Dear Martyn,
Numerous external databases, resources and software have contributed
significantly to the quality of the PDBe database and its web
applications. We gratefully acknowledge all these contributions,
including those from CCP4 at:
http://www.ebi.ac.uk/pdbe/?tab=aboutus&subtab=acknowledgements
Note that we also list all current (and past) funders at:
http://www.ebi.ac.uk/pdbe/?tab=aboutus&subtab=funding
Regards,
Gary.
On 14/03/2013 10:55, MARTYN SYMMONS wrote:
Ah yes a new logo...
But it might be of interest to hear in this forum what has happened to
the CCP4 logo that used to appear on the PISA and Fold pages in
acknowledgement of the support from the BBSRC on the underlying
algorithms for these services.
It is only by acknowledgement of the contribution of projects such as
CCP4 that we can establish a continuing funding stream for the
improvement of scientific software. I distinctly remember that this
was acknowledged by the presence of the CCP4 logo on appropriate pages
in the old PDBe website. Surely there is still space for that
acknowledgement too?
Yours perplexedly,
Martyn
Dr Martyn Symmons
Cambridge
------------------------------------------------------------------------
*From:* Gary Battle <[email protected]>
*To:* [email protected]
*Sent:* Thursday, 14 March 2013, 10:27
*Subject:* [ccp4bb] PDBe website update: What's new
Dear all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org
<http://pdbe.org/>) releases new and improved tools and services. Our
first website update of 2013 features:
1. A new weekly overview of new biology in the PDB
2. Improved searching of EMDB entries with rapid filtering of results
3. New features for visual analysis of EMDB entries
4. Improved pages with chemical-shift-validation information for NMR
entries
5. Easy sharing of PDBe pages
--------------------
1. A new weekly overview of new biology in the PDB.
You can now view instances of new biology in the PDB including Pfam
families, GO terms and UniProt entries that appear in the archive for
the first time. For example, this week’s release includes the first
structure ever from a member of the "Alternative Oxidase" Pfam
sequence family
(http://www.ebi.ac.uk/pdbe/searchResults.html?display=latest&tab=xref
<http://www.ebi.ac.uk/pdbe/searchResults.html?display=latest&tab=xref>).
Note that two kinds of "new biology" are shown: cases where an
existing Pfam family etc. maps to a newly released structure in the
PDB for the first time, and cases where an existing PDB entry maps to
a new entry in Pfam, GO, UniProt, CATH or SCOP.
2. Improved searching of EMDB entries with rapid filtering of results.
We have made searching the EMDB easier by implementing search filters
that enable you to rapidly narrow down the set of search results.
Filters based on experimental details, journal, organism etc. can be
applied when searching (http://pdbe.org/emsearch) or browsing the
contents of the archive (http://pdbe.org/embrowse).
3. New features for visual analysis of EMDB entries.
We have introduced several new features to aid visual analysis and
validation of EMBD entries, including:
* A volume-estimate graph that shows how the enclosed volume of a
map varies with the contour level (e.g.
http://pdbe.org/emd-5357/analysis).
* A Fourier-shell correlation (FSC) curve used to estimate the
resolution of single particle maps (e.g.
http://pdbe.org/emd-5357/analysis).
* A residue-based atom-inclusion chart that can be used to assess
the quality of fit of PDB models to an EMDB map (e.g.
* http://pdbe.org/emd-2017/analysis).
* An image showing the overlay of any deposited masks on a map,
that show segmentations or some particular feature of an entry
(e.g. http://pdbe.org/emd-1206/analysis).
(Note that not all features are available or applicable for all entries.)
4. Improved pages with chemical-shift-validation information for NMR
entries.
We have improved the presentation of information on the validation of
chemical shifts with VASCO. The redesigned webpages now show
statistics on the assigned chemical shifts, any referencing
corrections and a list of atoms with unusual chemical shifts values
(e.g. http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr).
5. Easy sharing of PDBe pages.
Regular visitors of the PDBe website may have noticed some small
changes to the headers of our pages. The new headers include feedback
and sharing buttons on every PDBe webpage. If you want to share what
you find on one of our pages with friends or colleagues, use the share
button to post the URL on Facebook, Twitter, etc. or to email it. If
you have suggestions for improvements, please let us know by using the
feedback button.
You may also have noticed our new logo. Based on a motif that is found
at all levels of structure, we hope that our new logo will quickly
become synonymous with the provision of high‐quality information about
3D molecular and cellular structure. Our new logo and guidelines for
its use are available from our website at http://pdbe.org/logo
As always, we welcome your comments and suggestions through the
feedback button at the top of every PDBe webpage.
Gary.
--
Gary Battle
Protein Data Bank in Europe (PDBe)
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope
--
Gary Battle
Outreach Coordinator
Protein Data Bank in Europe (PDBe)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
Tel: 01223 49-4654
email: [email protected]
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope
