[Protein-crystallography] PDBportfolio - slideshows of salient
images for all your favourite PDB entries
Gerard DVD Kleywegt
(by gerard from xray.bmc.uu.se)
Thu Mar 10 11:56:44 EST 2011
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 comes with a legend that
explains what is shown and one or more links that provide further information.
If you have ever wanted to show off your favourite or own structure(s) on your
website, PDBportfolio provides an easy-to-use alternative to a static image.
Examples of uses include:
- the PDBe summary pages for all PDB entries, for instance:
- the summary pages of the Uppsala Electron Density Server, for example:
- on your own webpages, for example:
The images/legends cover a number of categories of information, including:
- Quaternary structure - the largest assembly identified by the authors or PISA
- Deposited model - a cartoon and a surface representation are shown
(separately). The cartoon is coloured by chain and shown with non-polymeric
entities as space-filling (CPK) models. The surface is coloured by atom
properties using some simple rules (a la PyMol). For protein-DNA/RNA complexes,
only the protein surface is shown
- Domains - domains as defined by SCOP, CATH and Pfam are highlighted on the
structure in separate images. A unique colour is used for each type of domain
and each domain is rendered as a cartoon of that colour; the domain boundaries
are further indicated by a semi-transparent surface of the same colour around
the domain. Different surface styles are used to help in distinguishing
multiple occurrences of the same domain
- Compounds - small molecules are shown with their binding environment.
Compounds that are most likely experimental additives (such as glycerol) are
ignored. Of the remaining ligands, at most three different ones are shown
- Experiment - for X-ray entries, a B-factor putty is shown and red surface
patches indicate where crystal contacts occur. For NMR entries, the entire
ensemble of models is shown. For EM entries, the map is shown (and sometimes a
PDBportfolio can be used to display information about a single or multiple PDB
entries. PDBprints can also be shown to provide additional information about
the entry or entries (see http://pdbe.org/pdbprints for more information).
The PDBportfolio user-interface contains a number of elements, including:
- buttons that control the speed and allow you to start/stop the slideshow or
go to the next or previous image
- an entry/image-selection pull-down (if you select an entry or a category of
images, only the images belonging to it will be shown)
- action icons (below the images) - these allow you to get more information
about the information category of the current image, download an archive with
all the images plus the PyMol scripts used to generate them, and see a page
with all the images and legends in one table
- the legend for most images contains links to pages with further information
The information used to generate the images (e.g., mapping of Pfam or CATH
domains) is taken from the PDBe search database and will thus be kept
up-to-date "automatically" (as far as you as a user are concerned - see
http://pdbe.org/sifts for more information about what goes on under the hood).
To the right of the control buttons you will find a help icon - this will take
you to the following page:
This page also contains details on how to incorporate the widget in your own
webpages. It's so simple that even yours truly can do it...
We welcome your comments, bug reports and feature requests on this widget.
Please use the feedback button at the top of any PDBe web page.
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin from ebi.ac.uk
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