Proteopedia:Development
From Proteopedia
Rehovot, June 2017
AH and JP working side by side during AH's visit to Weizmann
- 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 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.
- Planned: add a button within the popup window that will allow to refresh the state of model, retrieving it again from the original page. This avoids the need to call again the popup window and load again the JSmol object (so a quicker experience)
- The option for display of the resize buttons is now part of the JSmol Extension for MediaWiki.
- The JSmol object is written to the page not during, but after page complete loading (if applicable, see below).
- The option for delaying Jsmol insertion is now part of the JSmol Extension for MediaWiki.
- An animated (rotating) GIF for the model or scene is displayed initially in place of the JSmol object (when the gif file is already available).
- A new button (“Display Interactive Model”) is shown below the image, for the user to decide showing the JSmol model instead of the image.
- The option for display of the image is now part of the JSmol Extension for MediaWiki.
- Planned: a (semi)automated procedure for generating and saving the collection of animated GIFs for Proteopedia pages (all, most visited?).
- Planned: consider whether the "simplified model" is no longer needed and we may go straight from the rotating image to the full model display.
- 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.
- When entering page Edit mode, JSmol for the 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).
- (work in progress) Whenever a model is loaded (seeded pages at least), information will be filled into the page content:
- The caption below JSmol will be updated.
- Type of model: macromolecular assembly or asymmetric unit.
- Number of models if NMR.
- Resolution if applicable.
- The user may change the model between macromolecular assembly and asymmetric unit (as long as the files are available)
- Initial implementation of a special Proteopedia category to display mutations in proteins, and the template page for that.
- 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.
- Reads the data from the matching data page.
- Includes a panel showing the sequence of the protein, with all mutations listed.
- Includes the JSmol model.
- Clicking on the mutations will display them in the 3D model.
