Scene authoring tools: Difference between revisions

The '''Scene authoring tool''' (SAT) is used to create and edit molecular scenes.  Scenes created using the ''Scene authoring tool'' can then be inserted into [[Proteopedia]] pages. This is a reference page explaining everything. For a tutorial introduction, see [[Proteopedia:DIY:Scenes|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory videos, e.g. [https://youtu.be/P-LsB2U8rNM].

The ''Scene authoring tools'' are accessible when you are editing a page.  Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box where all the wikitext of the page lives--here you can change the text of the page.  If you scroll down some, near the bottom, you'll find in bold letters '''SAT (Scene authoring tools) [show]'''.  Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (not <Structure> or <StructureSection> tags), there will be access to the SAT. In this case, first edit the page to include one (using the [[Image:Structure buttons.JPG|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.

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To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia).  Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia upladed file" and click load.

There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

The "currently loaded" text area under the Jmol viewer window displays the name of the currently loaded file. Several files can also be loaded into Jmol, one at a time, using the "append" button. Note that by default Jmol will not display both together; they will be in different frames which you need to manage.

The first input box shows the current page name (if you want to start with a scene from a different page, enter the page name here). Next, you proceed to choose the scene name using the drop-down selector (all scenes associated with the entered page name will be listed).  Once a scene is selected, all of its versions are available for selection using the drop-down version number menu.  When a version number is selected, that version of the scene is loaded onto the Jmol applet that is part of the ''Scene authoring tools'' and the description that was given to the scene is also recalled.  At the same time, the wikitext that is needed for insertion of the scene into the page is displayed.

Each distinct scene has 3 parameters to distinguish it from all other scenes: pagename, scenename, and versionnumber.  A scene's "pagename" is automatically determined by the name of the Proteopedia page on which the scene was initially created.  The scenename is given by the user.  The versionnumber is incremental: If no scene by the given name exists for the given page, then the first version will be version 1.  If there exist previous versions of the same scenename on the same pagename, then the newest saved version will not overwrite older versions of the scene, but will instead be automatically saved as the newest version (by incrementing the versionnumber by one).  A scene's full name is in this format: Pagename/Scenename/Versionnumber (e.g. Hemoglobin/Cavity/14). Current scenes have numerical page names (e.g. 77/778341/Ballstick/1). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. Inspection of the first couple of lines of the file shows, after the keyword "documentBase", that it originated from a user page.

[[Image:SAT controls outside of tabs.JPG|400px]]

These controls are available no matter which tab is open. You can select "ALL" or "NONE" to quickly select all or no atoms. To see which atoms are selected, use the controls next to "Show Selected with Halos".  If you have something selected, you will see your selection highlighted by yellow halos.  These halos are NOT part of your scene and have no impact other than to indicate to you what atoms are currently selected.