... and why don't we move on from pdb format to something a bit more
modern ?
i think it would only require a handful of programmers to agree on this
and the rest would (have to) follow.
i.e. if coot and refmac could both read and write something more modern
we'd have a huge part of ccp4 world
That is the plan and hopefully with help of people from pdb coot, buster,
phenix, refmac, ccp4 programs will all use mmcif with ligand descriptions
inside.
Good will is there, a little bit work is needed.
Regards
Garib
On 25 Jan 2012, at 08:15, Ingo P. Korndoerfer wrote:
... and why don't
Le 24/01/12 21:18, Dale Tronrud a écrit :
On 01/24/12 11:52, Miguel Ortiz Lombardia wrote:
El 24/01/12 18:56, Greg Costakes escribió:
Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.
But then suppose that one merges data from a crystal that is degrading
On Jan 24, 2012, at 10:31 PM, Bart Hazes wrote:
For some RNA viruses the rate of mutation is so high that they basically
sample a flat region of the fitness-landscape. If you could take two
individual viruses out of this sample to establish two independent infections
than over time each
Tassos reports:
1. None of the twenty test-users was satisfied with any of the two
solutions - and each was annoyed for a different reason.
This suggests that the choice of ELN is not the most difficult part of the
adoption process. Maybe the test users at the NKI were annoyed by the idea of
Dear all,
A postdoctoral position is available in Oxford Biochemistry for combined
crystallographic and NMR studies of centriolar proteins. The advert is
below and applications can be made online until Feb. 20th.
Regards,
John Vakonakis
--
Dr. Ioannis (John) Vakonakis
Wellcome Trust
Begin forwarded message:
Date: January 24, 2012 7:16:42 PM EST
To: Bart Hazes bha...@ualberta.camailto:bha...@ualberta.ca
Subject: Re: [ccp4bb] quasispecies
This remark brings to mind a paper published recently by Ariel Fernandez and
Mike Lynch:
Nature 474:502, 2011: Non-adaptive Origins of
Hi Yuri,
If you don't like Python, like myself (and I'm not alone, it
would seem), you could try Ruby (http://www.ruby-lang.org/en/). Some
examples of PDB file manipulation are below (taken from [1]).
The language is a great improvement in Perl and Python in my opinion, but
the downside
Dear all,
A beamline scientist position is available at the EMBL Hamburg Unit in Small
Angle Scattering in the
research group of Dr. Dmitri Svergun.
I attach the Vacancy Notice below. Deadline for application is 4th March 2012.
Applications should be directed to:www.embl.org/jobs
regards
Hi Yuri,
To add something nobody else has mentioned yet.
If you are interested in statistics and analysis you may find
interesting the R package. There is an excelent module, called Bio3D for
the analysis of protein structure and sequence data. Have a look here:
Dear Gregory and Darren,
Thank you for your answers. They have been very useful.
2012/1/24 Gregory Verdon gregory...@gmail.com
it possible that the protein is toxic (even when slightly expressed from
your possibly leaky pET vector), so that e.coli select for mutations that
kill expression of
MacCHESS is pleased to announce that the BioSAXS Essentials III Workshop
will once again be offered at Cornell University.
*BioSAXS Essentials III: Getting Started in Biological Small-Angle X-ray
Solution Scattering*
*
*Date:*February 24-26, 2012
Dear Crystallographer
Following my pitch on behalf of the British Crystallographic Association (BCA)
at the 2012 CCP4 Study Weekend in Warwick, I wanted to encourage any interested
macromolecular crystallographers to become members of the Association.
The UK will host the European
Toxicity of target proteins in pET vectors can manifest itself without DE3.
Some people suggest E. coli polymerases causes low level of expression. The
observed mutation rate is thousands of fold higher than what the textbooks
say. Its easy to tell toxicity from other causes of heterogeneity.
We've seen nice in vivo activity (on purpose) from proteins cloned under T7
promoters but transformed into non-DE3 cells. In fact, friends working with
more zesty enzymes who wanted a more tunable in vivo assay have had to mutate
the ribosome binding sites for proteins under T7 promotors to
Dear All,
A Research Technician position is available at the High Throughput
Crystallisation laboratory of the EMBL Grenoble Outstation.
You will find the details in the link below.
http://www.embl.de/aboutus/jobs/searchjobs/index.php?newlang=1newms=srsearchregion=670
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