Proteopedia:Development
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Essen, Germany, June 2017
JP Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.
Rehovot, Israel, June 2017
AH and JP working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from JS
During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.
Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.
- The JSmol object is now written to the page not during, but after page loading has completed.
- Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
- A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
- Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
- A new button [Display Interactive Model] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
- The image is replaced with the JSmol model also whenever the user clicks on a green link.
- An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
- The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
- Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
- The [popup] button is still available as an independent option.
- The popup window now has a new extra button, [update], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
- All the above-mentioned new options have also been added as part of the [Extension for MediaWiki], for use in other websites.
- When entering page Edit mode, JSmol for the Scene Authoring Tool (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
- Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
- The PDB id (read from the server).
- Number of models if NMR. This is read from the server or from within JSmol.
- Resolution if applicable. (Implementation is pending)
- Type of model: biological assembly or asymmetric unit. This is read from the Proteopedia server.
- When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
- The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
- For seeded pages, any user has now a choice to display the model of either biological assembly or asymmetric unit, as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
- When a page is written in a language other than English and its title has been set as recommended (that is, Title of page (language)), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: Spanish, French, German, Italian, Czech, Russian, Turkish, Chinese.
Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.
- A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
- The display page, also editable,
- Has a regular content area, editable by users.
- Reads the data from the matching data page (access limited).
- Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
- Includes the JSmol model.
- Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
- The display in JSmol may be animated between wild type and mutated residue.
