Hinxton, UK)
and that will hopefully interest some of you:
- Software Engineer/Scientific Programmer - to work on database integration
a
Hi folks,
If you have been trying to access PDBe or other EBI services today, you may
have found them to be less than responsive. There has been a major hardware
failure today and the EBI systems team is trying hard to fix things. However,
you may find that many services are unavailable and ma
wwPDB statement on Retraction of UAB PDB entries
-
In its December 4, 2009 issue, the Journal of Biological Chemistry (JBC)
retracted an article by H.M. Krishna Murthy et al. describing the structure of
dengue virus NS3 serine protease published 1
And if you liked SPASM, you'll love the SPASM web-server that Mark Harris has
made:
http://eds.bmc.uu.se/eds/spana.php?spasm
The decapeptide search is similar to the quest for left-handed helices
described in the original publication.
Recipe:
- from the start page, upload a small
Summary of this thread:
FUC-MAN-NAG-NAG-NAG
Merry Flying-Spaghetti-Monster-mas (*) everybody!
--Gerard
(* http://www.venganza.org/)
**
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology U
Is there any parameter which i had to check.
Yes, the contour levels of your mFo-DFc map...
(My guess is that you are contouring at an arbitrary low level - say, "3
sigma".)
--dvd
**
Gerard J. Kleywe
Is there any convention to define the order of the two terminal nitrogens
(NH1 and NH2) of the arginine side chain. For example, should the name NH1 be
assigned to the nitrogen that is in trans position with respect to the CD
carbon, and NH2 to the nitrogen in cis (or viceversa)?
Yes there is
Thanks Stephen!
I was going to suggest that, but I was afraid of the self-appointed CCP4BB
Gestapo that has been seen goose-stepping in this neighbourhood recently
(Tassos recently accused me of becoming mellow and diplomatic in my dotage, so
I hope I've set the record straight now). However,
Hi Tim,
Maybe it's too early in the day for me, but why can't electrons be a unit? You
seem to be confusing physical (in-)divisibility of an entity with the symbolic
use of fractions of that entity in calculations. We can speak of the average
number of cows per acre of land without having to c
But it still won't solve Miri's problem. I think what she is asking for is a
program that detects which atoms should be matched to which, irrespective of
their names (i.e., not assuming they are called " CA ") and order (i.e., not
nicely sequential such as amino-acid residues), and then applies
eficient at the moment, but that seems worth trying.
Steve
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Gerard DVD Kleywegt
Sent: Friday, February 26, 2010 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D fitting
But it still won't
:
How about LSQMAN ?
with ATOM_types Side_chain ?
That should do the trick.
J?rgen
P.S. sorry it's not really a CCP4 related program, but I use it very
frequently in conjunction with the CCP4 suite :-)
On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote:
On Fri, 2010-02-26 at 16:50 +0100,
So it's really a non-CCP4 non-solution...
--G
On Fri, 26 Feb 2010, Pavel Afonine wrote:
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB &
Dear PDBe users,
The Protein Data Bank in Europe (PDBe; pdbe.org) will retire the OCA search
system in October 2010. Users and developers relying on this service are
advised to direct their links to the OCA site at the Weizmann Institute
instead - http://oca.weizmann.ac.il/oca-bin/ocamain
De
You may also want to look at some other structures at similar resolution and
see what the density and interactions for their sulfates look like. E.g., if
you go to HIC-Up, get to the SO4 page and then click on the link to EDS
statistics - http://xray.bmc.uu.se/hicup/SO4/so4_eds_stats.html - it w
Now open for registration:
EMBO Practical Course 'Computational aspects of protein structure
determination and analysis: from data to structure to function'
Dates: 6-10 September 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Registration Deadline: 23 July 2010 - 12 noon (GMT)
Accep
The Protein Data Bank in Europe has *three* openings for software engineers or
scientific programmers (one-year contracts):
(1) The PDBe Team has an opening for a software engineer or scientific
programmer to work in the NMR (Nuclear Magnetic Resonance) project. The post
holder will work with
PDBe launches its redesigned website (pdbe.org)
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The Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched its
redesigned website with lots of new features, enhancements and improvements.
This so-called "Midsummer Make-over" is the first
The Protein Data Bank in Europe (PDBe; pdbe.org) has a vacancy for the Project
Leader Electron Microscopy position.
For more information:
http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/w_10_059_ebi/index.html
PDBe is the founder of the worldwide archive of 3D cryo-EM data, the Ele
Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB
accession code, or by searches based on information regarding, for instance, a
publication, a molecule name, a sequence or a related 3D structure. While
these methods are valuable for locating a specific PDB entry or grou
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