PDBportfolio is a widget to display slideshows of images that convey information about one or more PDB entries, that also provides links to relevant resources for further analysis of aspects of these structures. PDBportfolio is used on the PDB Atlas pages of PDBe (example) and also can be included in your own webpages (example).

Main categories of images

  1. Validation percentiles: An image depicting the comparison of key quality metrics of this entry with all other entries in the PDB archive and a subset of entries with comparable resolution. This image is prepared according to the recommendations of wwPDB Validation Task Force (Read et. al.).
  2. Biological assembly: An image for the largest assembly is displayed, by preference the one defined fully or partly by the author. The software used to predict assemblies during entry deposition is PISA.
  3. Deposited coordinates: A cartoon and a surface representation are shown. 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. For protein-DNA/RNA complexes, only the protein surface is shown.
  4. Domains: SCOP, CATH and Pfam domains are highlighted on the structure. A unique colour is used for each type of domain. Each domain is rendered as a cartoon of that colour and 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.
  5. Ligands: Ligands that are most likely experimental additives (such as glycerol) are ignored. Of the remaining ligands, at most three different ones are shown.
  6. Experiment: A structure in the PDB is intimately connected with the experiment that determined it. Images are available for in case of the X-ray, NMR and EM entries. For X-ray entries, an image shown a B-factor putty is shown and red surface patches therein show where crystal contacts occur. For NMR entries, the entire ensemble of models is shown. For EM entries, the map is shown and sometimes a fitted model is shown.

User interface of the PDBportfolio widget

To start with, there is a prominent green/white start button obscuring the first image in the widget. Upon a click, the button disappears and the slideshow starts. The image below shows the state of the widget after this button is clicked.
There are two versions of the widget. In the first, you can view images for more than one entry and select those images using a dropdown menu. PDBprints of the entries are also shown in the same widget. The second version (used in the PDBe Atlas pages) shows the PDBportfolio images for a single entry - it does not show the PDBprints and image selection dropdown menu.

The PDBportfolio user interface contains:
  • Play buttons: These are for playing and pausing the slideshow, making the slideshow go faster or slower, moving forwards and backwards in the slideshow after pausing it, and jumping to the first or the last image.
  • Image selection: It can be sometimes useful to be able to jump to an image of interest, especially when many entries are listed together in the same widget. The image selection dropdown has a hierarchical structure which allows you to select one image or a category of images.
  • PDBprints: This is a widget itself. It pictorially depicts salient aspects of an entry, such as citation, sample preparation, experiment type, taxonomy and presence of types of molecular components. It also links to pages that provide more information on these aspects.
  • Image: The static images (generated with PyMOL) that are displayed in the slideshow.
  • Legend: The legend consists of a concise header and a more detailed description of what the image is about. Description can be scrolled if necessary. The legend also contains links to relevant resources for further analysis (e.g. Pfam, CATH, SCOP, PDBeFold, PDBeMotif).
  • Links icons: The details icon takes you to a page containing more details on the image category. The download icon allows you to download a zipped archive containing all images and the PyMOL scripts used to create them. The listing icon takes you to a table of images, descriptions and scripts. The help icon takes you to this page.

How to include the PDBportfolio widget in your own pages

A PDBportfolio widget can be included in your own webpages very easily, e.g. if you want to showcase the structures solved in your lab.
  • Include the necessary javascript, preferably in <head>
    <script src='//www.ebi.ac.uk/pdbe/widgets/js/essential.js' type='text/javascript'></script>
    <script src='//www.ebi.ac.uk/pdbe/widgets/js/basic.js' type='text/javascript'></script>
    <script src='//www.ebi.ac.uk/pdbe/widgets/js/pdbportfolio.js' type='text/javascript'></script>
  • Include stylesheet and javascript for PDBprints if you are using the multi-entry version of the widget.
    <link type="text/css" rel="stylesheet" href="//www.ebi.ac.uk/pdbe/widgets/css/pdbprints.css">
    <script src='//www.ebi.ac.uk/pdbe/widgets/js/pdbprints.js' type='text/javascript'></script>
  • In the HTML layout of your page, add a div at a suitable place with a distinct id to host the PDBportfolio widget.
    <div id="portfolio_1cbs">
  • Include the javascript call to configure and start the PDBportfolio widget at a suitable place in your webpage, e.g. in the window.onload function.
    <script> window.onload = function() {
    new YAHOO.PDBe.ImagesWidget('portfolio_1cbs', '1cbs').show(); // single-entry version
    } </script>
    or, <script> window.onload = function() {
    new YAHOO.PDBe.ImagesWidget('portfolio_1cbs', '1cbs,1cbq,1cbr', 1).show(); // multi-entry version
    } </script>
  • Arguments to the ImageWidget() are:
    • div id: id of the host div element. This must be supplied and has no default value.
    • PDB entries: one or many (comma-separated) PDB entry codes, e.g. '1cbs', or '2x9t,1kx8,100d'. This must be supplied and there is no default value.
    • PDBprints flag: a flag to indicate whether or not to show PDBprints, in other words, whether to use the first or second version of the widget. This is null by default (do not show PDBprints, i.e. the single-entry version), or can be set to 1 to display the PDBprints (i.e. the multi-entry version.


When it comes to creating images to highlight exactly what you want, you might want to customize a PDBportfolio image further. You may download the PyMOL scripts used to make these images, enhance them and make your own images.
You may also use PDBportfolio images as they are or ask us for a higher quality image. We are happy for you to use the PDBportfolio images in your reports as long as you acknowledge the source.


  1. If there are more models than one in a PDB entry, then the first model is used to make most images, except NMR ensembles where all models are shown.
  2. The number of images for ligands has been restricted by showing only one instance of ligand-type, and ignoring ligand-types that are most likely experimental additives.
  3. Pfam domains can have overlapping definitions. We identify sets of non-overlapping Pfam domains and make one image for each such set. Hence, there can be multiple images for Pfam domains.


We welcome your comments, bug reports and feature requests on this widget. Please use the feedback button at the top of this page.


  • PDBportfolio images have been created using the excellent and popular protein visualization tool PyMOL (The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC).
  • Images for the biological assembly and the NMR categories are produced by the PDBe annotation staff. EM images are produced by the EMDB staff at PDBe.
  • The slideshow is based on the YUI carousel control from YAHOO! developer network.